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Since the Y-chromosome can only pass from male to male child, it would seem to pass intact. Thus, a boy's Y-chromosomes would, I guess, be the same as his father's. Going backwards, would not all men have identical Y-chromosomes for this reason, being somewhat like mitochondrial DNA?

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  • $\begingroup$ Because the Y stops recombining and has a small population size it is expected that variation will be rapidly depleted. Mutations still occur on the Y which can maintain some within population variance. ncbi.nlm.nih.gov/pubmed/26230387 $\endgroup$ – rg255 Sep 17 '15 at 6:19
  • $\begingroup$ There is a difference between an evolutionary process and a genetic process so to speak: you don't need recombination for evolution. A lot of organisms use cloning to generate "offspring", but these evolve as well because of mutation. $\endgroup$ – Willem Van Onsem Sep 17 '15 at 11:08
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Actually, no. There are also recombination prone regions of the Y chromosome that recombine and exchange material with X chromosomes, and these are called pseudoautosomal regions (PARs).

Y chromosomes can be used similarly to mitochondrial DNA to build up profiles of ancestry, but the sequences used for this purpose lie outside PARs, in the non-recombining region.

What about seqeuences outside PARs, do they show genetic variation?

As pointed out in the comments, PARs comprise only 5% of the Y chromosome, but even in the non-recombining regions of the Y chromosome studies in well-characterised populations have found that the mutation rate can approximate autosomal mutation rates in some regions of the chromosome, and exceed them in others.

What processes, other than recombination, drive mutations?

There are loads of different mechanisms by which mutations in general can be generated, including exposure to UV, free radicals, tobacco smoke, aristolochic acid, and perhaps most importantly spontaenous deamination of methylcytosines, which is an age related mutational process, proofreading errors inherent to DNA polymerases. Also, it is well known that in sperm, with age the mutation rate goes up throughout the genome. While UV is unlikely to be a prominent mutagen as was pointed out to me in the comments insofar sperm are concerned, factors like smoking still play a role.

An illuminating read about mutational processes and the mutational footprints they leave in genomes, as understood from studying cancer genomes, is here.

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  • $\begingroup$ Ok, but those regions are only 5% of the chromosome. Is the other 95% the same in all men? $\endgroup$ – Imprisoned Rhesus Sep 17 '15 at 1:38
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    $\begingroup$ Nope - those regions too are subjected to mutations at various rates, that in some well characterised populations approximate the autosomal mutation rate in some regions of the Y chromosome, with other regions showing elevated mutation rates. nature.com/ng/journal/v47/n5/full/ng.3171.html $\endgroup$ – Ankur Chakravarthy Sep 17 '15 at 1:51
  • $\begingroup$ Without recombination, how is the chromosome mutating? I know that it might get struck by a cosmic ray or something, but barring that, how? $\endgroup$ – Imprisoned Rhesus Sep 17 '15 at 2:15
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    $\begingroup$ There are loads of different mechanisms by which mutations can be generated, including exposure to UV, free radicals, tobacco smoke, aristolochic acid, and perhaps most importantly spontaenous deamination of methylcytosines, which is an age related mutational process, proofreading errors inherent to DNA polymerases. Also, it is well known that in sperm, with age the mutation rate goes up throughout the genome. nature.com/news/… $\endgroup$ – Ankur Chakravarthy Sep 17 '15 at 2:30
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    $\begingroup$ @AnkurChakravarthy please can you edit all of your comments into the body of your answer: they make it a much stronger answer, and it means they will be preserved long after the comments are deleted (comments are ephemeral, questions and answers are to keep) $\endgroup$ – EnergyNumbers Sep 17 '15 at 6:36

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