Male fertility and sperm count influenced by Y-chromosome haplogroups

[Maciamo]

The main function of the Y-chromosome is to regulate male fertility, including testes size, sperm count, sperm motility, and possibly also (perhaps indirectly) the bias towards more male or female offspring. Indeed a higher sperm count or motility has been associated with increased chances of fathering boys rather than girls.

This may well explain the success of some Y-DNA haplogroups over others. Wars and conquests are not the answer to everything. If some lineages produce more boys, in a mixed population of haplogroups, given enough time they will become naturally dominant and eventually replace other, less competitive lineages.

Some Y-DNA haplogroups, or mutations found within specific regional subclades, have been identified as a cause of lower male fertility.

Haplogroup E1b1b has a higher incidence of azoospermia in Italians

[Maciamo]

More on the association between low sperm motility or reduced sperm count with some y-haplogroups :

Y chromosome haplogroups may confer susceptibility to partial AZFc deletions and deletion effect on spermatogenesis impairment

The findings indicate that some monophyletic Y chromosomes may be associated with predisposition to specific subtypes of partial AZFc deletion and adverse effect on spermatogenesis. Although these deletions were not confirmed with gene dosage analysis, the results suggest that Y chromosome background is an important factor that affects partial AZFc deletion formation and its contribution to spermatogenic failure.

AZF deletions and Y chromosomal haplogroups: history and update based on sequence

Evidence for the association of Y-chromosome haplogroups with susceptibility to spermatogenic failure in a Chinese Han population

This study provides evidence for the association of Y-chromosome background with impaired spermatogenesis, suggesting that Y variations play a role in the occurrence and even the severity of spermatogenic failure.

The haplogroup implicated in impaired spermatogenesis in the Chinese population is O3*.

The association of Y chromosome haplogroups with spermatogenic failure in the Han Chinese

The results indicated that the prevalences of hg K* in the control and the case population were 0.78% (4/515) and 2.80% (8/285), respectively. The difference between the frequencies of the hg K* in the infertile males and the normal control population was significant [odds ratio (OR) = 3.69; 95% confidence interval (CI) = 1.10–12.36] (P = 0.028). However, in the other haplogroups no significant differences were found. In conclusion, Y haplogroup-K* might bear a risk factor of male infertility, and the individuals in the haplogroup need to be further examined.

K is the ancestor of 90% of Y-DNA lineages in the world. But K* has virtually disappeared, except if some isolated parts of Asia, including western China. New mutations arose that obviously conferred an advantage over K*, so that only the men with the new mutations passed on their Y-DNA.

Spermatogenic ability is different among males in different Y chromosome lineage

The results show that the mean sperm concentration correlates with Y chromosome type. Moreover, the occurrence of azoospermia is related to one particular Y chromosome lineage. Thus, males with a certain haplotype are at a disadvantage for fathering children. The difference of spermatogenic ability among men is important not only in pursuing male competition as in the past but also as relates to the future of modern human males.

The haplogroup in question is D. This is not surprising as it was the first with C to reach Asia, but now survives only in isolated regions like Japan, Tibet, Yunnan, some Indonesian islands or the Andamans.

Identification of a Y chromosome haplogroup associated with reduced sperm counts

We found that one class of Y chromosome, referred to as haplogroup 26+, was significantly overrepresented (27.9%; P < 0.001) in the group of men with either idiopathic oligozoospermia (defined as <20 x 106 sperm/ml) or azoospermia compared to the control Danish male population (4.6%). This study defines, for the first time, a class of Y chromosome that is at risk for infertility in a European population

The haplogroup numbers were taken from the Europe-wide study of Rosser et al. (2000). Based on the geographic distribution and the STR markers given, hg26 correspond to haplogroup Q.

