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Strange Y-Chromosome Bottleneck: Male Diversity / Population Collapse?

EnolaGaia

I knew the job was dangerous when I took it ...
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Among the benefits of advances in genetic testing and analysis are capabilities for analyzing genomic data from thousands of years ago. This permits some initial clues to prehistoric and ancient population features and distributions. Given the relatively sparse (fossil) data and the novelty of the technologies, the results should be treated as tentative or suggestive.

You've probably seen articles discussing what genomic research suggests about the rise and dissemination of human ancestors in the distant past.

There's a lesser-known mystery that's surfaced in such retrospective genomic research concerning the possibility of a notable collapse affecting human males alone, occurring somewhere between 5,000 and 10,000 years ago.

This story began in 2015, with the publication of the following article:

A recent bottleneck of Y chromosome diversity coincides with a global change in culture
Genome Research. 2015. 25: 459-466
https://genome.cshlp.org/content/25/4/459.long

Abstract
It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

(Full article @ the URL cited above)

The research was originally aimed at finding clues relating to the 'Out of Africa' scenario. It turned out that in addition to their originally expected results, the team discovered what appears to be a marked 'bottleneck' in Y-chromosome (i.e., exclusively male) diversity circa 10,000 years ago. This bottleneck could represent a radical narrowing of male genetic diversity or even a collapse in the human male population.

If interpreted in terms of population, the estimated figures could be taken to suggest up to 17 times as many females as males during the bottleneck period.

The cause of this bottleneck wasn't clear, and the 2015 paper suggests it must have been related to non-biological (e.g., cultural) changes:

(NOTE: Estimated regional population is denoted by Ne )

... The surprisingly low estimates of the male Ne might be explained either by natural selection affecting the Y chromosome or by culturally driven sex-specific changes in variance in offspring number. As the drop of male to female Ne does not seem to be limited to a single or a few haplotypes (Supplemental Fig. S3), selection is not a likely explanation. However, the drop of the male Ne during the mid-Holocene corresponds to a change in the archaeological record characterized by the spread of Neolithic cultures, demographic changes, as well as shifts in social behavior (Barker 2006). The temporal sequence of the male Ne decline patterns among continental regions (Supplemental Fig. S4B) is consistent with the archaeological evidence for the earlier spread of farming in the Near East, East Asia, and South Asia than in Europe (Fuller 2003; Bellwood 2005). A change in social structures that increased male variance in offspring number may explain the results, especially if male reproductive success was at least partially culturally inherited (Heyer et al. 2005). ...
 
"Doctor, you mentioned the ration of ten women to each man. Now, wouldn't that necessitate the abandonment of the so called monogamous sexual relationship, I mean, as far as men were concerned?"

"Regrettably, yes. But it is, you know, a sacrifice required for the future of the human race. I hasten to add that since each man will be required to do prodigious... service along these lines, the women will have to be selected for their sexual characteristics which will have to be of a highly stimulating nature"
 
More recently ...

This new article on Live Science summarizes the conundrum and describes a recent simulation study suggesting the rise of strongly patrilineal societies and warfare might explain the apparent bottleneck.

Why Do Genes Suggest Most Men Died Off 7,000 Years Ago?
Modern men's genes suggest that something peculiar happened 5,000 to 7,000 years ago: Most of the male population across Asia, Europe and Africa seems to have died off, leaving behind just one man for every 17 women.

This so-called population "bottleneck" was first proposed in 2015, and since then, researchers have been trying to figure out what could've caused it. One hypothesis held that the drop-off in the male population occurred due to ecological or climatic factors that mainly affected male offspring, while another idea suggested that the die-off happened because some males had more power in society, and thus produced more children.

Now, a new paper, published May 25 in the journal Nature Communications, offers yet another explanation: People living in patrilineal clans (consisting of males from the same descent) might have fought with each other, wiping out entire male lineages at a time. ...

That ratio of 17 females for every one male "struck us as being very extreme, and there must be another explanation," said senior study author Marcus Feldman, a population geneticist at Stanford University in California. According to their new explanation, the male population didn't take a nosedive, but rather the diversity of the Y chromosome decreased due to the way people lived and fought with each other. In other words, there weren't actually fewer males, just less diversity among the males.

