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Y Chromosomes in the News and #MeToo

The firing of CBS CEO Leslie Moonves for his alleged history of revolting attacks on women and the upcoming one-year anniversary of Ronan Farrow’s seminal New Yorker piece on Harvey Weinstein and of Alyssa Milano’s #MeToo tweet echoing Tarana Burke’s 2006 call-to-action got me pondering the Y chromosome.

Genomically speaking, the diminutive Y is the only thing that distinguishes males from females (see “Y Envy.”) Both sexes have X chromosomes, and although mitochondrial DNA passes from females to all offspring, we all have mitochondria. Only the Y is the male’s alone.

If size matters, the Y chromosome loses. The human X has about 1500 protein-encoding genes compared to the Y’s 231, some of which have counterparts on the X. Only a handful of Y genes, in the “male-specific region” of the chromosome, are uniquely male. They include the SRY gene that determines maleness and a few others that control fertility.

So the Y chromosome can tell us some interesting things about the male of the species.

I’d love to peruse the Y chromosomes of Les Moonves, Harvey Weinstein, Charlie Rose, and a few other notables to see if they perhaps share a gene variant controlling testosterone. Maybe they are descendants of Genghis Khan. His Y chromosome genetic marker pattern was famously found in 16 Asian populations at an astounding frequency of 8%, making up ∼0.5% of the Y chromosomes in the world. Calculations using mutation rates suggest origin of the distinctive chromosome in Mongolia abut 1,000 years ago. Genghis and his many male descendants spreading their seed explains the genetic evidence.

Other studies of the Y, in diverse species, are eclectic and intriguing. Here are a few recent ones:

War, What Is It Good For?

Between 7,000 and 5,000 years ago, the diversity of DNA sequences comprising human Y chromosomes plummeted, extrapolated from contemporary DNA sequence comparisons, geography, and history and using mutation rates as a molecular clock. Such population bottlenecks often reflect an event, such as poaching reducing the cheetah populations in Africa into a state of near-genetic uniformity. Tian Chen Zeng, a sociology major at Stanford, wondered what happened to men during that time to make their Y chromosomes so alike.

Zeng, his computational science major friend Alan Aw, and biology professor Marcus Feldman used computer modeling of population dynamics to deduce what might have triggered the plunging genetic diversity among men known as the “post-Neolithic Y chromosome bottleneck.”

The trio started with the fact that groups in Africa, Europe, and Asia at that time were patrilineal – the male ancestral line determined membership. Even though the Y chromosomes differed genetically among extended families, within the groups the tiny chromosomes were remarkably uniform in DNA sequence.

Their hypothesis: a major event wiped out entire groups, leaving only a few families to repopulate, which would drive a classic bottleneck.

The answer: WAR. Simulations that diminish each patrilineal group instead of wholesale disappearances didn’t lead to a bottleneck. “Historical and geographical patterns of cultural interactions could explain the patterns in genetics,” said Dr. Feldman, who is extending the approach to explain other sociological scenarios. Their work is published in Nature Communications.

Making Dingoes Great Again

Y chromosome and mitochondrial DNA sequences reveal that dingoes came to Australia twice, traversing a land bridge that extended from Papau New Guinea, 8,000 to 10,000 years ago. The diversity of Y chromosomes among the wild dogs suggests that the males have gotten around a lot more than the females and have picked up DNA from all sorts of canines, domestic and wild, mostly within southeastern Australia. Kylie Cairns, from the University of New South Wales and colleagues suggest ways to keep dingoes distinct, such as dog owners using “improved dingo-proof fencing.” The study appears in  Ecology and Evolution.

Supermales!

Flowering plants have sex chromosomes too. In garden asparagus, males are XY, females XX, and YY “supermales” are bred in the greenhouse. Crossing females (XX) to supermales (YY) produces all XY males, which are valued crops because they live longer and aren’t full of pesky seeds.

(Piet Beurskens)

Before the recent sequencing of the asparagus genome, at the University of Georgia, breeders had to conduct time-consuming backcrosses to distinguish XY from YY, but have now identified genetic markers to speed up the process. Plus, better understanding of the genes that determine sex have made it possible to “manipulate the asparagus Y chromosome to convert males to females or hermaphrodites,” said Jim Leebens-Mack, professor of plant biology and senior author on the study, which was published in Nature Communications.