The haplogroup with the highest sperm count in the study was hg1, which unsurprisingly is R1b, followed by hg3 (R1a) . This supports my hypothesis that R1a and R1b became dominant in Europe, in spite of their late Bronze-age arrival, thanks to a genetic predisposition to father more boys compared to other haplogroups. Indeed, a higher sperm count is one of the principal factors in raising the chances of having a boy rather than a girl.

The fourth haplogroup in the study, hg2+, represents haplogroup I. The difference in sperm count between I and Q is not huge (41.4 against 30.8 mill/ml) in comparison to R1b (75.8 mill/ml).

Krausz et al. explain that :

Most of the hg26+ men have very low sperm counts. Sperm counts within this range are associated with very poor reproductive success and, in the absence of assisted reproduction, these chromosomes will be rapidly eliminated from the population. Taking into account the hg26+ frequency in the Danish population (∼5%) and assuming a mean selective disadvantage for these chromosomes of 0.5, this Y chromosome lineage would disappear from the Danish population within 12 generations.

With such a fast replacement rate, it could even be imagined that R1b arrived later than 2500 BCE in Western Europe, in fairly small number, and still would have become dominant without any massacre of indigenous men nor polygamy required.

Considering that other studies have found that haplogroup E also had a low sperm count by European standard (but probably higher than most subclades of hg A and B), it is easy to imagine how R1b (V88) could have boomed in some parts of Africa. Once the haplogroup penetrated a tribe, the proportion of R1b to haplogroup A, B or E would rise very quickly, explaining how it could reach over 95% in some tribes of North Cameroon.

[Maciamo]

More concrete data linking specific Y-DNA haplogroups (N1 and D2a) to decreased male fertility.

AZFc Deletions and Spermatogenic Failure: A Population-Based Survey of 20,000 Y Chromosomes (Rozen et al. - 2012)

There are two previously reported instances in which the prevalence of an AZFc-region deletion varies strongly by population: (1) the high prevalence of the b2/b3 deletion around the Baltic Sea is due to the prevalence of haplogroup
N1 chromosomes, all of which contain the b2/b3 deletion, and (2) the high prevalence of the gr/gr deletion in Japan is due to the prevalence of haplogroup D2a chromosomes, all of which contain the gr/gr deletion.

The article also says that gr/gr-deleted chromosomes are overrepresented in haplogroup R1a (which is defined by the SRY10831 mutation, a rare occurrence of a mutation in the sex-determining gene of the Y chromosome). It's not clear what effect this has on fertility though.

[LeBrok]

Interesting read, thanks.

[MOESAN]

some remarks of mine
an old HG (or an old SNP defined HG) is comdamned to disappear in big populations, not everytime by the effect of a natural selection but by the fact that mutations occurs that modify the HG naming: after all we (Eurasians) are descendants of Y-DE: it decreased, but not by selection, only by gaving birth to other "HG's" - if I have correctly understood the Hgs system, the official separation (names) between Hgs is an arbitrary one - (someway like saying latine is dead, without looking at romances languages)
impact not very easy to calculate:
the spermatozoids speed? were there spermatozoids races organized to find the champion out? as a whole, the X spermat's took profit as the Y ones in a given HG bearer - so, theorically, more Y ones but in some proportion more X (females) ones - and the females in a population were not trying ("tasting" sexually) every male they mate on the street or the meadow? if in a population were mixed bearers of different Hgs with different mobilities of spermats, if a female had only the same husband or man, it would be the frequence of sexual rapports that had importance, not the HG of the man: the milliards of spermats in a "performance" would have provided enough quantity to give birth to a children, whatever his Y or X HG... I think the female (mother)'s health would have been more important at last - and mobility of spermats concern X spermats too not only males, but females too:
perhaps the other characteristics of an HG could play here: more boys at birth in a population, by the effect of greater mobility of Y compared to X (the sexual chromosom, not the haplogroup!!!), but girls healthier than boys: in old times, more males birth mortality or low age males mortality (the problem of more warriors males fall down here?), so very soon, more females than males( but they died often enough when giving birth): but if an HG is linked to more health, more resistance (to what? question...) then fewer young males dead: then, YES, maybe, more representants of the concerned HG?...
not so simple, I believe...
good night, oidhche mhath, nos vad

