The Invisible History of the Human Race
Page 25
• • •
The amount of time between the discovery of genetic and genomic knowledge and the transfer of that knowledge to the public has been extraordinarily brief and possibly completely unprecedented. As of 2014 a small handful of well-known companies—Family Tree DNA, 23andMe, and AncestryDNA.com, as well as National Geographic’s Genographic Project—and services offer a selection of DNA tests and genealogical connections to the general public. Depending on which service you buy, you can have up to 111 segments of your Y chromosome analyzed (if you’re male), some or all of your mtDNA, and most of your twenty-two non-sex chromosomes. (23andMe also looks at health and traits; see chapter 14.) Once you have your data, you can also use do-it-yourself or noncommerical sites like Promethease, SNPedia, Interpretome, and Dodecad to interpret it. The genetic genealogy companies often investigate many more places in the genome than were considered in academic studies of just a few years ago. When it comes to personalized genetic research, many individuals can afford what most researchers can’t, which means that the banks of genomes held by Family Tree DNA and other companies are essentially crowdfunded, uniquely valuable libraries. Indeed, the biggest collections of Y chromosomes and mtDNA in the world are found at Family Tree DNA, not at research facilities.
What do these extraordinary companies look like? After all, the genome is a treasure house; it’s the Library of Congress many times over, all stacked on top of the long-lost library of Alexandria. I wanted to see the genome made visible, so I visited Family Tree DNA, the first genetic genealogy company, founded in 1999 in Houston, Texas. On a day of crushing heat I drove from Houston’s airport through the urban sprawl to an undistinguished office building to meet with Bennett Greenspan, a showman with a Texas accent and a nontrivial moustache.
Greenspan settled in for a talk, but when I asked him if I could see where they analyzed the DNA, he said, “It’s pretty boring.” “No, no,” I insisted, “I’ve never seen a DNA lab before. It will be fascinating.” He took me to the suite’s back rooms, where samples of DNA sent in by customers were opened. The room looked exactly like the back room of an office complex in exurban Houston. It was small. There was furniture. There were windows too. In one corner a machine made slight chugging noises. Greenspan was right. Once you have the right machines, you don’t need a lot of space or gleaming paraphernalia to uncover the mysteries of the human race.
Greenspan showed me where the sample, usually provided by the customer in the form of saliva or a cheek swab, first goes into a machine that isolates the DNA from everything else. The next machine was what he called the shake-and-bake or, more formally, the PCR (for polymerase chain reaction) machine. The DNA goes in, he explained, and then they “heat it up and cool it down, and heat it up and cool it down, and every time they do, it makes more and more DNA. The idea is to magnify the amount of DNA so you end up with more needles than haystack.” Once that is done, the DNA is placed in “the world’s most expensive freezer,” which holds about eighty thousand samples frozen at minus twenty degrees Fahrenheit. When the samples are taken out to analyze, it’s done by robot to eliminate potential human error. Next comes the analysis. Depending on the test, the sample goes through yet another machine, this one with fluorescent magnetic beads. If the segment of DNA that they are looking for is present in the person’s sample, it will attach to the beads.
Typically companies provide a graphic representation of a customer’s chromosomes, and if members of the same family have their genome analyzed, they can superimpose the respective images over each other and see exactly where their DNA overlaps. It may well be obvious to you that the shape of your sister’s eyes is the same as yours, but now you can also see that you share an identical segment of chromosome 3, among others, and that you are literally constituted from the same raw materials at many places all over your genome.
All the companies offer an interpretation of what your genome reveals about your ancestry. You might find, for example, that your Y chromosome is usually found only in men from Africa or Europe or India or Mongolia. You may discover that a certain sequence of letters in your autosomal DNA is typically found in someone with Finnish heritage or Korean ancestry. Only a few years ago the world of science was turned upside down when it was discovered that in ancient times two nonhuman species contributed to the human genome. Now, for a small fee, some companies will analyze how much of your genome comes from Neanderthals. (More about Neanderthals and our other sister species, Denisovans, in chapter 12.)
Greenspan gets personally involved in helping customers solve mysteries from the past. One woman wrote to him and said that even though her family had no Jewish ancestry that she knew of, her grandfather’s given name was Herschel, and her father and his brother were given Herschel as a middle name. A few years earlier she had found an art print hidden behind a painting that had belonged to her grandfather. It was dated 1891, and someone had written “L’Shana Tova,” a Hebrew new year’s greeting, on it. Family Tree DNA tests of her DNA showed that it was likely that she was, in fact, Jewish.
Another woman who was raised Catholic in Spain came from a family with an oral tradition of Jewish ancestry that dated back twenty generations. Greenspan found that the woman’s mtDNA matched people who were from places like Spain, Greece, Algeria, Bulgaria, and Turkey and that they were all, indeed, Sephardic Jews. She asked Greenspan to write her a letter that she could take to a Jewish court to apply for issuance of a letter of return, a formal acknowledgement that she was Jewish.
