Influence of Y-chromosomal DNA mutations on behaviour and reproductory success

[Maciamo]

The human Y chromosome contains only 86 genes, compared to 20,000 genes on the 45 other chromosomes. While most mutations defining Y-DNA haplogroups lie in non-coding regions of the Y chromosome, a few other take place in actual genes. One of the most important among these genes is SRY (sex-determining region). In rare cases when the SRY gene is translocated to the X chromosome, it causes the XX male syndrome (a person with two X chromosomes who should be a woman but is actually a man). Likewise, XY individuals with defects or deletions in the SRY gene end up with female characteristics (Swyer syndrome). Mutations in that SRY genes are therefore bound to have serious effects on the carrier. It is perhaps not a coincidence then that several of the most successful Y-chromosomal haplogroups are defined by a SRY mutation. This is the case for:

- Haplogroup BT (SRY1532.1, aka SRY10831.1) : the entire branch of humanity that split from haplogroup A some 70,000 years ago, when Homo Sapiens first decided to leave Africa and colonise Eurasia. Some of the earliest descendants of BT were haplogroups C and D, who colonised most of Asia and Oceania, and probably also entered Europe.

- Haplogroup E (SRY4064, aka SRY8299) : the most successful of all African male lineages, which also spread around the Middle East and Europe during the Neolithic.

- Haplogroup O2b (SRY465) : a major male lineage in Japan, Korea and Manchuria. It is associated with the Yayoi colonisation of Japan from Korea from 500 BCE.

- Haplogroup R1a1 (SRY10831.2!, aka SRY1532.2! => reversion of the BT mutation above) : a lineage which underwent one of the most spectacular expansions in human (pre)history soon after the SRY mutation emerged, conquering half of Europe and a big part of Asia, from Anatolia to Siberia and India. Note that R1a lineages lacking the SRY1532.2! mutation (R1a* defined by the M420 mutation) are almost extinct today.

- Haplogroup R1b-M167 (SRY2627) : the most common R1b subclade in Catalonia.


Here are other apparently important mutations in the coding region of the Y-chromosome.

- Haplogroup DE (M1, aka YAP) is defined by the Y-chromosome Alu Polymorphism (YAP) insertion, the most well-known unique event polymorphism (UEP), estimated to have occured 65,000 years ago.

- Haplogroups J (12f2.1) and D2 (12f2.2) are defined by the same 12f2 STS polymorphism, linked to the deletion of the L1PA4 element in the HERV15yq2 sequence block. The HERV gene stands for Human endogenous retrovirus. Recombinations in HERV15 have been linked to changes in fertility.

- Haplogroup R (M207, aka UTY2) : the most successful male lineage in western Eurasia is defined by a mutation in the UTY gene (ubiquitously transcribed TPR gene).

- R1b-M222 (USP9Y+3636) : the presumed lineage of Niall of the Nine Hostages, found chiefly in northern Ireland and southern Scotland. Defects in the USP9Y gene can cause azospermia and infertility. We can therefore assume, considering the quick expansion of this haplogroup since the early Middle Ages, that the USP9Y+3636 mutation improved fertility (more swimmers) in men who have it.

- Haplogroup T* (M184, aka USP9Y+3178) : the defining mutation of the whole haplogroup T is also on the USP9Y gene.


The effect of Y-DNA on behaviour

The phenotypic effects of the Y chromosomes are still unclear, apart from conferring distinctly male characteristics. There are many attributes which distinguish men from women. Some are physical (hairiness, more muscle, taller body, squarer jaws, etc.), but many are purely behavioural (aggressiveness, dominance, ambition, rational/logic thinking, problem-solving, inventiveness, seduction/courting tactics, etc.).

The success of some lineages in specific environments may lie in mutations increasing one of several of these attributes. Human societies vary greatly depending on their geographic environment (hot, cold, fertile land, dessert), and their stage of historical development (hunter-gatherers, Neolithic, metal age, feudal society, modern society). Behavioural traits that are successful in one particular geographic and socio-historical environment may be at a disadvantage under different conditions.

I believe that this may be why some haplogroups have prospered at specific time and place in history. Men living in a warlike and highly hierarchical Bronze-age society, where chieftains have many wives or concubines, will have more chances of success if they carry genes that make them more aggressive and socially dominant. In a society where elaborate courtship is determinant in men's reproductive success, aggressiveness may end up being detrimental. Concretely that may be why R1a1a prospered during the Bronze Age and societies where it is dominant today are still more aggressive than average (Russia, Pakistan) and have a culture in which male courtship is not preponderant. I have noticed that populations with high levels of haplogroup J2a (Italy, Greece, Turkey, Lebanon, Jewish community) are typically merchant cultures, in which men are known for being smooth talkers, shrewd negotiators (haggling culture), and perhaps skilled seducers too. That may have something to do with mutations in haplogroup J2a. J1 people are also quite commercial-minded, though appear more aggressive and less the Casanova types.

