Tag Archives: tracing DNA tribe

The vanishing Y chromosome

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It was a cold day for Vancouver. He looked out of the window, past the drooping branches of the cedar trees. The sky was clear. He checked the clock. It was just before six in the morning. The alarm was set at six twenty. He got up and shuffled to the bathroom, preparing for the day. It was Monday, and the start of another week. He was back in Vancouver, after a week in Houston, Texas.
By the time he left home, it was seven in the morning. Temperature had dropped a few degrees below freezing. There was no snow. The car had gotten a bit cold in the garage overnight, so he switched the Air conditioner on, setting the internal temperature to 19 degrees. His thoughts veered to the issue of the speeding Y-chromosome.
He knew the last of the 23 pairs of chromosomes in his DNA was the sex determining one. He knew XY makes a male and XX makes a female. He knew the Y-chromosome comes down from father to son, but does not go to the daughter. Y-chromosome and its DNA trace could therefore be analyzed to track paternal ancestry of a person. He had actually gotten it done for his own genes, and was proceeding with more detailed tests on the same item, hoping to peer further into his ancestral footprints.
Females do not inherit this Y chromosome, and therefore, this method of paternal ancestry cannot be used on females.
But that was not what was bothering him. This Y-chromosome had apparently evolved rather fast for humans, and the difference in this area between humans and chimps are far greater than the average difference in the entire genome of man and chimp.
He sipped his cup of coffee, and lifted his camera to the eye. He was topped at a traffic light, and the view in front showed not only the street and the city, but also the mountain range in the distance, with its snow covered peaks and the floating traces of clouds against a low contrast blue-gray sky. It was pretty. He knew the scene would change minute to minute, as the sun prepared to emerge over the sky. He squeezed off a shot, and then another. Setting the camera down on the passenger seat, he eased the car forward again. The light had turned green.
What bothered him, was the gossip that the human Y-chromosome was rotting, and on its way to extinction. Some believed it because it had, over the millions of years since it became sex determining item for mammals, been losing sections of itself, thereby getting smaller and smaller, compared to its partner, the X chromosome. Today, the human Y-chromosome apparently had lost 97 percent of its original content The story was, according to papers coming out, started 300 million years ago, as the mammalian class separated itself from the others.
However, the monotremes, such as the platypus, apparently had a different system of sex determination, based on five pairs of chromosomes, and perhaps closer to the birds than the rest of the mammals. But when it came to placental mammals, the 23 chromosome was pretty much the sex determinant, out of which the X-chromosome remained healthy and able to repair itself from defects through recombination, while the Y apparently shut itself off from recombination hundreds of millions of years ago, and since then had been losing sections of itself continuously.
He had another sip of coffee. But, apparently, it was not all lost, and the male humans need not panic, yet. If the reports now coming out of MIT researchers are to be believed, the Y-chromosome went into a sort of free fall initially, but later more or less steadied itself, perhaps through process of natural selection. If someone had a miniscule and non functioning Y chromosome, he could not produce male off springs, and would therefore go extinct himself, leaving the field ripe for more successful holders of Y-chromosome.
Whatever the reason, a greatly shrunk liliputian Y-chromosome was stable, and here to stay.
He scratched his chin and turned the car into West Hastings street, within sight of his office. He wondered if and how he might insert that fact about the incredible shrinking Y-chromosome, into the story of Neil, as he dealt with his job, his Indian perspective on life in Canada, and his dealings with a burgeoning romance with Mabel, while the same time having to deal with the emergence of a second woman. He might write a few pages on it in the evening, he decided, as he pulled his car into the entrance driveway to the underground parking.
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Neil was slightly self conscious. He had put on a clean shirt and a a red pullover. He had actually stood before the bathroom mirror and watched himself for a while, and combed his unruly hair once more. This was an activity he was normally not known to engage in. But today, he had taken some trouble to actually fish out a cologne and dab his face with it after shaving.
The thing was, he was taking Mabel out of a date. This was the first time he was taking anybody out on a date in Canada. And if one discounts the few more or less forgettable events during his last vacation in India, and the trip to Shanghai, China, this was the first time in many years that he was taking a girl out. He had felt mildly apprehensive.
The other problem he had was deciding where to take her. Dinner was easy. Though he was not a wine connoisseur, he had been around the world enough to get around in international cuisine. He was not much of a drinker and did not really enjoy spending hours in a pub. Also, he was not a good dancer and did avoided noisy night clubs. The collective din of the dim lit and crowded atmosphere gave him a headache, and he felt out of place. He identified  this to be a problem, since many of his colleagues and folks he knew did like hanging out in pubs and nightclubs.
So he had asked Mabel out for a movie and a dinner. They had a choice of movies that were running in the cineplex nearby. The movie about Edgar Hoover was one. But somehow, watching a movie about a power hungry ugly gay man that secretly kept tabs on senators did not seem to be the best choice for a first date with a pretty woman.
Then there was a documentary about the history of Detroit. Neil decided to discount that too. Also, an Indian hindi movie with English subtitles was on, but he did not want to push that one on Mabel. Besides, he was not fond of formula movies in Hindi. He did not know if the movie was formula or above average, but did not feel enthusiastic about finding out.
Finally, he had decided to ask Mabel if she might like to see a film about a trailer park teenage girl that had stolen a car and driven a few hundred miles to a city she had never been to before, to search for a father she had never seen before either. Mabel had agreed readily, on phone. In fact, she did not seem to care which movie he liked to see, and was equally agreeable to see any. And after the movie, he said he’d like to take her to dinner in a Vietnamese restaurant. Mabel had agreed to both. She even told him, jokingly, that she was still keen to learn about the incredibly shrinking Y-chromosome and what he had so far found from the report on the DNA analysis of his own Y-chromosomes.
And so, here he was, standing at her door, feeling slightly anxious and same time elated. He was fourteen years older than Mabel. He did not know if this was a wise thing to do. And yet, here he was.

