From DNA to New Cousins & Ancestry

Posted on January 2, 2016 by Roger Gosden

The back of a Cornflakes box is a good deal more absorbing than another person’s family tree. Genealogy is a rather personal game of history. Our interest seems to gain momentum with age, which may unfortunately mean we are too late for an older generation to explain gaps in our family history.

Surveys show the majority don’t know or remember or care about the names of our great grandparents or further back; perhaps we need to put a face on an ancestor for a name to mean something. As one of that majority, I knew little about my background or where my ancestors lived and are buried. But searching for records through online ancestry services and discovering remote cousins using DNA hooked me in a way that poring over parish records or deciphering gravestones never could. Technology is making genealogy into a new craze and for absorbing TV, like Finding Your Roots and Who Do You Think You Are? This post is mainly for people who want to dig up their ancestors but haven’t yet gotten started. It won’t say much about my family tree (I promise), but aims to convey what I found interesting or worrying after enrolling in Ancestry, 23andme, and Family Tree DNA. Yes, I signed up for all three because they are not exactly the same services, and I wanted to check if results were the same.

After paying the one-off sign-up fee or subscription, each company mails the customer a specimen pack to be returned with a cheek swab or spittle sample for DNA analysis. You have the option of contributing your data to the company’s genetic diversity studies (I did) and keeping your data private from other subscribers (I didn’t because I wanted unknown relatives to find me). A few weeks later an email announces your results are ready for perusal online.

If asked, I would probably say ethnicity doesn’t matter a whole lot to me. That sounds virtuous, doesn’t it, but I admit it was the first result I checked, along with predictions of my physical characteristics. Perhaps deep down there was a sliver of anxiety in case I was never told my full story, but DNA would be truthful. The data showed I am 98% Northern European. It predicted brown eyes, undetached earlobes, no cleft in my chin or wet earwax, and that I can smell sulfurous metabolites in my urine after eating asparagus. I didn’t need to spend a hundred bucks to learn what I already knew, but these confirmations gave me confidence in the other results.

Aside from 263 genetic variants handed down from my Neanderthal ancestors (blogpost of November 18, 2014), I found the mix of European origins that made me was rather interesting. I am like one of my mother’s cake recipes, made of every kind of fruit and nut plus a smack of Oriental spice. That’s common for Brits. I have an admixture of DNA from the British Isles and Ireland, a fair amount from Scandinavia (those Vikings and Danes), a little Western European (French and German), and a dab of Southern European (2%) and Middle Eastern, probably Ashkenazi Jewish (<2%).

Map my origins

Map my origins

Although all three tests confirmed European ancestry (98-100%), there was a lot of variation within that category, especially for the British Isles (14/52/69%) and Scandinavia (6/7/27%). The differences definitely reflected the haplotypes selected for testing by the companies, but also perhaps the definition of what a national origin means. It’s hard to define what it takes to be 100% “British.” Would that imply an ancestry strictly prior to the Norman Conquest (not much French), or before the Scandinavian and Saxon invasions (no Norwegian, Swedish, Danish or German heritage), or afore the Roman Conquest (no Italians or their allies)? If so, only an Ancient Briton or Celt would qualify, and I very much doubt any exist today. Besides, a strict definition might exclude that most glorious “English” king, Alfred. The companies are silent on this question, so you can choose what you want to think. If your roots are in America, north or south, you will probably have an even larger smorgasbord of origins. Congratulations!

A mixed origin is biologically reassuring and makes nonsense of some kinds of ethnic pride. There was a time and place in history when ethnicity was undiluted by recent immigration, but hard to find today.

Mum_and_Dad_headstone_1Ancestry research using DNA is greatly helped if you have data from both parents, although even if they are not available your own results can say something about their backgrounds. The mitochondrial genome is a tiny ring of DNA inherited from our mothers, and we share it with our brothers and sisters. My maternal haplogroup is K1a11 which originates in the Middle East and traveled to Europe through the relatives of Otzi the Ice Man. My brothers and I inherit our father’s haplogroup I1 from his Y chromosome, which is common in Scandinavia. None of us is blond and blue-eyed, and none have the financial sagacity of Warren Buffett who has the same haplotype. It’s not surprising.

Genetics is not destiny, not really. Scientific or artistic genius very rarely run in families, and hardly ever more than two generations. And consider Bill Maher and Bill O’Reilly, one a leftish political satirist and the other a host on Fox News Channel. They are at opposite poles of the political spectrum, yet have a common Irish ancestor way back. No surprise there either, but I digress.