I have noticed before a correlation between industriousness and haplogroup R in Europe and O in East Asia. Overall it is probably the whole macro-haplogroup NOP (including Q and R) that predisposes men to a higher level of activity. One consequence of this is that countries or regions with high levels of combined haplogroups N, O, Q and R tend to be more productive, and therefore usually richer than others. It doesn't work at the individual level though, because individual wealth depends on many other factors, such as income equality, wealth redistribution, individual intelligence, skills (e.g. money management) and traits of character (e.g. parsimony). It also depends heavily on the political and economic system in place in that country. That is why Eastern Europe became considerably poorer during the Communist era, but is now catching up with Western Europe (at least countries with high levels of haplogroups R and N).


Adaptations of male fertility to the local environment and climate

I have long been intrigued by the fact that some haplogroups seem to have prospered in one specialised environment. Here are some examples:

- Haplogroup N appears to be particularly well-adapted to very cold climates (northern Scandinavia, Finland, Baltic, northern European Russia, Siberia). N is actually the predominant haplogroup pretty much everywhere in Eurasia above the Arctic Circle. This is odd considering that many other haplogroups (I1, R1a, R1b, Q, C3, O...) could have colonised the Arctic region, but for some reason it is always N that makes the majority of the population. This may simply have to do with a mutation that makes sperm more resistant to extreme cold in men belonging to haplogroup N. That would explain why, in the long term, even Baltic people with no Uralic connection an hardly any Mongoloid admixture (Lithuanians, Latvians) ended up with such high percentages of N. It may simply be an adaptation to the local climate.

- Haplogroup E doesn't seem to do well in colder countries. E1b1b colonised most of Europe as far as the British Isles during the Neolithic, but didn't survive well (definitely less well than the indigenous I1 and I2). That may be for the opposite reason that I cited above for N, namely that spermatozoa of men belonging to haplogroup E may be more resistant to heat, but less resistant to cold.

- Haplogroup J1-P58 is found mostly in very hot desert environments, and is not as common in other climates in places conquered by the Arabs during the expansion of Islam. For example, J1-P58 is less common in Lebanon than in Algeria, despite being closer to Saudi Arabia.

[Fire Haired]

Those are cool and interesting theory's but I think you would agree it is a lot a lot a lot more complicated. R1b in the Near east and Europe is almost all under R1b1a2a L23 which started maybe 10,000ybp. R1b1a2a1a L11 did not arrive into western Europe until 5,000ybp R1b1a2a1a2b S28 probably did not spread into Italy and most of central Europe till Urnfield culture from 3,200-2,730ybp. Plus the Germanic and Italo Celtic tribes who conquered western Europe so you would put them as the aggressive war like kind of like Indo European branches of R1a but they also had maybe 30-50% of other haplogroups it is rare to find anyone who is 60% or more under one Y DNA haplogroups. I think the reason Germanic Italo Celtic R1b1a2a1a L11, Balto Slavic R1a1a1b1 Z283, and Indo Iranian(maybe also Tocharian) R1a1a1b2 Z93 conquered is not because of their haplogroup but because they are all Indo Europeans and have similar cultures. Russians today are known to be tough but they were beat up pretty well by the Vikings well almost everyone in Europe was. There is actulley a Russian family who told me traditional Russian folk stories about very big warriors who used to raid people and they said their Vikings I don't know it would be cool if it was. The R1a1a1b1 Z282 eastern European tribes from what I know did not defeat Germanic tribes Vandlas and Goths and really no one beat the Huns. I don't think you can declare one people groups is natural more aggressive than another or has a certain instinctually personality. There are some stero types of French being spoiled bratty wimps and their Gaulic ancestors were known as some of the most war like people in the ancient world. And Romans and Greeks saw them as primitive and wild. Look at European Royalty traditions how fancy and organized it is and I am pretty sure it goes back to Franks and other Germanic western European kingdoms in the early middle ages. Then when you compare those Germanic kingdoms like Franks the description of the Rus Vikings according to Ibn falden they were very dirty and primitive and nothing like that even though both Rus and Franks were Germanic.

You made the point in a thread how modern Italians traits don't really fit Ancient Romans. I don't think we should generalize characteristics of people groups because it is really complicated they wont always fit into a certain stero type.

[Fire Haired]

Are you saying I1 is indigenous to the British isles and before Neolithic I really doubt you actulley believe that. Germanic migrations and Vikings are deifntley the source. I am sure there are some Y DNA haplogroups in British isles that came before Neolithic but under 1% I don't know of any i2a2a1 probably came with Celts and I2a1b3 in Neolithic.

[bicicleur]

I find this a very interesting question, but I think it is very speculative to draw conclusions.
Like haplogroup N, they were the first to colonise Siberia after the LGM.
But are they better adapted to cold because of some gene in the Y-chromosome or did they develop some gene for better cold-resistance in the autosomal region afterwards by natural selection?
It's the story of the chicken and the egg : which one was first?

