Counting Chromosomes
A blog of random musings on genealogy, genetics, and history
Red hair and freckles
Her parents both have brown hair.
Is that proof DNA skips a generation?

Q: I've been in touch with a gentleman who says that he is related to my deceased father's family line. His family tree shows this—six generations back—but on GEDmatch he doesn't match me, my two siblings, or two known 1st cousins. He told me that DNA will skip a generation, and insists that if I don't match him I'll probably match his son, whose test results, autosomal and Y-chromosome, are pending. I have no male immediate family members to test the Y-chromosome. I know we don't all get the same DNA from our ancestors, but aren't we limited to the DNA of our parents? Nothing new could show up in his son that he doesn't have but that his father, the son's grandfather, did, correct?

A: Assuming the gentleman and his wife aren't related—e.g., their great-grandparents were a case of two brothers marrying two sisters, making them double 2nd cousins and allowing differing autosomal DNA segments to pass down from both lines—you are absolutely correct. Without pedigree collapse in our trees, and relatively recently generationally speaking, there should be no surprises in the son's results. I'm going to digress a moment before addressing the skip-a-generation thing.

Detour to Imputation

I'm hedging my bets by saying should because the outcome may depend upon where those results are viewed. If on GEDmatch, I can say "no" with greater assurance. With the recent algorithm updates at MyHeritage as an example of how assumptive math plays a greater role in our DNA interpretations than we may realize, they have begun using a form of genotype imputation to "stitch" together two small, otherwise insignificant segments into a larger one that becomes meaningful for matching purposes.

We'll talk more about imputation at a future date, but the basis of the theory is the same for MyHeritage's segment "stitching" as it is in the mechanisms that allow us to compare atDNA results from the Illumina OmniExpress chip (which was used in most of the 10 million test kits now out there) and the new GSA chip, even though only 23% of the SNPs (single nucleotide polymorphisms) tested are the same. The concept is simple: with a database that is large enough and comprehensive enough, we can assumptively but reliably fill-in the blanks.

The easiest example to illustrate this idea is language. If you are a native (or extremely fluent) speaker of English, you have many years of using the language in a structured way, have learned and ingrained both spellings and common phrasing and syntax, and have used English words millions and millions of times throughout your life. That's the comprehensive database you bring to the task. When you see this, your brain can almost instantly supply the missing letters for you:

Word Imputation

 
"Mary had a little lamb." Right? And 99.9% of the time that assumption would be correct. But it can never be 100% correct simply because there might be something in that one-tenth of one percent that throws us a curve. What if the girl in question had been named for an Irish ancestral line, O'Mara? And what if, for some unfathomable but entirely possible reason, she decided to conceal a very small tree branch?

"Mara hid a little limb" fits the defined criteria, even if unlikely. It's all about pattern recognition and, while very good, machine pattern recognition may never be completely perfect and incontestable. As a hypothetical, this is one way a son might seem to have atDNA matches on the paternal line that the father does not.

Digression into imputation done. Is the "skip a generation" thing only a genetic fantasy? Not at all. It has, however, nothing to do with what we typically consider matching data for genealogy. This is another digressive rabbit hole that I will only spend a little time on, but "skip a generation" refers to dominant and recessive genes, and the expression of those genes. Let's quickly consider a gene that determines hair color.

Red Hair and Freckles

Red hair is a recessive gene. A child's pair of genes can be either homozygous (identical from both parents) or heterozygous (one gene type from the father, the other type from the mother). Geneticists usually display the dominant with a capital letter, and the recessive with a lowercase letter; let's call them "R" and "r" in this case. If both the mother and the father are homozygous dominant, they would both be indicated by "RR," neither would have red hair, and neither have a recessive gene they could pass on to their children. None of their kids or their kids' descendants would have red hair.