[MOESAN]

that said, yes, if some HGs are so bad in reproductive ability, they can disappear swifter than expected - but here the ability to give birth to more children concern males AND females, and other genes, as a whole, autosomals distinct from the ones of chromosomes X and Y, would encrease too in the population

[Maciamo]

some remarks of mine
an old HG (or an old SNP defined HG) is comdamned to disappear in big populations, not everytime by the effect of a natural selection but by the fact that mutations occurs that modify the HG naming: after all we (Eurasians) are descendants of Y-DE: it decreased, but not by selection, only by gaving birth to other "HG's" - if I have correctly understood the Hgs system, the official separation (names) between Hgs is an arbitrary one - (someway like saying latine is dead, without looking at romances languages)

You are right about this. It depends what you call a haplogroup. One could say that haplogroup K is almost extinct, or that it is the most common haplogroup in the world, depending on whether you could its descendants or not.

[gidai]

The main function of the Y-chromosome is to regulate male fertility, including testes size, sperm count, sperm motility, and possibly also (perhaps indirectly) the bias towards more male or female offspring. Indeed a higher sperm count or motility has been associated with increased chances of fathering boys rather than girls.

This may well explain the success of some Y-DNA haplogroups over others. Wars and conquests are not the answer to everything. If some lineages produce more boys, in a mixed population of haplogroups, given enough time they will become naturally dominant and eventually replace other, less competitive lineages.

Some Y-DNA haplogroups, or mutations found within specific regional subclades, have been identified as a cause of lower male fertility.

Haplogroup E1b1b has a higher incidence of azoospermia in Italians

I did an exercise calculating a simple scenario.

I try to see what happens if at one point in time, two diferent populations, each with its own Y haplogruop, 1 and 2, mix together, let's say in proportion of 1 to 99. At the initial moment the Y haplogroup 1 population represent only 1% of the mixture, and fertility is the same for both populations, but because of any biological reasons there is a difference between the number of boys and girls who are born in families of men of haplogrup 1 and 2. I assumed that from 10 offsprings, males 1 have 6 boys and 4 girls, and males 2 have 4 boys and 6 girls.
Then I calculated what would happen with the frequency of this two haplogroups in the mixed population over the next generations. Their evolution is spectacular.

1(%) ... 2(%)

1 .........99 --> initial
1,49.....98,51
2,22.....97,78
3,3.......96.7
4,86.....95,14
7,12.....92.88
10,32....89,68
14,72....85,28
20,56....79,44
27,97....72,03
36,81....63,19
46,63....53,37
56,72....43,28 --> XII generation (300 - 360 years)
66,28....33,72
74,68....25,32
81,56....18,44
86,9.....13,1
90,87.... 9,13 --> XVII generation (425 - 510 years)
93,72.... 6,28
95,73.... 4,27
97,11.... 2,89
98.05.... 1,95
98,69.... 1,31
99,13.... 0,87 --> XXIII generation (575 - 690 years)
99,42.... 0,58
99,61.... 0,39

Since the XII generation (300-360 years), the haplogroups proportion has changed in favor of Y haplogroup 1.
In the XXIII generation (575 - 690 years) haplogroup 2 is already below 1%.

Other important effects:
a) - Mitochondrial haplogroup of the population 2, which represented 99% at the beginning, will increase, reaching almost 100% in a verry short time.
b) - Although haplogroup 1 has become overwhelming, in fact the initial autosomal genetic heritage proportion of the mixture is kept, 1 to 99.
c) - This may explain the success of the new branches of haplogroups, some of which spread very rapidly against the oldest one or his own basal branches, that were widespread before. Otherwise their chances of spreading would be virtually non-existent...