[LeBrok]

I find this a very interesting question, but I think it is very speculative to draw conclusions.
Like haplogroup N, they were the first to colonise Siberia after the LGM.
But are they better adapted to cold because of some gene in the Y-chromosome or did they develop some gene for better cold-resistance in the autosomal region afterwards by natural selection?
It's the story of the chicken and the egg : which one was first?

I agree, till we know what these genes do, it will be just speculations. Most of the mutations were adaptational/evolutionary response to the environment. There are some that were just mistakes but with very little consequences to health of a male, therefore carried forward as well to next generations.

[Angela]

Correlation also doesn't mean causation.

I do think there are a few studies looking at the fertility rates of different y dna clades, but they are from before the era when sub-clades were discovered. This would require a lot more research, in my opinion, but of course it's true that even a small percentage difference could, over time, have a big impact.

Oh, and the research would have to distinguish and unravel various issues affecting fertility. It's not all about sperm counts, motility etc., as fertility is a much more complicated issue, which is also affected by the compatibility of the male and female in terms of immune response as only one example.

[nordicwarrior]

Correlation also doesn't mean causation.

I do think there are a few studies looking at the fertility rates of different y dna clades, but they are from before the era when sub-clades were discovered. This would require a lot more research, in my opinion, but of course it's true that even a small percentage difference could, over time, have a big impact.

Oh, and the research would have to distinguish and unravel various issues affecting fertility. It's not all about sperm counts, motility etc., as fertility is a much more complicated issue, which is also affected by the compatibility of the male and female in terms of immune response as only one example.

Great point. And there's also the "battle" between the X side and Y side that Ridley talks about in his book Genome. How much of an influence does the maternal code have on "selecting" the male genes. I recommend this book for further explanation.

[Angela]

Great point. And there's also the "battle" between the X side and Y side that Ridley talks about in his book Genome. How much of an influence does the maternal code have on "selecting" the male genes. I recommend this book for further explanation.

Thanks for the recommendation.

[Maciamo]

I find this a very interesting question, but I think it is very speculative to draw conclusions.
Like haplogroup N, they were the first to colonise Siberia after the LGM.
But are they better adapted to cold because of some gene in the Y-chromosome or did they develop some gene for better cold-resistance in the autosomal region afterwards by natural selection?
It's the story of the chicken and the egg : which one was first?

The point is that I do not think that haplogroup N was the first in Siberia. There are good chances that I1 was in Finland and Scandinavia before and that N only arrived with the Uralic expansion, which only started 5000 years ago. Finnish and Sami languages only split from each others some 2500 years ago. In Siberia it is clear that haplogroup Q was there at least 13,000 years ago, when the Bering Strait was still frozen, since they crossed over to the American continent. So while the N prevalence nowadays ? It's certainly not a technological one. R1a could have overtaken all N populations in Siberia during the Bronze Age, as they conquered most of the Middle East and South Asia, and went at least as far east as Mongolia. Since R1a and Q also evolved in southern Siberia, I doubt that the length of adaptation is determinant. It may just be a matter of luck in acquiring the right mutations.

[Maciamo]

Three weeks ago, it was reported that American biologists were able to produce healthy offspring in mice using the sperm of male mice whose Y-chromosome had been amputated of all but two genes. In other words, the Y-chromosome of mice only needs to genes to be able to achieve reproduction. The two genes are SRY to make a testis and Eif2s3y to allow spermatogenesis to proceed in some cells to the point where you can use them to fertilize an egg. No human equivalent has been found for Eif2s3y yet, but it surely exists and may be spread out on my than a single gene.

What is interesting is the confirmation that the SRY gene is one of the the bare essential genes on the Y-chromosome. It is therefore doubly interesting that important top-level Y-DNA haplogroups should be defined by SRY mutations, as explained above.

[Power77]

Can XX males who have some translocated Y-genetic material(such as SRY) get a paternal/Y-DNA haplogroup? Or is the entire Y-chromosome needed for such an assignment? I'm a bit confused!

[Maciamo]

I have found out that other main haplogroups are defined by mutations in the coding section of Y-chromosomal genes.

- Haplogroup B2b1a1 (MSY2.1): found in central Africa

- Haplogroup M2a (SRY9138): found in Papua New Guinea and the Solomon Islands

- Haplogroup O1 (MSY2.2) is defined by mutation in the male-specific region of the human Y chromosome (MSY), which seems to recombine frequently with the X chromosome and is associated with spermatogenic functions. One of the most successful lineages in Southeast Asia, which may have originated in southern China where it still makes up 25% of the male lineages.

- Haplogroup O1b2 (SRY465) : the main branch of O1 found in Austronesian peoples of Taiwan, the Philippines, Indonesia, Melanesia, Micronesia, and Madagascar.


I am not sure about the three following mutations, but they don't seem to be a regular SNP's.

- Haplogroup B2b1 and Haplogroup K (50f2/C aka DYS7C): both share the same mutation in a DYS (a unique Y-DNA segment, although not necessarily in the coding region). Note that K is the ancestral lineage of 80% of Eurasian people.