Mabel opened the door and smiled. She had this wide smile that transformed her face. She exuded a natural radiance and lack of pretense, an ability to put people at ease. She was mostly casual in her dress. Neil remembered her mostly wearing blue jeans or pants, more often than not with a baseball cap on her head. But today, she had dressed herself. Her hair was shiny and free flowing. She had on a dress and a sweater. She had a scarf around her neck. She looked lovely. Neil was conscious again at her youth, and their age difference.
‘Hi’ he greeted her, slightly awkward. ‘You look lovely’.
Her smile widened. She stepped back and pirouetted. She was aware of his eyes on her. She did not dress for a party, and they were only going to a movie and a dinner. But she had taken the trouble of dressing herself enough for the occasion. She was thrilled that he finally asked her out for an evening. This had been a six year wait for her. She fell for him the first time they met, when she was a mere sixteen years old and still in school.
The last weekend was the watershed event finally, when she grabbed his face and kissed him, taking the initiative. That had lead to them spending the night together at his place. This was hopefully to be the beginning of an affair that would end in them staying together for life. She had not yet announced anything to anyone. She had already been planning on how they might spend some of their weekends. She was going to accompany him on his birding trips around Vancouver. She had already borrowed a field guide and was reading up on the flora and fauna of the area. She had been an outdoors woman and knew as much as the next person about the local plants and animals. But that was not going to be enough. She intended to develop a passion and a level of curiosity about the surroundings that would match Neil. His curiosity about the natural world around them had rubbed off on Mabel over the years. She had inadvertently started reading up on plate tectonics, continental drift, climatology, ice age glaciation and a whole lot of other things. It even influenced her decision on the part time college course she started taking.
She wanted a career in line with her uncle’s business, in construction, interior and landscape decoration and building of homes. But same time, she now had opened another horizon for herself, and was studying architecture on one side, and geology on another. Neil, without any conscious effort, had played a large part in her decisions to go for college, and in selection her subjects.
To her, the age difference did not count. Difference in their race was irrelevant, and would not matter to her, although she suspected Neil was bothered a bit about both issues.
She smiled and winked back at Neil, causing his eyebrows to go up. ‘I dressed up for you. Like ?’

Neil stepped into the room and gathered her in his arms.

Old woman sacrifices herself

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It was one of those days. First, Tony did not like the title of this blog. He toyed with a number of alternatives, including naming a few of the giant mammals that went extinct between ten and twenty thousand years ago.
This was the time frame that was to provide one of the threads in his story. Many remember this as the phase of the last ice age of the planet.  It may well be that the earth was losing some of its ice coverings, while at the same time early humans were getting more adept at exploring hitherto uninhabited regions of the world. His maternal lineage was probably moving along the Eurasian landmass at this time, as revealed by reports of the analysis done on his mitochondrial DNA.
And Tony was trying to write up on this imaginary trail of an ancestral female that morphed from generation to generation, moving from one era and landscape through to the next, till they come into historical times, and the scene gets fuzzy. Clarity was to come as the second thread of the story, of a young Indian engineer meets up with his past. The story is not supposed to end there. The mitochondria that he carried would not be passed to the next generation. Only females did that. But he had sisters, and the line would continue, at least in the foreseeable future, onto a few more generations.
But, meanwhile, he was to weld the past with the present, which involved a Canadian woman, or perhaps two. Tony scratched his head and went back to constructing a scene that involved either a mammoth, or a saber tooth cat, or perhaps a shivatherium, that would confront an elderly woman in the central asian steppes.