“I would have discounted her story pretty much out of hand as almost unprovable or almost unbelievable that a family could for twenty generations pass on that they were part of this minority group,” Greenspan told me. “I always worry when we deal with oral history without dealing with the DNA because I think that the difference between telling stories and telling truth is multiple sets of evidence.”
• • •
After fewer than fifteen years in business, personal genetics companies have made possible a genetic-based social networking that makes the social networks of the early 2010s look like child’s play. Customers of 23andMe, Family Tree DNA, and AncestryDNA can discover an extraordinary collection of genetic cousins and track not just their families but specific segments of DNA in their genome. By combining the records research of millions of people with the analysis of their DNA, users can build an actual copy of their human network over the last few hundred years or longer and find their individual place within it.
Companies alert customers when another customer has one or more largeish segments of DNA that look exactly the same. Geneticists say these shared segments have “identity by descent,” meaning they are the same because we got them from the same person. The implication is that the segment has been inherited by both customers from a common ancestor. Accordingly, the company will describe the DNA matches as a “relative” or a “cousin.” Fundamentally, the more closely related you are to someone, the more segments you will have in common, and the longer they will be.
It is said that autosomal DNA can take you back at least five generations. The probability of identifying a third cousin using autosomal DNA is roughly 90 percent, a fourth cousin 50 percent, and a fifth cousin 10 percent. Greenspan said he knows of people who have definitively identified eighth cousins with autosomal DNA. It’s hard to believe that these boundaries won’t be extended further as the science develops.
With a large enough group of descendants in a single family line, it is even possible to rebuild the genome of the dead. The genome of each living person could be used as a virtual puzzle piece with which to reassemble much of the genome of the group’s common ancestor. It is theoretically possible, though no one has yet done it, to reconstruct individuals who have left no trace in written history at all. “With enough people,” Woodward said, “you could project back and rebuild the population of Leigh in Lancashire, England, in 1850.”
A few years ago Blaine Bettin
ger, an intellectual-property lawyer with a background in molecular biology, began a personal search for the DNA of his great-grandmother. Born in 1889, she lived so long that Bettinger, who is thirty-eight, met her as child. She was adopted, he said, so he knew nothing about her genetic background. Yet she was “an incredibly strong woman who had a big impact.” There are traits in Bettinger’s family—he thinks of them as ripples—that seem to emanate from her. In order to explore her and her influence on his family, Bettinger started collecting the DNA of her descendants so that he could isolate some of what they inherited from her.
With the help of two of her grandchildren, he has been able to identify thirty-five segments of DNA spread over almost every chromosome that came from her and her husband. His next step is to find relatives who match through those isolated segments so that he can prize apart which segment came from her and which came from him. As well as convincing members of his family to participate, Bettinger uses cousin matching to find others who overlap on those segments.
Wading through the personal-genomics options and analyses can be daunting for people who have not thought much about their own genes before. Bettinger ordered his first DNA test in 2003, when companies offered to read around 175 markers on the autosome; now the tests examine just under 1,000,000 markers. As a result, Bettinger has become a leader in the genetic genealogist community, part of a select group of individuals who help people understand their cousin networks and what their DNA may tell them, much of it through his popular blog, TheGeneticGenealogist.com.
CeCe Moore, another genetic genealogist and blogger (YourGeneticGenealogist.com), became interested in the subject when she began to put together a family tree for a niece who was getting married. “Little did I know, it’s addicting,” she said. “And I’m one of those obsessive-compulsive types.” Moore used to work as a TV producer but is now a genetic genealogy consultant for the television shows Finding Your Roots, with Henry Louis Gates Jr. and Genealogy Roadshow. She has essentially developed an entirely new class of career, not just explaining and interpreting the ins and outs of DNA but being a genetic detective who helps clients find the missing. Now she eats, lives, and breathes DNA all day, she said, and often through the night as well.
One of the growing uses of genetic genealogy is for adoptees to find families, and Moore, who is the administrator of the Adopted DNA Project at Family Tree DNA, is regularly asked for help. “I get e-mails from people literally every day who found out they’re not who they thought they were genetically,” she said. “They come out as a half-sibling to their sibling, who they thought was their full sibling. This is happening all the time. It usually turns out that the father isn’t the father. I’ve also been contacted about what looks like a baby switch in the hospital.” One of Moore’s earlier cases involved tracking the family of someone who was left on a doorstep in 1916, but in the past year she has been contacted on behalf of half a dozen individuals who were abandoned as newborns, some found in dumpsters.
Sometimes people don’t get the ancestral result that they expect. They assume that they are Irish, but the test says their DNA is more like that of a Russian Jew. “This is just my experience,” Moore added. “It could be that people are drawn to testing who always felt like they didn’t fit in or always had a question in their mind, but the numbers are very high.”