The longer you are an active subscriber to a genealogical service the more information that rolls in because other people join and some become sharers. If you go public with data, you will soon see your DNA matching other people’s and learn the strength of the match (%) and the corresponding segments (in cM). Your parent or child should of course have a 50% DNA match with you, but after gaining that reassurance it’s most interesting to scroll through the lower entries. There are likely to be hundreds of other matches in descending order of relatedness. Some of them provide a picture and short bio, and even an email for contacting them, but most on your list are likely to be anonymous or never reply to your inquiries. I suspect they don’t have anything to hide: they enrolled mainly for the health data that can be downloaded (next post) or never return to the page for updating DNA relatives.

You will undoubtedly have some surprises. For me it was the large number of American matches, more than any other nationality, because I had no idea about any ancestors migrating ahead of me. As for the British people expected to be on my list, perhaps they are more wary of sharing details in case they reach a nosy government or genetic stalkers.

My wife had the happy discovery of an unknown third cousin through a DNA match. She lives only an hour away from us and owns property that their common ancestor farmed in the early days of Colonial America. She is a super cousin because they share over 1% of their DNA, meaning they might be doubly descended from their ancestor. Lucinda is also distantly related to her daughter-in-law’s family. My surprise was to find my wife’s half-sister and brothers in Texas are my remote cousins, probably through an Irish ancestor I never knew about.

You have to be ready for a jolt when you delve into history, and I’m still waiting for one. Luckily, I haven’t found any felons or slave-owners in my family tree, nor relatives of that man with a black toothbrush mustache who died in 1945. Phew! But be prepared to hear from people trying to find living relatives. Two women who were adopted as children have contacted me, but I couldn’t give them any leads to a living parent or sibling because we are too distantly related. Another contact has been trying to establish a link between us and a billionaire hedge-fund owner; thankfully, that inquiry has gone silent. No doubt some people have used these services instead of standard paternity testing, and I have reason to believe an oral sample doesn’t need as much scrubbing as the instructions recommend. Padlock your toothbrush if that worries you.

Besides filling the missing names on a family tree, tracing ancestors back for say seven generations to the 17th century reveals many interesting details and documents. For example, registrations of births, marriages and deaths, military records, census data, ocean crossings and immigration data, not to mention convictions for felonies, are represented online from scanning of original documents. Perusing these materials was a moving experience because it personalized those who had contributed to my existence by revealing the little details I would never have known otherwise. There is a risk, however, that family stories that have grown fonder in the telling through the generations can turn out to be flawed or fanciful, so prepare for dissonant emotions.

One person who contacted me was searching for a royal connection, so I was glad I couldn’t help her. She left me wondering why anyone wants to be connected to a lineage that is marred by an unhealthy degree of inbreeding in the past. Remember hemophilia was passed down by Victoria, and the famous jaw of the Royal House of Habsburg? European royal families constantly intermarried. Queen Victoria married her first cousin, Prince Albert of Saxe-Coburg, an admirable and brilliant man whom anyone would be proud to call a relative. But whatever parts of the genome contributing to his gifts (probably minor) were mixed and diluted in the following generations. A dynasty endures through its heirs, but not by passing down a founder’s peculiar genetic merits.

Lastly, I was musing about King Richard III, the last of the Plantagenet kings of England who was killed at the Battle of Bosworth Field in 1485. The grave was excavated in a Leicester carpark in 2013 and his identity was confirmed from DNA and spinal curvature. Ricardians strive to repair his reputation brought down by Shakespeare, and in some circles there is a cachet if you can prove descent from Good King Richard.

Think about it. He lived over 21 generations ago. If you can trace your branches back to the trunk that connects to his close relatives (he had no children) you have a claim to the Plantagenet crown, but it’s vanishingly slender. DNA is diluted by half at every new generation, so if we assume no interference by intermarriage or asymmetric recombination or medieval milkman (some assumptions!), you share 221 of his DNA, or less than one part in a million. It is meaningless to feel honored by descent from some bigwig if he or she is that remote. But there is a wonderful conclusion here: ancestry research reminds us we are all connected, and if we need to boast we can all claim a relationship to our greatest heroes in history. It’s all a matter of degree, because we are all cousins.

Next Post: What Price Genetic Privacy?

 

Posted in Biomedical, Health | Tagged , , , , , , , , , | Comments Off on From DNA to New Cousins & Ancestry

Peace in 2016

Posted on December 30, 2015 by Roger Gosden

Tennyson message for New Year 16 font

Inner Hebrides, Scotland

Isle of Rhum

Posted in Memoir, Other, Seasons in Virginia | Tagged , , | Comments Off on Peace in 2016

Time Long Past

Posted on December 18, 2015 by Roger Gosden

“Christmas comes round faster every time, Roger, and the years go by more quickly when you get to my age.” Grandma’s warning was also the annual refrain we heard from a lot of older folk as we grew up, and now as we climb into her years we nod agreement.