American Lion - wikipedia

The woman in question would likely be separated from her clan during a hunting expedition that went wrong. While her immediate clan remained two hundred yards away, a group of the giant mammals, angry and afraid, were preparing to make a last stand against the spear throwing humans, when they chanced upon the woman.
There were a few things that was special about this woman – who was called Suta by her clan. She had, on an earlier blog, represented as a small girl sleeping in a cave during a winter storm. Now she was old. She carried a piece of mitochondrial DNA that was to pass on its copies down thousands of years all the way to Sunil Dustidar, or Neil Dusty, of British Columbia, Canada, in the year 2012.
But she was not alone. She had with her a kid – a small daughter, huddling wide eyed behind her, as she crouched, holding a piece of stone, and hissing at the approaching animal.
In the story, she would end up sacrificing herself, and injuring the animal enough to let her small daughter dash for her life, to the security of the rest of her clan – running the gauntlet of hostile animals in the central asian steppes, her tiny feet making small tracks on the wet snow as she dashed between rocks and ran, crouching. She was barely five years old, but was an expert runner and tree climber. She was hoping to reach the line of young fir trees beyond the gully ahead of her, surprising a group of giant rodents that were a cross between rabbits and skunks.
Meanwhile, the old woman, Suta, had been gored, or bitten, by the animal that felt trapped by the hunting humans on one side, and the stone throwing woman on the other. Tony could not decide what animal it should be. A saber toothed cat would likely bite her somewhere. He remembered reading somewhere that a human skull bore puncture marks of a saber toothed cat. But biting a skull appeared to be a bad way or attaching a human. The puncture marks might have been after the human had died. Perhaps the skull had rolled out into a stream bed and the cat was trying to crack the skull to get as the rotting brain.
But in the cast of Suta, an attacking carnivore should use the most economical and efficient way to kill a prey. A bit at the neck? Or stomach ? In the story, the animal would attack the woman partially as self defense. And the woman would ensure that the animal’s attention remained on her, thus allowing her baby to escape to safety. And while all this was going on, her own clan were frantically yelling and grunting, and throwing spears. Tony did not know how good the clan would have been in handling fires. Could it be that they learned the tricks of wrapping dry reeds or wine around the spear handle, soaked in animal fat or bitumen, and light a fire before throwing those burning lances ?
Such a tactic might not be any better than throwing a spear with a sharp stone at the front designed to pierce the skin and embed deep into the prey. But it might have the psychological effect of panicking the animals into irrational behavior and coax them out of their corners and into the open. It might also scare them away from attacking Suta and her baby.
If not saber toothed cats, it would be mammoths. It could be cave lions of Eurasia. It could be a sivatherium. When it came to saber teethed cat or cave lions, Tony felt unsure than a hunting party of late pleistocene humans would attach a predator of that kind. Also, it was almost certain that predators did not move in large herds, and would more likely to ambush the humans rather than humans ambushing them. So, a predator could be accidentally caught in the cross fire between the hunting party, and the giant herbivores.