- Haplogroup N (LLY22g)

- Haplogroup O2b1 (47z aka DXYS5Y)


SNPs defining haplogroups are not always mutations (replacing one letter by another), but also insertions (adding one or several letters) and deletions (cutting out one or several letters). Whereas mutations within a gene can be synonymous (the new sequence makes the same amino acid and therefore conserves an identical gene function), insertions and deletions are generally very disruptive and typically cause frameshift mutations, potentially altering whole genes. Little information is available at the moment on the effect this may have on the Y chromosome. Nevertheless, most top level haplogroups seem to be define by insertions and/or deletions.

- A00 : G->del at 2656961
- A0 : TTA->del at 15024287..15024289
- A0b : T->del at 2710309
- A1 : G->del + GATA->del at 21926041..21926042
- BT : del->T at 21907538
- B : del->T at 21878072..21878073
- B2b1a1 (the same as above) : ins 4bp->del 3bp at 15015500 (the same as in haplogroup O* below)
- C* : insertion of 9 bp between 21714378..21714386 + GTT->del at 15180103..15180105 + C->del at 2815407
- DE* : deletion -> ALU insertion at 21610891..21612014
- D1b : del->ins 1 bp at 21751917
- E* : del -7T-> ins 8T at 17644332..17644338
- E1b1a : del->GAGA at 16809478..16809479
- E1b1b-M84 : T->del at 21898363
- G* : 5 insertions at 24986774, 26620522, 27341881, 5674986 and 6753301 + 3x del->AT at 24987775..24987776, 26621523..26621524 and 27340875..27340876 + CA->del at 21153068..21153069
- G2a2b2 : del->A at 2888607 (same as R1b)
- H1a1 : insertion of 2 bp at rs2032675
- I* : GT->del at 15027529..15027530
- I1 : A->del at 18077293
- I2a2a-M284 : ACAA->del at 22750461..22750464
- J* : insertion of 1 bp at 21779295
- J1a2 : T>del at 7570823
- J2a1f (M419) : AAAAG->del at 15467906..15467910
- J2a1b3 (L218) : AAG->del at 21739941..21739943
- L1b : insertion of 2 bp at rs13447360
- N* : del->C at 15422968..15422969
- N1c1a1a (L1026) : TA->del at 21892577..21892578
- O* : insertion of 5 bp at rs2032678 + ins 4bp->del 3bp at 15015500
- O2a1-M121 : ins->del -2 bp at 21907170
- O2a1-M134 : C->del at 21716218
- O2a1-M117 : ins->del -4 bp at 21765312..21765315
- O2a4-M333 : del->G at 14847516..14847517
- R* : ACTGCATGCCTTACA->del at 9878852..9878866 (15 bp deletions !)
- R1a : CTGT->del at 16693280..16693281
- R1a1a1 : insertion at 15031111..15031120
- R1b : insertion of 4 bp at rs2032615 + del->A at 2888607 + G->del at 15668048
- R1b-M73 : insertion of 2 bp at rs2032634
- R1b-M18 : del->AA at 21733162
- R1b-L176 : del->AAAAC at 21779256..21779257
- R2a1 : del->A at 14871881..14871882
- T* : del->AACA at rs2032676
- T1 : T->del at 18162486..18162487

Just like for mutations in the coding region of Y-DNA genes, I don't think it's a coincidence that insertions/deletions happened exactly among lineages that would see a dramatic expansion. The ins/del mirror gene mutations in haplogroups BT, B2b1a1, DE, E, J, N and R.

But insertions and/or deletions can more generally be said to define the majority of top-level haplogroups, including A00, A0, A1, BT, B, C, DE, E, G, I, I1, J, N, O, R, R1a, R1b, T and T1. Note that haplogroup F and P didn't make the list and are almost extinct now. Haplogroup H also isn't listed and H2 became almost exictinct, while H1a1 got a new mutation and prospered.


Note that very major haplogroups that have had tremendous historical success at some point in human history, including haplogroups C (9 ins, 4 del), E (8 ins, 7 del), G (5 ins, 4 del), O (9 ins, 3 del) and R (15 del), have the highest number of insertions and/or deletions.

Even relatively deep clades are not ordinary. N1c1-L1026 is the main Finno-Ugric branch, which means the European branch of that otherwise Asian haplogroup. Genetic adaptation to European X chromosomes? In the same line, R1b-M73 is the Asian branch, and R1b-M18 the African branch of an otherwise mainly European haplogroup. Since the X and Y chromosomes do interact with one another, it's not impossible that these are all adaptations to racially different X chromosomes, with a long divergent evolution.

I1 and I2-M284, the two most successful I lineages outside Slavic countries are the only ones with insertions or deletions, and they define exactly I1* and the M284 mutation itself.

R1b-L176 is the most successful subclade of DF27 and achieved remarkably high frequencies in Catalonia in a relatively short time since the Iron Age.

G2a2b2 was the main haplogroup of European Neolithic farmers, and as such was the main Y-haplogroup in Europe for several millennia.