If it has a correspondent in reality, among other things this can explain manny "sudden population extinctions" if we take into account only Y haplogroups. But these extinctions do not exist autosomaly!
I think, that could mean a fast expansion at high proportion of R1b, R1a, neolithic G2a or other Y haplogroups without too big migrations.
So, probably, mixing with other small groups, some populations switch Y chromosome, but their genetic heritage remain at high level until today.

What do you think?

[Megalophias]

Variants that shift the sex ratio one way or the other can exist (though I don't know if any are known in humans). This is a form of genomic conflict, where part of the genome gets replicated more at the expense of the rest of the genome (and the rest of the genome will tend to evolve ways to prevent this). It sometimes happens in plants, where mitochondria and chloroplasts (being maternally transmitted) sometimes develop ways to promote production of female over male offspring, and this can become common within a species. But in the long term it is counterproductive, because when females predominate males will have a big advantage, so nuclear DNA will evolve ways to suppress it.

Your example, besides having an extremely high sex ratio change, assumes that a population with a Y chromosome that's suppressing XX sperm from being formed is interbreeding with a population with mitochondria that are suppressing XY sperm (or something like that) - both of these opposite (and rare or possibly nonexistent) things at once. What are the chances? And now you have sons with both selfish Y DNA and selfish mtDNA, does their sex ratio return to normal, or are they less fertile, or what?

[gidai]

Probably things are more complex. It's just a simplistic scenario. But it seems to lead to effects that I understand that have been observed or can explain what is happening in reality.
Proportions of boys/girls at birth of 0.9 to 1.16 exist in some populations. Places with the highest rate of newborn boys or sexually mature men are in the Caucasus, Middle East, South Asia, Balkans, Central Asia, North Africa. In those places I read that new Y haplogroups and subclades are believed to have appeared, which could expanded if the scenario is reality in fact.

[gidai]

Some data about countries with high new born boys/girls sex ratio that looks interesting I think.
China is likely to be influenced by demographic policies now, and make the global average rise to 1.07. But it is interesting to see new born boys/girls rate in smaller countries like those from Caucasus and the Balkans, and these are areas where new mutations are thought to have occurred over time.

Country/region	at birth (WDB estimate, 2012)[5]
China	1.19
Azerbaijan	1.16
Armenia	1.15
Georgia	1.11
Korea, South	1.10
Solomon Islands	1.09
Samoa	1.08
Papua New Guinea	1.08
Suriname	1.08
Montenegro	1.08
Serbia	1.08
Republic of Macedonia	1.08
India	1.08
Kazakhstan	1.07
Cyprus	1.07
Afghanistan	1.07
Iraq	1.07
Vanuatu	1.07
Micronesia, Federated States of	1.07
Ireland	1.07
Greece	1.07
Bosnia and Herzegovina	1.07
Singapore	1.07
– World	1.07
Albania	1.07
Hong Kong	1.07

[Corrado]

China, Korea, and maybe Vietnam could possibly be explained by sex-selective abortions, but I'm not sure that's a viable explanation for the discrepancies in the Caucasus or Oceania, since I presume abortion is either illegal, highly discouraged, or just not readily available in those countries. Of course, even if abortion is illegal or otherwise restricted in a certain country, doesn't mean they don't occur, but I have a hard time believing the sheer volume of illicit/concealed abortions would be high enough to skew the total sex ratio of newborns in an entire country in any case.

EDIT: I spoke too soon, at least in regards to the Caucasus countries. A quick perusal of Wikipedia (what can't you find on that site?) shows that abotion is both legal and fairly common in both Azerbaijan and Armenia, and Armenia has actually tried to explicitly curb sex selective abortions recently. So the sex ratios at birth for those two are definitely likely the result of artifical selection. However, abortion is illegal in Papua New Guinea and Vanuatu (Vanuatu in particular seems very stringent), so there might be a little more going on there.