But what if each parent were "Rr," in other words carry both a dominant and a recessive gene? Neither of them would have red hair because the dominant gene is in control, but they could both pass an "r" recessive to one or more of their children. So they could have three children, one each "RR," "Rr," and "rr." The first would not have red hair and could not pass along the red-hair recessive gene. The second, like her parents, would not have red hair but would be able to pass along either the dominant or the recessive gene. The third would have red hair, and could only pass along the recessive red-hair gene.

This is how DNA can skip a generation. Nothing actually skips anything, of course. But it can most certainly appear like it when one grandparent has red hair, both parents have dark brown hair, and their daughter then turns out to have lovely scarlet locks.

Bottom line is that, as you noted, you can only get your 3 billion base pairs of DNA from two places: your mother and your father. We're purposely going to ignore unusual cases here, like some forms of stem cell transplantation or future CRISPR genetic engineering. That said, you get only approximately 25% of each of your grandparents DNA. In fact, Graham Cooper at UC Davis looked at 1,500 real-world DNA tests and determined that roughly one in 200 grandchildren would obtain only about 10% of his or her autosome from one of the paternal grandparents. With each generation, things get shuffled up more and more.

Diminishing atDNA Returns

What this means is that if you and a cousin share an ancestor six generations back—as is possibly the case with your newly-discovered cousins—a lack of autosomal DNA matching is not evidence disproving the relationship. In fact, the odds we share any detectable DNA at all worsen rapidly the more distant the cousinship. A study headed by Brenna Henn (formerly the head scientist for 23andMe) demonstrated that only 45.9% of your 4th cousins will share any detectable DNA with you at all, and that drops to 14.9% for 5th cousins: your 4g-grandparents and six generations. At that level, your odds of matching an actual 5th cousin are 11:2, or two matches showing for every 13 cousins tested. This is one reason autosomal DNA triangulation, as a process, is really much more complex and detailed than some assume it to be.

If the common ancestor is in both your and your new cousin's direct paternal lines, then yDNA testing could assist with validating the relationship. The Y-chromosome doesn't go through crossover at meiosis, and is passed down intact from father to son unchanged save for occasional—but typically quite slow—generational mutations. This means the male taking the test doesn't necessarily need to be your sibling or father. If your father has a living brother or you have a known male 1st cousin on that paternal descendant line, then yDNA testing could give you and your new-found cousin evidence substantiating a relationship back to that 4g-grandparent MRCA.

Oh, and by the way. While red hair is recessive, having freckles is a dominant trait...even though the same gene, MC1R, is responsible for both! Ain't genetics grand?

Oxford Ancestors
Oxford Ancestors Ltd. closes.
Databases to remain for "a few more months."

Bryan Sykes, MA PhD DSc, launched the company Oxford Ancestors (Kidlington, Oxfordshire, England) in May of 2000, the same month that Family Tree DNA in Houston, Texas, first began selling genealogical DNA tests. These were the first two companies to offer genetic genealogy tests directly to the public.

Sykes just announced the closure of Oxford Ancestors. On the company's website he wrote:

Oxford Ancestors is closing down after 18 years. I have enjoyed those years immensely and it has been a rare privilege to have you send me your DNA from all over the world. We started because I wanted people to be able to share in the excitement of the research being done in university laboratories like my own in Oxford but rarely reaching beyond the halls of academe. That has all changed now and cheap DNA tests are widely available, even if their meaning is sometimes dubious.

He also noted, "In practical terms, all outstanding orders will be fulfilled in accordance with our Terms and Conditions and the databases will operate as usual for a few more months."

The company was founded due to Sykes's belief that his book, The Seven Daughters of Eve (see below), which was set for publication in the spring of 2001, would help create a market for direct-to-consumer DNA testing. The book, describing seven top-level mtDNA haplogroups of Europeans, was one of the first about ancestry and genetics to reach a popular audience. And Sykes was correct: it helped stimulate an interest in genetic genealogy that, as we know, has led to a significant retail industry with several of millions of people already tested.