E-M84 is the main Levantine/Jewish subclade of E1b1b, and a particularly successful branch.

O2a1 subclades M117, M121 and M134 are all major East Asian lineages. In the 2002 phylogeny there were simply known respectively as O3e1, O3a and O3d.

[Azzurro]

I have found out that other main haplogroups are defined by mutations in the coding section of Y-chromosomal genes.

- Haplogroup B2b1a1 (MSY2.1): found in central Africa

- Haplogroup M2a (SRY9138): found in Papua New Guinea and the Solomon Islands

- Haplogroup O1 (MSY2.2) is defined by mutation in the male-specific region of the human Y chromosome (MSY), which seems to recombine frequently with the X chromosome and is associated with spermatogenic functions. One of the most successful lineages in Southeast Asia, which may have originated in southern China where it still makes up 25% of the male lineages.

- Haplogroup O1b2 (SRY465) : the main branch of O1 found in Austronesian peoples of Taiwan, the Philippines, Indonesia, Melanesia, Micronesia, and Madagascar.


I am not sure about the three following mutations, but they don't seem to be a regular SNP's.

- Haplogroup B2b1 and Haplogroup K (50f2/C aka DYS7C): both share the same mutation in a DYS (a unique Y-DNA segment, although not necessarily in the coding region). Note that K is the ancestral lineage of 80% of Eurasian people.

- Haplogroup N (LLY22g)

- Haplogroup O2b1 (47z aka DXYS5Y)


Also of interest are the insertions and deletions within the Y-chromosomes, which could potentially cause a series of nonsynonymous substitutions, including missense mutations that alter amino acids and therefore gene function. Little information is available at the moment on the effect this may have. Nevertheless, quite a few top level haplogroups also possess these.

- A00 : G->del at 2656961
- A0 : TTA->del at 15024287..15024289
- A0b : T->del at 2710309
- A1 : G->del + GATA->del at 21926041..21926042
- BT : del->T at 21907538
- B : del->T at 21878072..21878073
- B2b1a1 (the same as above) : ins 4bp->del 3bp at 15015500 (the same as in haplogroup O* below)
- C* : insertion of 9 bp between 21714378..21714386 + GTT->del at 15180103..15180105 + C->del at 2815407
- DE* : deletion -> ALU insertion at 21610891..21612014
- D1b : del->ins 1 bp at 21751917
- E* : del -7T-> ins 8T at 17644332..17644338
- E1b1a : del->GAGA at 16809478..16809479
- E1b1b-M84 : T->del at 21898363
- G* : 5 insertions at 24986774, 26620522, 27341881, 5674986 and 6753301 + 3x del->AT at 24987775..24987776, 26621523..26621524 and 27340875..27340876 + CA->del at 21153068..21153069
- G2a2b2 : del->A at 2888607 (same as R1b)
- H1a1 : insertion of 2 bp at rs2032675
- I* : GT->del at 15027529..15027530
- I1 : A->del at 18077293
- I2a2a-M284 : ACAA->del at 22750461..22750464
- J* : insertion of 1 bp at 21779295
- J1a2 : T>del at 7570823
- J2a1f (M419) : AAAAG->del at 15467906..15467910
- J2a1b3 (L218) : AAG->del at 21739941..21739943
- L1b : insertion of 2 bp at rs13447360
- N* : del->C at 15422968..15422969
- N1c1a1a (L1026) : TA->del at 21892577..21892578
- O* : insertion of 5 bp at rs2032678 + ins 4bp->del 3bp at 15015500
- O2a1-M121 : ins->del -2 bp at 21907170
- O2a1-M134 : C->del at 21716218
- O2a1-M117 : ins->del -4 bp at 21765312..21765315
- O2a4-M333 : del->G at 14847516..14847517
- R* : ACTGCATGCCTTACA->del at 9878852..9878866 (15 bp deletions !)
- R1a : CTGT->del at 16693280..16693281
- R1a1a1 : insertion at 15031111..15031120
- R1b : insertion of 4 bp at rs2032615 + del->A at 2888607 + G->del at 15668048
- R1b-M73 : insertion of 2 bp at rs2032634
- R1b-M18 : del->AA at 21733162
- R1b-L176 : del->AAAAC at 21779256..21779257
- R2a1 : del->A at 14871881..14871882
- T* : del->AACA at rs2032676
- T1 : T->del at 18162486..18162487

Just like for mutations in the coding region of Y-DNA genes, I don't think it's a coincidence that insertions/deletions happened exactly among lineages that would see a dramatic expansion. The ins/del mirror gene mutations in haplogroups BT, B2b1a1, DE, E, J, N and R.

But insertions and/or deletions can more generally be said to define the majority of top-level haplogroups, including A00, A0, A1, BT, B, C, DE, E, G, I, I1, J, N, O, R, R1a, R1b, T and T1. Note that haplogroup F and P didn't make the list and are almost extinct now. Haplogroup H also isn't listed and H2 became almost exictinct, while H1a1 got a new mutation and prospered.