Humans have 23 pairs of chromosomes that carry most of our genes. Of these, the 23rd pair is what determines our sex: Whereas females have two X chromosomes, males have one X chromosome and one Y chromosome.

Because offspring inherit one chromosome from each parent, genes usually get shuffled around, increasing the diversity across species. But the Y chromosome, having no female counterpart, doesn't get shuffled, so it stays pretty much the same from grandfather to father to son (save for any mutations that occur, which explains why the Y chromosome does differ among males).

War might've caused the Y chromosome bottleneck

To test their theory, the researchers conducted 18 simulations in which they created different scenarios for the bottleneck that included factors such as Y chromosome mutations, competition between groups, and death. Their simulations showed that warfare between patrilineal clans could have caused this so-called "Y chromosome bottleneck," because the members of each patrilineal clan would have very similar Y chromosomes to each other. So, if one clan killed off another, it would also slash the chance of that family's Y chromosome moving on to offspring.

In the researchers' simulations in which patrilineal clans didn't exist, however, the bottleneck didn't occur.

What's more, there was no such bottleneck in the women of the time, as is shown by mitochondrial DNA — a type of DNA that's passed down only from mother to child.

"In that same group, the women could have come from anywhere," Feldman told Live Science. "They would've been brought into the group from either the victories that they had over other groups, or they could've been females who were residing in that area before."

As an example, he added, if you look at colonization throughout history, people generally "killed all the men and kept the women for themselves."

Monika Karmin, a population geneticist at the University of Tartu in Estonia who was not part of the new study, told Live Science that the "beauty of their study" is the way the researchers framed their hypothesis and demonstrated that "fighting clans are indeed likely to cause a drastic drop in male genetic diversity. ...

FULL STORY: https://www.livescience.com/62754-warring-clans-caused-population-bottleneck.html
 
Here's the recent published study cited in the Live Science article:

Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck

Abstract

In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000–7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among these groups. Our analysis shows that this sociocultural hypothesis can explain the inference of a population bottleneck. We also show that our hypothesis is consistent with current findings from the archaeogenetics of Old World Eurasia, and is important for conceptions of cultural and social evolution in prehistory.

FULL ARTICLE: https://www.nature.com/articles/s41467-018-04375-6
 
In case you'd like a visual aid for the phenomenon, here's the key figure from the Karmin et al. (2015) article cited in post #1.

The graph on the left illustrates Y chromosomal (exclusively patrilineal) diversity, and the graph on the right illustrates mitochondrial DNA (exclusively matrilineal) diversity. The 'collapse' is seen as the dramatic downward 'notch' in the left-hand graph.

F2.large.jpg


From: Karmin et al. (2015)
Available via Creative Commons Attribution / Non-Commercial license.
SOURCE: https://genome.cshlp.org/content/25/4/459.long
 
Among the benefits of advances in genetic testing and analysis are capabilities for analyzing genomic data from thousands of years ago. This permits some initial clues to prehistoric and ancient population features and distributions. Given the relatively sparse (fossil) data and the novelty of the technologies, the results should be treated as tentative or suggestive.

You've probably seen articles discussing what genomic research suggests about the rise and dissemination of human ancestors in the distant past.

There's a lesser-known mystery that's surfaced in such retrospective genomic research concerning the possibility of a notable collapse affecting human males alone, occurring somewhere between 5,000 and 10,000 years ago.

This story began in 2015, with the publication of the following article:

A recent bottleneck of Y chromosome diversity coincides with a global change in culture
Genome Research. 2015. 25: 459-466
https://genome.cshlp.org/content/25/4/459.long



(Full article @ the URL cited above)

The research was originally aimed at finding clues relating to the 'Out of Africa' scenario. It turned out that in addition to their originally expected results, the team discovered what appears to be a marked 'bottleneck' in Y-chromosome (i.e., exclusively male) diversity circa 10,000 years ago. This bottleneck could represent a radical narrowing of male genetic diversity or even a collapse in the human male population.

If interpreted in terms of population, the estimated figures could be taken to suggest up to 17 times as many females as males during the bottleneck period.