Crime Scene Conundrums

Mikkel M. Andersen from the University of Copenhagen and David J. Balding of the University of Melbourne and University College London tackled the limited utility of consulting Y chromosome sequences in forensics cases. The problem: many males have matching Ys, especially within populations and communities. The analysis appears in PLOS Genetics.

Many men share Y chromosome sequences (Mikkel Anderson)

The Y chromosome isn’t particularly valuable in the forensic setting to begin with. It’s small, has very few genes, and because there’s only one Y, it can’t exchange sections with a partner the way two X’s or a pair of autosomes can. That’s why Y chromosomes are alike, identical even, within an extended family. It was possible to deduce in 1998 that Thomas Jefferson fathered slave Sally Hemings youngest son Eston and perhaps others, from other of the president’s relatives who had the same Y. His only son had died in infancy. Ironically, the Jefferson Y belongs to a group that includes only about 1 percent of the world’s human Y chromosomes. Of course outing the distinctive chromosome just confirmed what many suspected.

Andersen and Balding argue that courts should be aware of the likelihood that even distantly related men might share a Y chromosome sequence, and so other evidence is critical. They have developed software to assist Y chromosome forensic analysis, especially with mixtures.

Mummy Half-Brothers

Despite the paucity of information on the Y, sometimes comparisons allow distinctions. Consider the “two brothers” of the Manchester Museum’s Egyptian mummy collection. Recent DNA sequencing of their Y chromosomes, published in The Journal of Archaeological Science, rewrote the story of their parentage. Khnum-nakht and Nakht-ankh, who lived around 1800 BC, were discovered at Deir Rifeh, a village 250 miles south of Cairo, in 1907.

(Manchester Museum)

The men were buried together and hieroglyphic inscriptions on the coffins indicated they were the sons of an unnamed local governor. But when Egyptologist Margaret Murray unwrapped them in 1908, she concluded that their skeletons were too different for them to have been brothers. She suggested that one had been adopted.

More recently, researchers from the University of Manchester extracted DNA from the mummies’ teeth to settle a long-standing disagreement over their kinship. A clue was that their mothers had the same name, and in fact both men shared her mitochondrial genome. But their Y chromosomes differed. Khnum-nakht and Nakht-ankh were half-brothers.

The Monotony of the Human Y – If It Ain’t Broke …

The human Y chromosome is littered with repeated DNA sequences. With all the fuss over protein-encoding genes, the subtext written in the repeats is often under-appreciated.

Levi Teitz, working in the lab of Y guru David Page at the Whitehead Institute and colleagues scrutinized Y sequences from 1,216 males in the 1000 Genomes Project. They report in The American Journal of Human Genetics that Y chromosome repeat numbers are remarkably alike among men, compared to repeat numbers in other species.

Consistency in DNA sequences, even noncoding ones, means that whatever the Y chromosomes of humans are doing, it’s working. Natural selection is favoring DNA sequences that lead to successful reproduction. The uniformity of human Y chromosomes also explains their relative uselessness in forensics, compared to more information-packed chromosomes.

#MeToo: Don’t Blame Biology, Sexual Assault is a Choice

It’s easy to see parallels in modern men behaving badly to the actions of Genghis Khan and his crew, to Thomas Jefferson and others who regarded their female slaves as property, to men at war over the millennia, and even back to the carousing dingoes.

But I’m not allowing the XYs who’ve been outed thanks to the Weinstein effect and the #MeToo movement, as well as those dumb enough to publicly brag about it, to blame their tiny weeny Y chromosomes for violence against women. Although in many mammalian species males physically dominate females, hormonally driven to reproduce, the human brain is supposed to enable a higher level of decision-making, of self-control, and of recognition of the abuse of power. Being inebriated and not remembering an assault, or defining an attack differently than the victim does, are not valid excuses.

The ever-growing list of XYs who deny or attempt to justify sexually violent behavior cannot blame their biology. It’s their choice.

 

 

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