The end of a year is when time tends to assault our thoughts. It doesn’t, of course, really change outside of Dr. Who’s TARDIS, but the perception matters for every time traveler, and is more urgent when there are fewer miles ahead than in the rear-view mirror of your life.

Shelley

As a perception problem, it’s more the territory of psychology than physiology or physics, and psychologists have had plenty to say about it. For one thing, they found that Eastern and Western cultures agree that time seems to speed up with age, although I would love to know if primitive (I prefer the “primal”) societies share the experience.

ClockOver a century ago, William James suggested time steps into a gallop because there are fewer memorable events or milestones ahead for marking the course of our lives—first day at school, graduation day, first kiss, first job, etc. By analogy, we lose sense of distance traveled on a road trip out of a city when the mile markers peter out in the countryside.

It may have been true in Victorian times that the years seemed to become more “hollow and collapse,” but I think the theory of collapsing time is bunkum now: our lives are rarely static at any age, as long as we are in sound physical and mental health. We dash through torrents of change (“firsts”) in family life, the workplace, and where technology, economics and politics impact our lives. We never reach a slow, meandering river before advanced age.

Psychologists have other theories for time. Some suggest it’s all about the choice of metaphor, that young people may represent time with ones that are more static (e.g., a calm ocean) than their elders (e.g., a speeding train). Others say that our false perception is simply a result of time getting progressively shorter as a fraction of our lives.

But a large study in Germany in 2005 found rather little evidence of any relationship to age, and those who said that time was going fastest admitted feeling under more pressure. Perhaps the mystery largely boils down to lifestyle. I have even heard children say that time is going too fast for them, and they have never been under more pressure to achieve goals and fill schedules. They have fewer empty hours than in my day, which I spent “wasting time” birding in the woods, and when they break from structured activities their brains often feverishly turn to games and social media on their phones and tablets. They keep the pressure on their fingertips.

I hear the poet who dreamt of dwelling in a small clay and wattle cabin to stretch time among the bean-rows and bee-hives.

Yeats poem

As I send this greeting to readers I hope they chill-out during the holiday season and at every other opportunity, so they can report a year hence that 2016 came round more slowly!

Next Post: We’re all Cousins in the Same Family

Posted in Memoir | Tagged , , , , | Comments Off on Time Long Past

The Strange Tale of a Chimera

Posted on December 12, 2015 by Roger Gosden

The Chimera had a serpent’s tail with the head of a lion and a goat on its monstrous body. That was a Greek myth, but real-life chimeras exist. They originate from the blending of cells from two fertilized eggs into a single body.

A chimeric man was identified in California recently after undergoing fertility treatment with his wife. She received intra-uterine insemination (IUI) with his sperm for a gynecological problem: it was successful and they had a son. There was nothing unusual in the case until a routine blood test revealed the boy had a blood type that didn’t match either parent. But how could a third party be involved in his conception? Since there was no doubt that she was his biological mother (no mix-up in the birthing center), the husband opted for a paternity test using a buccal cell sample.

It didn’t match his boy, even after retesting. Had the clinic accidentally mixed up his semen sample with one from another patient going through the service on the same day? Technocuckoldy happens.

The couple’s next stop was the office of a geneticist, before consulting their lawyer.

The geneticist suggested they send saliva samples from both dad and son to a personalized genomics company (23andMe.com). When the data came back the story suddenly changed from alarming to interesting.

The DNA of man and boy was a 25% match, not the 50% expected for normal paternity. Taken at face value, the result suggests the boy was a grandson or a nephew of the man instead of his son. But dad really was his biological parent because when his semen was carefully analyzed 10% of his sperm corresponded exactly to the boy’s DNA. The rest was from an unknown relative! There was a similar mix of origins in the man’s buccal sample, and probably in other parts of his body they didn’t test.

The geneticist deduced that the man was harboring cells originating from a twin brother who had vanished before birth. Dad was a chimera. Cells from his moribund twin had colonized his testicles when they were sharing a womb and became spermatogonia for making sperm after puberty.