The cause of this bottleneck wasn't clear, and the 2015 paper suggests it must have been related to non-biological (e.g., cultural) changes:

(NOTE: Estimated regional population is denoted by Ne )
Mad hypothetical idea-type thing...maybe they had an ancient form of SJW-led feminism and MGTOW?
We're seeing history repeat itself.
 
More seriously ...

From the 19th century onward there were some scholars who postulated there was an earlier stage of human social development in which females dominated the socio-cultural order. The popularity of this sort of theorization peaked in the 1990's before waning in the face of archaeological evidence failing to support - or in some cases directly refuting - certain aspects of the notion.

If this tentative indication of a male diversity bottleneck turns out to be valid, it could eventually lead to a reappraisal of gender dominance in prehistoric socio-cultural affairs and even the pendulum of scholarly opinion swinging the other way.

On the other hand, it might just as easily lead to a concept of a widespread socio-cultural motif even more male-dominated than the one we've known during our lifetimes.

These are examples of the potential ramifications that make me find this story very interesting ...
 
These are examples of the potential ramifications that make me find this story very interesting

I also find this very interesting!
As much as I would like to believe that we, at one time, lived in some female dominated Amazonian Utopia, (LOL!), what it really seems likely to be is what happens with the Mormons. The rich old powerful men get 30 wives, and their first pick of any young women coming of age (12 -15, btw) so the young men get no wives and get to have no children. The breeding "rights" get concentrated in the few "elders" (male) who mate with all the females.

This also fits roughly with the (supposed) timeline of the rise of agriculture, and the concentration of wealth within society. Which would've very quickly turned to the concentration of wealth within certain individuals, which equals power over those with less. The cycle, over time, just exacerbates the imbalance, and viola, you have the bottleneck.

And just as the graph shows, you can only push that so far, because you still need the general population to have a stake in the society you want to rule, other wise you have no power over them. They will just up and walk away. They have no family to support or protect, so you can't threaten them with much.

Also, the fact that the majority of us may be descended from a small group of greedy, power hungry, sex mad dictators could explain a lot!!!
 
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... The breeding "rights" get concentrated in the few "elders" (male) who mate with all the females.

This also fits roughly with the (supposed) timeline of the rise of agriculture, and the concentration of wealth within society. Which would've very quickly turned to the concentration of wealth within certain individuals, which equals power over those with less. The cycle, over time, just exacerbates the imbalance, and viola, you have the bottleneck.
...

Yep - that's one of the scenarios that most clearly resonates with the timeframe, the shift from hunter / gatherer to settled / agrarian lifestyles, and the downturn in male diversity (if seen as a collapse in variance rather than a collapse in male population).

There are all sorts of spins one can project onto this evidence.

Perhaps the most important aspect of this is that it essentially opens up another dimension of potential understanding regarding that critical period. In the past, we've had to rely on the artifacts and burials left behind, then try to retro-project ideas about the people who lived then.

With this genomics-based data, we're now afforded a chance to deal with evidence concerning the people themselves.
 
We hear that the quality - if not the quantity - of modern sperm ain't what it used to be. The blame has been laid at the door of science with its pesky plastic compounds. Maybe this time around that is true! Might there not have been previous drops in male fertility due to environmental factors, such as volcanic debris etc? :mattack:
 
We hear that the quality - if not the quantity - of modern sperm ain't what it used to be. The blame has been laid at the door of science with its pesky plastic compounds. Maybe this time around that is true! Might there not have been previous drops in male fertility due to environmental factors, such as volcanic debris etc?

It's conceivable, but ... An environmental factor would need to be quite widespread and something that affected males far more than females.

The apparent timeframe would put the collapse in the period when the Saharan region was in the last stages of shifting into the arid desert we know today, but that represents a relatively localized environmental stressor.

The estimated timeframe for the collapse's onset is some few thousands of years after the close of the Younger Dryas, so it's difficult to correlate that period directly to whatever happened.