Note that very major haplogroups that have had tremendous historical success at some point in human history, including haplogroups C (9 ins, 4 del), E (8 ins, 7 del), G (5 ins, 4 del), O (9 ins, 3 del) and R (15 del), have the highest number of insertions and/or deletions.

Even relatively deep clades are not ordinary. N1c1-L1026 is the main Finno-Ugric branch, which means the European branch of that otherwise Asian haplogroup. Genetic adaptation to European X chromosomes? In the same line, R1b-M73 is the Asian branch, and R1b-M18 the African branch of an otherwise mainly European haplogroup. Since the X and Y chromosomes do interact with one another, it's not impossible that these are all adaptations to racially different X chromosomes, with a long divergent evolution.

I1 and I2-M284, the two most successful I lineages outside Slavic countries are the only ones with insertions or deletions, and they define exactly I1* and the M284 mutation itself.

R1b-L176 is the most successful subclade of DF27 and achieved remarkably high frequencies in Catalonia in a relatively short time since the Iron Age.

G2a2b2 was the main haplogroup of European Neolithic farmers, and as such was the main Y-haplogroup in Europe for several millennia.

E-M84 is the main Levantine/Jewish subclade of E1b1b, and a particularly successful branch.

O2a1 subclades M117, M121 and M134 are all major East Asian lineages. In the 2002 phylogeny there were simply known respectively as O3e1, O3a and O3d.

Maciamo, thanks for these threads, keep up the great work! Got a question I saw some of your other threads similar to these, what is your opinion of J2a and its spread was it a successful line/movement? I know J2a is very general so lets say clades like M67 and M92 and their downstreams?

[Maciamo]

Maciamo, thanks for these threads, keep up the great work! Got a question I saw some of your other threads similar to these, what is your opinion of J2a and its spread was it a successful line/movement? I know J2a is very general so lets say clades like M67 and M92 and their downstreams?

The success of haplogroup can be seen by how frequent they are now, especially in comparison to the past. In that regard, haplogroups J2a, R1a1a and R1b-M269 were all extremely successful since the Bronze and Iron Ages.

I am trying to establish here if some sort of natural selection affecting fertility benefited some haplogroups more than others. If that is the case, beneficial mutations would have caused a change in fertility or sexual behaviour, or even male physical attributes associated with fertility or dominance, which gave them an edge over other lineages. When looking back at the Palaeolithic, other lineages would have long become extinct. And that is pretty much what ancient DNA is telling us. Plenty of Palaeolithic and Mesolithic lineages tested to date are in fact extinct. That includes some C1a2, I* and I2* subclades that don't exist anymore, but also R1a and R1b branches (e.g. in Mesolithic Karelia and Samara) that didn't leave any descendants today. While the success of Bronze Age haplogroups can be attributed to superior military technology (bronze weapons, horses, chariots), that doesn't work for most haplogroups since the Palaeolithic.

The earliest Out-of-Africa migration (among surviving lineages) was conducted by Y-haplogroups C and D. Yet, for some reason C was considerably more successful, colonising all Europe, the Middle East, North and South Asia, Oceania and later even the Americas, while haplogroup D ended up in secluded places like the Andamans, Tibet and Japan. Why is that? It could be just luck. But both C and D spread in all directions and developed into numerous subclades. Yet everywhere it is consistently C that left more descendants, even in regions where the two were found among the same ethnic groups. The only exception is haplogroup D1b in Japan. If if look at the list of insertions and deletions above, haplogroup C is defined by 13 of them, while D has none, but D1b has one. We don't know at present if C and D spread together from Africa or if they represent separate migrations. But in any case, they would have met very early on and lived together for over 50,000 years until the present. In other words, natural selection was at work for longer between these two lineages that between practically any other two lineages in Homo sapiens prehistory. It could be that D was even more common at first, but that a very slightly improved fertility for C men (yeah, I heard it too :) ) increased its frequency by a fraction of a percent at each generation. Over 50,000 years , or even 10,000 years for that matter, haplogroup C would have almost entirely replaced D in most communities. Haplogroup D could have survived only in specific isolated communities where a founder effect among the first settlers gave them 100% of D and 0% of C to start with. In Japan's case, a new special ins/del mutation for D1b was selected early (about 45,000 years ago) and allowed that lineage to survive.

In Africa, the most ancient lineages that survive today (A00, A0, A0b, A1, B) were all founded by de novo ins/del events. Probably not a coincidence. The oldest among them, A00, is about 250,000 years old and pre-dates the appearance of Homo sapiens by some 150,000 years! Then came one new haplogroup 60,000 years ago, haplogroup E, that got a series of 7 deletions and 8 insertions in one place on its Y chromosome in one go. Those deletions altered the SRY (sex-determining region) gene at the tip of the Y chromosome. That apparently had dramatic effect on the fertility of the carrier, as haplogroup E became the overwhelmingly dominant male lineage in Africa, that no amount of genetic diversity and sexual competition from other haplogroups managed to overcome. In fact, E1b1a got four more fertility-boosting deletions and became the main lineage in Sub-Saharan Africa.