Straight-tusked Elephant - wikipedia

If not mammoths, a sivatherium provided an attractive alternative. A giant giraffe like animal with multiple horns on its head and a mouth that might have resembled a modern tepir – this animal carried the improbable name of a hindu God. Why it carried shiva in its name, Tony was not sure – but such a name and an animal might add variety. Cornered and injured, it was massive enough to attack and gore a single wild haired human, especially an elderly woman wearing animal skin and brandishing small stones.
In the other half of the story – Neil was trying to piece together the thread of his ancestral lineage. Since the last blog, several things had happened. He had ended up sleeping with Mabel a few times a week, and stopped feeling awkward about it. His initial hesitation, because of the difference in age, as well as the perception of race, had not completely vanished, but were no more troubling him. Man was a creature of habit, and had a habit of getting used to things. Mabel certainly brought a degree of thrill and happiness that was missing in his life. She looked positively radiant some of the time, and very pleased with herself in general.
Neil guessed they were sort of dating each other, and were kind of paired up. His idea of dating normally involved taking a woman out for an evening of eating, or drinking, or watching a movie or something. But Neil had done none of those. If they went out together, more often than not in involved walking around in sandy shores or among thick vegetation in some nature park. Neil would normally be hauling a heavy camera and lens mounted on a tripod – the whole contraption balanced on his shoulder as he moved. Mabel would also have a backpack with additional photography gear of Neil. But lately she started adding sandwiches, fruit juice, water, and even a birders field guide to her pack. Neil did not like carrying field guides, but refer to them later, back in his car, or back home. But Mabel wanted to catch up on the general identification of birds. She was soon to learn the difference between different kinds of swifts, martins and swallows, or gulls, or birds of prey, and waders.
She loved spending time with Neil, and Neil was getting used to having another person with him on his days of bird watching.
There was going to be complications coming into the cozy relationship developing between Neil and Mabel. They were not aware of it yet.

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Cave bear worship - wikipedia

Cave Paintings of ice age eurasian animals - wikipedia

The story was soon going to have some sort of a triangle. There needed to be either another woman, or another man or both. Tony was more inclined to create another woman, a single mother with a child. He even named her Karen.
Two months ago, Tony did not have a clue on the plot for the story. But that was two months ago.
Tony stopped typing and put away the laptop for a while. He was hungry. He spent the last few hours walking about in the Galleria mall in Houston and move through the stores of Macy, Sacks fifth avenue, Sony, Apple, and a number of others, without finding a single thing he wanted to buy. The closest he came to purchasing anything was a half sleeve white sweater in Macy. But they had small sizes and extra large but no Large size, which was the right size for him. Just as well, he really did not need a white half sleeve sweater, even if it looked nice.
Why he was there? Well, he had finished his work ahead of time, and instead of returning home to Vancouver on Sunday, he tried to rebook his flight a day earlier, but failed. So, he essentially had a day to spare. He decided against going out to the art galleries, or the nature parks, or search out some friends there. The walk in the mall was more to do with stretching his legs and getting some exercise.
Sitting near the fountain inside the mall, he had read up two newspapers, the Financial Time, and Houston Chronicle. He was unimpressed by the trivia but liked a few articles, especially in the pink Financial Times.
Papers had their share of news about the fighting republican candidates that wishes to challenge Obama in the coming presidential election. He found the news mostly boring, and also silly.
Nobody discussed real politics, or real economics, or real anything anymore.He had left the papers and moved on. Perhaps another shopper would find a better use for them.
He had stopped at a spot where baby dogs were on sale for potential pet owners. The dog pups were a hit among young children. There were no price tags, so Tony did not know how much they cost.
Back to the hotel, which was across the street from the entrance to the mall, Tony had sat at the bar and had a beer, trying to watch a basketball game on the wide flatscreen TV there. Unimpressed, he came up and started writing about Suta and her sacrifice.
The item had a link with his own immediate ancestry, going back a few hundred years. He had learned, from his father and his uncle, that their ancestors had one deformed male that actually grew to adulthood and produced off springs that made it possible for the lineage to continue.
But the deformation was not from birth. As a child, he was apparently attacked by a tiger in what is today Bangladesh. His mother, a tiny sari clad woman, had chased and attacked the tiger holding a sort of machete. The tiger, or perhaps it was a tigress, got furious, dropped the bleeding child and grabbed the mother, killing and dragging her off to the marshes. She had sacrificed herself for the sake of her baby. That baby, now deformed for life, survived. Tony had heard of that story, from his own father and his fathers elder brother.
That was linked to his paternal ancestry. But in the story he was writing, he decided to attach a similar incidence, pushing it back to the Pleistocene-Holocene boundary, and moved it from his paternal, to his maternal ancestry.
But now, it was time for a hearty meal. Tony decided to walk back into the mall. He had seen a nice restaurant and bar that was better than the coffee shop in the hotel. He was planning to have a glass of wine, a very large salad, and perhaps a cheese cake.
He put put on his wind cheater, took his iPad, and walked out of the hotel, mulling about a saber toothed tiger, a four tusked mammoth, and a shivatherium, and how a tiny woman might sacrifice herself to save her daughter, thus allowing her mitochondrial DNA to survive through another ten thousand years all the way to the present.