Chimerism sounds strange and deeply abnormal, but it is a natural phenomenon. In a few species it is a normal process, even a necessary one. Perhaps the weirdest example is the deep sea angler fish, the one with gaping jaws and a dorsal fin modified like a fishing line that serves as a lure for prey. Those are the females. The males were overlooked for a long time because they are tiny. Instead of mating in a conventional way (perhaps they don’t dare), they become absorbed into a female’s body after fusing with her. It is not a final death for a male because his blood vessels join up with hers, enabling some of his cells to survive, including the all-important sperm cells. The female becomes a chimera after receiving the male fertility transplant, which enables her to be self-fertilized.

Strictly speaking, anyone who receives a transplanted organ or bone marrow from a donor is a chimera. But in mammals most chimeras originate from sharing a placental circulation in pregnancy, and this occurs regularly in marmoset monkeys. In cattle it can have biological consequences.

Freemartin cows were recognized as far back as Ancient Rome because they are sterile, which is bad news for farmers. The 18th Century anatomist John Hunter realized they only occur when a female calf has a twin of opposite sex. Conceived as genetic females, freemartins are affected by hormones carried over from blood circulating in their male sibling. Male fetuses have much higher levels of testosterone and AMH, hormones that masculinize the body and cause the uterus to shrivel.

Cross-circulation rarely causes these effects in other species, although in humans it accounts for some rare intersex abnormalities, and can create nutritional deprivation in a twin with a shared placenta.

We used to make chimeric mice with four genetic parents for tracing cell lineages during development. When an 8-cell embryo from a black x black mated mouse and one from a white x white mating were “unshelled” and fused to make a single large embryo, the pup born after transfer to a surrogate mother was piebald. Chimeric pups were sexually normal with a few exceptions that were either intersexes with a testis and an ovary or had an “ovotestis.” Although fusion was almost 100% efficient in the Petri dish, the shell (zona pellucida) prevents chimerism at early stages of pregnancy in women by covering sticky surfaces that might cause embryos to adhere to each other or dangerously attach to the wall of the fallopian tube during passage to the uterus. Human-animal chimeras are now hot in experimental biology, but that’s another topic.

In Aldous Huxley’s Brave New World, human freemartins created at the Hatchery were not chimeras but made by a purely chemical process. These low caste females were sterile, asexual women with beards. The history of using physical differences to debase or abuse people is old and agonizing, but chimeras have avoided that fate and I have never even heard the name used as an insult. That’s because they generally go unnoticed until a genetic test reveals more than one zygotic origin in the same individual, or a striped pattern of sunburn raises a question of why the skin cells were differentially sensitive to u-v radiation.

Chimeras are more common than we realize, and I even wonder if I am among their ranks. I heard that I had a vanishing twin, although that doesn’t necessarily imply I am like the man at the California clinic who is carrying cells from a deceased fetal twin. Nor is that remote possibility something I worry about, and it wouldn’t give me the creeps even if I had brains cells from a brother or sister fetus. Fetal cell transfer is no more spooky to me than an organ transplant, and a good deal more natural. But the fact of a vanishing twin sometimes causes me to muse how my life would be different if he or she had lived.

Next Post: Mighty Mitochondria

 

Posted in Biomedical | Tagged , , , | Comments Off on The Strange Tale of a Chimera

Chimps Head for Retirement

Posted on December 1, 2015 by Roger Gosden

In 1871, the now-extinct Hornet magazine published a cartoon of Charles Darwin looking like a human-ape chimera. It was not meant kindly.

Charles Darwin

The Hornet Magazine

We might suppose that progressive Victorian thinkers would have embraced chimps, gorillas, orangs, etc. as newly-found cousins. Perhaps some did, but lonely captivity in bare “prisons,” laboratory experimentation, and hunting continued.

It takes a long time for ingrained attitudes about the “beasts” to change, even when evidence mounts about their cognition and suffering. It’s ironic that medical research which adopted apes for human ends has raised appreciation of them as sentient beings that insists on a higher ethical standard of care not much different to what we demand for ourselves. Jane Goodall, the foremost chimpanzee expert and advocate, urges, “Surely we should treat them with the same consideration and kindness as we show to other humans; and as we recognize human rights, so too should we recognize the rights of the great apes?”

There was a recent instance of how attitudes are changing when the head of the NIH announced that the last 50 chimpanzees in federal laboratories will be retired to a sanctuary for the rest of their lives. The published reasons for freeing the chimps was utilitarian and couched in unemotional waffle (“the need for research has essentially shrunk to zero”), but I’m sure that public opinion influenced the policy. Pictures of apes in cages, separated from their babies, and communicating with people in sign language open our hearts to them as we see more of us in them and vice versa. We are unashamedly sentimental about our pets, and why not for our simian cousins too? This might sound surprising coming from a writer who sometimes used animals in research (never primates), but it’s not shameful to admit a change of heart. The treatment of animals as only subjects of curiosity, cuisine and companionship can evolve to something greater, although I can’t say how far the ineffable feelings can go.