The same thing happened repeatedly with all other major haplogroups. Every time, new beneficial insertions and/or deletions were positively selected over the generations and replaced all other side lineages. That is essentially how haplogroups developed. Take 100 Y-DNA lineages descended from a recent ancestor. One of them possesses a new fertility boosting mutation. What is going to happen? The carriers of this Y chromosome will have more children, or at least more sons, as higher sperm count and motility has been linked to an increased propensity to father sons (because male spermatozoa swim faster but die more easily in the uterus, so a high number of fast swimmers equates to a higher chance of having a boy). The X chromosome will develop new adaptations of its own to counterbalance those effects, but that process takes time and only works as long as men mate with women from their own tribe or ethnic group, where those newly evolved X chromosomes are present. When men start conquering vast expanses of land in a short time and mating with indigenous women, as has happened with Bronze Age Indo-Europeans and later Spaniards and Portuguese in the Americas, it is very likely that these conquerors, if they possess Y chromosomes with heightened fertility, will end up having a biased sex-ratio that slightly favour boys, thus quickly spreading their Y-DNA. This is one of the reasons why new Y-DNA haplogroups typically spread faster outside their original ethnic group than within it, where X chromosomes have had time to adapt progressively to each new Y-boosting mutation.


To answer your question about J2a, you will notice that haplogroup J is defined by the 12f2 STS polymorphism, linked to the deletion of the L1PA4 element in the HERV15yq2 sequence, but also by an insertion in a different region. Then two J2a1 subclades possess additional block deletions: the Iranian J2-M419 and the Levantine J2-L218, right under M67. But overall I think that the success of J2a1 owes quite a lot to its political and military success since the Kura-Araxes period, be it with the ancient Anatolians (Hurrians, Hittites, etc.), or of course the Phoenicians, Greeks and Romans.

When I originally posted this thread three years ago, I only considered mutations within Y-chromosomal genes as important for improvements in fertility. I have since considered that insertions and deletions may be just as important. There is maybe another factor I haven't considered yet that also plays a role in fertility. It could be the role played by the X chromosome itself, and not just on the woman's side, but also for men, as the X chromosome also plays a role in male health and fertility. Autosomal genes could also play a role, such as the way a woman's body's immune system reacts to spermatozoa. Some are more aggressive than others, which can lead to female infertility (the immune system destroying all 'foreign cells'). A lower immune response would favour boys as male spermatozoa swim faster but are killed off more easily. The same is true for the cellular acidity, which is in part regulated by mitochondrial DNA. Members of haplogroups U and K have more alkaline cells, which tends to favour boys as male spermatozoa survive better in alkaline environments. A too welcoming uterine environment (low immune reaction + alkaline uterus) would skew the sex ratio toward more boys.

[Azzurro]

The success of haplogroup can be seen by how frequent they are now, especially in comparison to the past. In that regard, haplogroups J2a, R1a1a and R1b-M269 were all extremely successful since the Bronze and Iron Ages.

I am trying to establish here if some sort of natural selection affecting fertility benefited some haplogroups more than others. If that is the case, beneficial mutations would have caused a change in fertility or sexual behaviour, or even male physical attributes associated with fertility or dominance, which gave them an edge over other lineages. When looking back at the Palaeolithic, other lineages would have long become extinct. And that is pretty much what ancient DNA is telling us. Plenty of Palaeolithic and Mesolithic lineages tested to date are in fact extinct. That includes some C1a2, I* and I2* subclades that don't exist anymore, but also R1a and R1b branches (e.g. in Mesolithic Karelia and Samara) that didn't leave any descendants today. While the success of Bronze Age haplogroups can be attributed to superior military technology (bronze weapons, horses, chariots), that doesn't work for most haplogroups since the Palaeolithic.

The earliest Out-of-Africa migration (among surviving lineages) was conducted by Y-haplogroups C and D. Yet, for some reason C was considerably more successful, colonising all Europe, the Middle East, North and South Asia, Oceania and later even the Americas, while haplogroup D ended up in secluded places like the Andamans, Tibet and Japan. Why is that? It could be just luck. But both C and D spread in all directions and developed into numerous subclades. Yet everywhere it is consistently C that left more descendants, even in regions where the two were found among the same ethnic groups. The only exception is haplogroup D1b in Japan. If if look at the list of insertions and deletions above, haplogroup C is defined by 13 of them, while D has none, but D1b has one. We don't know at present if C and D spread together from Africa or if they represent separate migrations. But in any case, they would have met very early on and lived together for over 50,000 years until the present. In other words, natural selection was at work for longer between these two lineages that between practically any other two lineages in Homo sapiens prehistory. It could be that D was even more common at first, but that a very slightly improved fertility for C men (yeah, I heard it too :) ) increased its frequency by a fraction of a percent at each generation. Over 50,000 years , or even 10,000 years for that matter, haplogroup C would have almost entirely replaced D in most communities. Haplogroup D could have survived only in specific isolated communities where a founder effect among the first settlers gave them 100% of D and 0% of C to start with. In Japan's case, a new special ins/del mutation for D1b was selected early (about 45,000 years ago) and allowed that lineage to survive.