Suta at the Riviera

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She woke up with the sound of howling winds. It rattled the stone buttressed flaps of leather across the narrow entrance to their cave. Puffs of snow burst through the narrow gaps and settled at the entrance. The stone below was cold, and her bed was lined with soft soil and leaves, on which she had part of a wooly rhinoceros hide, on which she had curled up with some dry grass and straw and another fox hide atop her. Hairs on her arms , back and legs had not grown much yet, and in any case, was not protection enough from the cold. Her mother had already left the cave, likely with Solu, their clan leader. Only baby Oth kept sleeping, curled around the wolf pup. Mama wolf had also gone, with the elders.

Suta gazed at the cave ceiling. The cave had earlier been used by bats, but abandoned since they themselves moved in. The strong smell of their excrement and urine made her heady at times, but every time the wind passed through the cave, the smell would go away for a few days. The cave had a narrow opening through which they could crawl out. The interior of the cave thinned out but did not end. A small shaft connected to the outside without the rocky mound. They would cover that opening with a stone slab, to prevent reptiles, wolverines and small critters from entering the cave. But when they needed the cave aired, they would open up both ends.
The cave was once also the home of a smilodon – a sabre toothed cat. Solu and his brother had fought and chased it away. Even now, the sabre tooth would occasionally pass by and growl at night, as if reminding them that it would like to have the cave back. Suta and her mother were not able to deter the smilodon from attacking them unarmed. But his mother had become and expert thrower or stone hand spears, a demonstration of which the sabre toothed cat carries on its hind flank as a scar, and learned to give them some distance in day time. A sabre tooth was an ambusher, and not a frontal attack predator – at least not for humans. Suta was still learning to throw a stone spear, but she was too small, and was more comfortable with the stone axe with the short wooden handle, used close to her body. She had once confronted a cornered fox with it and came out the winner, without getting bitten.
The cave was at the edge of a shallow lake in what in the future would be named the riviera. It would be a balmy popular oceanfront land of rich people. But in Suta’s time, it was a bleak, ice encrusted covered region in the grip of an ice age.
She was only six years old, and less than three feet tall. In another two years, she might find a mate and pair up either in their clan or go her own way. She did not know it yet, but she carried a piece of mitochondria, that, many thousands of years in the future, was going to end up in a woman of India, who would pass it to her son, who would be migrating to Canada, and sit down with a cup of coffee, and write about her times in the cave by the French riviera.
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Tony wrote this much, and leaned back in his chair, putting his feet up on the table, noticing that his big toes had some thick and fierce looking nails that were due for clipping. He sighed. He was never very good as chores of this kind. Fishing out the toe nail clipper from the shelf, he proceeded to tend to his toes, letting his thoughts go back to what he wrote.
The thing is – he was beginning to get an idea of a plot, and it was getting complex by the minutes.
First, there was this Canadian young woman, Mabel, that had taken an interest in Neil. Tony was never going to be a romance writer. So, Mabel was likely going to unsuccessful in getting Neil to commit himself for several hundred pages, and the reader by then would have given up.
But, there was a way out – and this involved writing about the fun detective work Neil was engaged in with regard to tracing his own paternal and maternal genetic lineage. Tony was going to get Mabel involved in it, and let the two of them figure things out from that point.
And then he was, perhaps in alternate chapters, add one more layer of complexity – that of a stone age women, who hypothetically carried the mitochondria that would end up, or rather, a sort of an imperfect copy of which would end up in Neil. And the story would sort of progress on two fronts – one more or less locked in time to the present, involving Neil and Mabel and the crazy world of today, while the other front would have the ice age cave woman gradually morphing through time, to end up a few generations ago into north-eastern Bengal, preparing the seeds that would eventually end with Neil himself, while Neils story would be very close to Tony’s own.
How is that for a story that had no plot, to end up having a hell of a complex one ?
The thing is, Neil did not know if it was normal for a cave dweller, ten thousand years ago in French Riviera, was expected to have hides of wooly rhinoceros. He did not know if the time, and the place was both right, for the now extinct animal. He did not even know if French Riviera area had any natural caves.
He did not know how much body hair folks had those days before the invention of fabric and clothing. He did not know at what age young women of the late stone age were consider to have reached the age of consent. Neil did not know a whole lot about ice age Europe. But, Tony suspected his maternal as well as paternal ancestors passed exactly through that land at that time.
And he was intrigued about it.

Ahh well, time to go to sleep.