The reason why animals, even apes, never deserved the protection of legal rights was, of course, because they are not human. They don’t have a brain and moral law that in our own estimation justified us as their emperors. The difference between Us and Them is that we regard ourselves as a benevolent species, for that’s what humane means. What a shocking self-deceit!

Most Victorians, irrespective of whether they believed the Creation Story or Evolutionary Theory, thought our species was destined to rule the Earth. The Darwinian revelation that we are a Johnny-come-lately species didn’t puncture that mental outlook, and modern ecology has struggled to fix a truer and more sustainable perspective against the resistance of economic and political forces. The justification for using and abusing animals was the same as that for the mistreatment and malice of other ethnicities of our own species—they were all dehumanized.  Lately, I have been musing when the divorce with nature began.

A new breed of eco-theologians, including the late Thomas Berry, admit that the three great monotheistic religions unconsciously helped to vindicate brutal treatment of animals and careless stewardship of the environment. When people lived much closer to the land as a source of production, there could be greater feelings of unity with the rest of creation, and less hubris exploiting its “goods.” The natural world was a divine revelation that preceded the Scriptures. Still today, some native religions teach that the land and its inhabitants, plant and animal, are sacred, and the sacrifice of an animal taken in a hunt was a sacramental act for some North American Indians.

If I try to pinpoint a time and place in history when Western attitudes changed I choose Medieval Europe. As a devotee of Aristotle, Thomas Aquinas taught that humans stand at the apex of nature’s hierarchy, owing no special moral responsibility to animals, which are only instruments for our use. When the Black Death arrived a hundred years later, killing a third to a half of the population, the church tried to soften the horror of temporal existence and the hard Augustinian doctrine of a broken world by focusing the minds of the faithful on the permanent reward of peace in heaven. With eyes fixed on such a great hope why should anyone bother about the Earth and its creatures? Wasn’t the great lover of creation, Francis of Assisi, just a sentimental monk?

Although the tide of faith started ebbing in the Enlightenment, attitudes towards nature and animal life remained harsh. The wild woods, mountains, and oceans, and the creatures they harbored were dangerous, not precious gifts. Beauty and its ally, security, lay in the towns and cities, and urbanization increased the drift from old feelings of communion with nature. Materialism and its goods had arrived. Pressed to choose a historical figure to represent the changing secular attitudes it’s hard to beat Descartes. He drew a metaphysical gulf between Mind and Matter. Since animals were assumed not to have a mind or self-consciousness (now repudiated), they were regarded as biological machines, mere matter not calling for special care.

The promotion of a bunch of chimps to a gentler life as senior citizens is a tiny example of how public sensibilities have evolved, although there is a long way to go before deep-seated religious and secular assumptions are replaced with more open and enlightened feelings that can bring us closer to our spiritual Earth home. We can expect to see more controversy and struggles over our management of animals—for food production, sporting entertainment, medical research—and I have no idea where they will end. But a quotation from Henry Beston holds a guiding light for me. He was a friend of Rachel Carson and like another temporary hermit in Massachusetts, Henry David Thoreau, he spent a solitary year in a cabin, but beside the ocean instead of a pond. He wrote in The Outermost House:

We need another and a wiser and perhaps more mystical concept of animals. Remote from universal nature, and living by complicated artifice, man in civilization surveys the creature through the glass of his knowledge and sees thereby a feather magnified and the whole image in distortion. We patronize them for their incompleteness, for the tragic fate of having taken form so far below ourselves. And therein we err, and greatly err. For the animal world shall not be measured by man. In a world older and more complete than ours they move finished and complete, gifted with senses we have lost or never attained, living by voices we shall never hear. They are not brethren, they are not underlings; they are other nations, caught with ourselves in the net of life and time, fellow prisoners of the splendor and travail of   the earth.

I guess old Darwin would have shared those feelings and welcomed the belated rediscovery we are making of caring for our real home, this shrinking world with its creatures whose destiny is more completely in our hands than ever. He might have enjoyed seeing his caricature in magazines, believed there was dignity in a hairy pelt, and reflected on Francis’s dream of an Earth family—Mother Earth, Brother Wind and Air, Sister Water, Brother Donkey, Brother Chimp, Brother Darwin.

Next Post: Sperm reveal Human Chimera

Posted in Animalia, Environment | Tagged , , , , | 1 Comment