Some sort of disease / plague might be a more plausible factor, particularly if one assumes males (generally) were the ones most likely to be operating 'afield' and interacting with other groups. It wouldn't need to be a fatal disease if it commonly resulted in male survivors' infertility. The modern version of mumps can wreak havoc on the testicles in pubescent and adult males, but residual infertility is relatively rare. A hypothetical ancient 'super-mumps' that ravaged males during that period might explain it. The disappearance of such a 'super-mumps' virus would be easily explained by invoking natural selection. If you render your host incapable of reproduction you lose your 'meal ticket'.

There are studies that strongly suggest diet can affect male fertility, but as far as I know this is still an issue requiring further research. One factor cited in the studies to date is a correlation between high intake of red meat and fats and infertility. One could speculate that those ancient folks who clung to hunting as their primary food source might have been relatively infertile compared to the new-wavers who settled down and grew crops.
 
Coincidentally, there might be one or more clues in this new New York Times article:

Secrets of the Y Chromosome

https://www.nytimes.com/2018/06/11/health/men-y-chromosome.html?partner=rss&emc=rss

For one thing:

Researchers have discovered that, contrary to longstanding assumptions, the Y chromosome is not limited to a handful of masculine tasks, like specifying male body parts in a developing embryo or replenishing the sperm supply in an adult man.

New evidence indicates that the Y chromosome participates in an array of essential, general-interest tasks in men, like stanching cancerous growth, keeping arteries clear and blocking the buildup of amyloid plaque in the brain.

As a sizable percentage of men age, their blood and other body cells begin to spontaneously jettison copies of the Y chromosome, sometimes quickly, sometimes slowly. That unfortunate act of chromosomal decluttering appears to put the men at a heightened risk of Alzheimer’s disease, leukemia and other disorders.

I find this tidbit even more interesting and potentially relevant ...

... Although human DNA has been found to contain vestiges of our dalliances with Neanderthals from about 50,000 years ago, none of those genomic imprints are on the human Y chromosome.

By the look of it, something specific to the Neanderthal Y chromosome ultimately proved inimical to human health and survival, and so any trace of the Neanderthal Y chromosome was ejected from the human gene pool like a poorly matched kidney.

The immune system analogy may be particularly apt. Fernando Mendez, a geneticist, and his colleague Carlos Bustamante of Stanford University reported that one of the notable differences between the human and Neanderthal Y chromosomes lies in a gene linked to transplant rejection.

Whatever the reason for the purification of the human Y over time, women’s equivalent X chromosome does not appear to have been similarly cleansed, with the result that women on average may be slightly more Neanderthal than men ...
 
@EnolaGaia , because of the World Wars of the 20th Century, the sudden absence of men on some western societies, paved the way for the liberation of the women (in the factories, offices, but also arts and even military), that filled the gaps left by the men when they left to war (had they came back or not). Wouldn't we have some hints of a similar tendency back in the time of the Y chromossome bottleneck, in your opinion?
 
@EnolaGaia , because of the World Wars of the 20th Century, the sudden absence of men on some western societies, paved the way for the liberation of the women (in the factories, offices, but also arts and even military), that filled the gaps left by the men when they left to war (had they came back or not). Wouldn't we have some hints of a similar tendency back in the time of the Y chromossome bottleneck, in your opinion?

The notion that the Y chromosome 'collapse' might be linked to warfare is one of the suggestions made to date. The researchers cited above showed an inclination to attribute the collapse to socio-cultural developments and events, within which heightened warfare / conflict would be an obvious candidate.

On the other hand, the apparent correlation of the estimated collapse trend across all regions suggests the change happened everywhere at roughly the same time. I'm not sure how well this fits with a primarily, much less a purely, socio-cultural cause. Different groups in different places were at different stages of development (e.g., onset of agriculture; shift to more settled lifestyles).

The problem is that the archaeological record is sparse for that critical time period, even if one considers only a single region.
 
The suggestion relatively few males contributed to the ongoing human genetic record isn't new. This 2008 item posted on FTMB suggests polygamy played a large role:

Polygamy left its mark on the human genome
forum.forteantimes.com/index.php?threads/polygamy-left-its-mark-on-the-human-genome.35021/
Link is obsolete. The current link is:
https://forums.forteana.org/index.php?threads/polygamy-left-its-mark-on-the-human-genome.35021/


In effect, this was an early hint at the socio-cultural interpretation of the story cited here in this thread.
 
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