By starting with the segments of DNA that people have in common on one or more chromosomes in genetic genealogy databases, Moore has found missing siblings and even parents. First she tracks back through the family histories of the genetic cousins to find a common ancestor among them, then she will attempt to work her way down again from the common ancestor to find the individual’s parents. “You build the tree up and then you build the tree down,” she said. “If a predicted second cousin shares great-grandparents with a person looking for their birth family (maybe great-great-grandparents, if they just happen to share a little more DNA than expected), we can build that tree down; we can see who lived in the right place at the right time, who was the right gender, and you can sometimes solve it.” Sometimes Moore has found a direct match, where it is quite obvious from the amount of DNA that two people have in common across many chromosomes that they are siblings or parent and child. She recommends that all her clients send their samples to 23andMe, Family Tree DNA, and AncestryDNA, which together have databases of over one million autosomes. “You have to fish in all three ponds.” Sometimes all that can be found about someone is her general ancestry: A recent client discovered that she was Mexican, which she had no idea was the case.
While many individual mysteries have been solved with genetic genealogy, if we change the focus to entire populations, shared chunks of autosomal DNA can take us much further back in time than even eight generations ago.
• • •
Modern culture is good at retaining general knowledge from the recent past, and since the invention of archaeology and paleoanthropology we’ve been able to recover some of the distant past too. Still, much of what we know about the ancients had to be effortfully uncovered. Though we may feel a kinship with figures from the nineteenth and eighteenth centuries or even the Picts, who lived a millennium ago, or the Romans from a thousand years before that, we have lost almost all sense of connection with most people who lived more than two thousand years ago. We have a reasonably good idea about some of their knowledge, which we’ve been able to work out from the traces they left. But we have little sense that that knowledge was passed on to us, not in the same way that we can confidently recognize the innovations and legacies of various significant characters over the last five hundred years, from Leonardo da Vinci to the Wright brothers.
Yet we are now on the cusp of boom times in deciphering the deep history of the world, because in addition to the commercial genetic genealogy companies, many scientific teams are devising different methods to get even further back into the past. They promise not only to illuminate chronologically and emotionally distant times but also to clarify the ways in which we remain connected to them. At the same time that the British team was devising a unique method for revealing the regional genetic blends of Britain, Peter Ralph, a professor of biology at the University of Southern California, and his colleague Graham Coop of the University of California at Davis were developing another way to dig into the history of Europe via its DNA. They examined the genomes of a group of 2,257 Europeans, divided into forty different populations, and identified all the small segments of DNA that any two people had inherited from a recent common ancestor. The goal was to understand the way people are related in modern-day Europe and, in the process, to learn how human networks have changed through time.
Ralph and Coop found that any two modern Europeans who lived in neighboring populations shared between two and twelve genetic ancestors in the previous 1,500 years. These foreign cousins are a testament to the fundamental interconnectedness of all people but also to how ultimately disparate we are: Twelve genetic cousins in another country after 1,500 years isn’t exactly grounds for a family reunion. A similar study found that in a sample of five thousand Europeans, there were tens of thousands of pairs of second to ninth cousins. According to Ralph and Coop, in the period between 1,500 and 2,500 years ago, a given pair of individuals would likely have shared one hundred or more genetic ancestors, which means they carried the same random segment of DNA passed down over all that time from an eightieth-grandparent—perhaps a Roman legionnaire, a Portuguese sailor, or a Greek shepherd. The farther apart people lived in Europe, the less likely it was that they shared genetic ancestors, although, say Ralph and Coop, they would still likely share some.
The way that genomes are cut, split, and shuffled across generations has significant consequences for their structure today. How do segments of DNA break apart and come back together again? I asked Ralph, who suggested that I re-create a lineage, at least on a tiny scale, to see how the process works. I returned to the kitchen table, and again sat there
with my genome before me, only this time it was made of paper, a red strip to symbolize all the genetic material I received from my mother and a green strip to represent all the DNA I received from my father. I wanted to follow half of my DNA back through the generations, so I set the green paper aside, which left me with half my genome—everything I received from my mother.
I chopped the red strip into twenty-three smaller bits to represent the chromosomes in my cells that were made by my mother and then passed on to me. Then I passed the strips farther up the table, symbolically sending them back up the tree to my mother. In order to get a sense of what her genome looked like, I then added another twenty-three strips of brown paper to represent the DNA that my mother did not pass down to me.
The funny thing about the set of chromosomes before me was that even though I was looking at my mother’s total genetic material, I was not looking at her actual chromosomes. The chromosomes she gave to me underwent a process of recombination before she passed them on. Segments of DNA were swapped between each pair, so that overall her chromosomes broke and then recombined on average about thirty-two times across the genome.
In order to unscramble the process, I chopped up the forty-six red and brown strips and swapped pieces between them. This was finicky work, so I settled for doing it just thirty times, which meant that most of the forty-six resulting strips had at least one red segment and one brown segment. These twenty-three pairs of mosaic strips represented my mother’s actual chromosomes.