In Africa, the most ancient lineages that survive today (A00, A0, A0b, A1, B) were all founded by de novo ins/del events. Probably not a coincidence. The oldest among them, A00, is about 250,000 years old and pre-dates the appearance of Homo sapiens by some 150,000 years! Then came one new haplogroup 60,000 years ago, haplogroup E, that got a series of 7 deletions and 8 insertions in one place on its Y chromosome in one go. Those deletions altered the SRY (sex-determining region) gene at the tip of the Y chromosome. That apparently had dramatic effect on the fertility of the carrier, as haplogroup E became the overwhelmingly dominant male lineage in Africa, that no amount of genetic diversity and sexual competition from other haplogroups managed to overcome. In fact, E1b1a got four more fertility-boosting deletions and became the main lineage in Sub-Saharan Africa.

The same thing happened repeatedly with all other major haplogroups. Every time, new beneficial insertions and/or deletions were positively selected over the generations and replaced all other side lineages. That is essentially how haplogroups developed. Take 100 Y-DNA lineages descended from a recent ancestor. One of them possesses a new fertility boosting mutation. What is going to happen? The carriers of this Y chromosome will have more children, or at least more sons, as higher sperm count and motility has been linked to an increased propensity to father sons (because male spermatozoa swim faster but die more easily in the uterus, so a high number of fast swimmers equates to a higher chance of having a boy). The X chromosome will develop new adaptations of its own to counterbalance those effects, but that process takes time and only works as long as men mate with women from their own tribe or ethnic group, where those newly evolved X chromosomes are present. When men start conquering vast expanses of land in a short time and mating with indigenous women, as has happened with Bronze Age Indo-Europeans and later Spaniards and Portuguese in the Americas, it is very likely that these conquerors, if they possess Y chromosomes with heightened fertility, will end up having a biased sex-ratio that slightly favour boys, thus quickly spreading their Y-DNA. This is one of the reasons why new Y-DNA haplogroups typically spread faster outside their original ethnic group than within it, where X chromosomes have had time to adapt progressively to each new Y-boosting mutation.


To answer your question about J2a, you will notice that haplogroup J is defined by the 12f2 STS polymorphism, linked to the deletion of the L1PA4 element in the HERV15yq2 sequence, but also by an insertion in a different region. Then two J2a1 subclades possess additional block deletions: the Iranian J2-M419 and the Levantine J2-L218, right under M67. But overall I think that the success of J2a1 owes quite a lot to its political and military success since the Kura-Araxes period, be it with the ancient Anatolians (Hurrians, Hittites, etc.), or of course the Phoenicians, Greeks and Romans.

When I originally posted this thread three years ago, I only considered mutations within Y-chromosomal genes as important for improvements in fertility. I have since considered that insertions and deletions may be just as important. There is maybe another factor I haven't considered yet that also plays a role in fertility. It could be the role played by the X chromosome itself, and not just on the woman's side, but also for men, as the X chromosome also plays a role in male health and fertility. Autosomal genes could also play a role, such as the way a woman's body's immune system reacts to spermatozoa. Some are more aggressive than others, which can lead to female infertility (the immune system destroying all 'foreign cells'). A lower immune response would favour boys as male spermatozoa swim faster but are killed off more easily. The same is true for the cellular acidity, which is in part regulated by mitochondrial DNA. Members of haplogroups U and K have more alkaline cells, which tends to favour boys as male spermatozoa survive better in alkaline environments. A too welcoming uterine environment (low immune reaction + alkaline uterus) would skew the sex ratio toward more boys.

Brilliant analysis, makes a lot of sense when you look at the large scope of things and the details, maybe J2a1 owes some of its success too as being a major maritime and trade culture as well, in the late bronze age the vast trading system from Egypt to Greece might have been an area where J2a1 thrived, the copper and precious metals trade might have been directly involved, what are your opinions on this? In terms of C is it found in Europe today? I guess it is really rare, even with G seeing that it was the major neolithic farmer haplogroup it is found at less than 10% in most European countries, it must also have had its difficulties.

[Regio X]

By the way: http://www.nature.com/nrg/journal/va....2016.106.html
3 Oct 2016

Abstract

"Once deemed heretical, emerging evidence now supports the notion that the inheritance of acquired characteristics can occur through ancestral exposures or experiences and that certain paternally acquired traits can be 'memorized' in the sperm as epigenetic information. The search for epigenetic factors in mammalian sperm that transmit acquired phenotypes has recently focused on RNAs and, more recently, RNA modifications. Here, we review insights that have been gained from studying sperm RNAs and RNA modifications, and their roles in influencing offspring phenotypes. We discuss the possible mechanisms by which sperm become acquisitive following environmental–somatic–germline interactions, and how they transmit paternally acquired phenotypes by shaping early embryonic development."