Dr. Bryan Sykes
Dr. Bryan Sykes

Dr. Sykes, Emeritus Professor of Human Genetics at the University of Oxford, has been a trailblazer in genetic anthropology and genealogy. In 1989, in the journal Nature, he was the first to ever publish a study that used extraction and testing of DNA from ancient bone fragments. And every genetic genealogist I known has, at some point, read at least one of Sykes's books.

Criticism

Critique, particularly of methodology and procedure, dogged some of Sykes's projects. Most notable are:

  • A 1997 mitochondrial DNA essay of a tooth from the 9,000-year-old skeleton of the Cheddar Man, which results were called into doubt by Bandelt, et al. (2005) over possible sample contamination
  • The odd case in 2003 of Thomas R. Robinson, an associate professor of accounting at the University of Miami, who received a call from Oxford Ancestors telling him he was a yDNA descendant of Genghis Khan; later, confirmational testing by Family Tree DNA disproved this assertion. (Wade, Nicholas, "Falling From Genghis's Family Tree." The New York Times, 21 June 2006)
  • The 2015 book, The Nature of the Beast (later retitled, see below), which details investigation into yetis in the Himalayas and Bigfoot in North America through DNA samples from purported hair samples. (Leake, Jonathan, science editor, "Scientist Savaged for Bigfoot Claim." The Sunday Times of London, 29 March 2015)

These notwithstanding, Sykes has cemented himself as a pioneer and innovator in the use of DNA in anthropology and genealogy. On the Oxford Ancestors' website, Sykes concluded that he will be leaving England in the summer of 2018 to live abroad and to devote more time to his writing.

Books by Bryan Sykes

Dendrogram
Clustering dendrogram from the study
Click image to read article at PLOS Genetics

Large-scale DNA studies focusing on Ireland are seeming to appear almost back-to-back. Last December in Scientific Reports, Gilbert, O'Reilly, Merrigan, et al. published "The Irish DNA Atlas: Revealing Fine-Scale Population Structure and History within Ireland." From that abstract:

The extent of population structure within Ireland is largely unknown, as is the impact of historical migrations. Here we illustrate fine-scale genetic structure across Ireland that follows geographic boundaries and present evidence of admixture events into Ireland.

Less than two months later, we had a new peer-reviewed article published by Ross Byrne, Rui Martiniano, Lara Cassidy, Matthew Carrigan, Garrett Hellenthal, Orla Hardiman, Daniel G. Bradley, and Russell L. McLaughlin in PLOS Genetics: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007152.

Titled "Insular Celtic Population Structure and Genomic Footprints of Migration," this study used haplotype-based fineSTRUCTURE

MyHeritage DNA Test Kit

MyHeritage made a big splash at RootsTech last week highlighting its new chromosome browser which initial reports indicate is nicely constructed, robust, and includes a true triangulation feature. The debut of the browser was in conjunction with the announcement of major improvements in the MyHeritage matching procedures and algorithms.

The announcements came not at RootsTech—which wrapped-up last Saturday in Salt Lake City—but a few weeks earlier on the MyHeritage Blog. It was at the massive RootsTech though, this year estimated to have had over 14,200 paid attendees, where attention on MyHeritage became front and center.

Anyone who took a MyHeritage DNA test, and anyone who uploaded DNA data from another service, will now receive more accurate DNA Matches; more plentiful matches (about 10x more); fewer false positives; more specific and more accurate relationship estimates; and indications on lower confidence DNA Matches to help focus research efforts.
     —MyHeritage Blog, 11 January 2018

Jonny Perl
Jonny Perl, DNA Painter
at RootsTech 2018 in Salt Lake City

DNA Painter, the autosomal DNA visualization tool for genealogy created and developed by Jonny Perl, has not only been gaining thousands of users in its seven-month existence, but on March 2 in Salt Lake City it was announced as winner of the 2018 RootsTech DNA Innovation Contest.

Jonny, a web and applications developer in England, has been involved in genealogy for over ten years, but took his first DNA test in December 2016. He admits that he was skeptical of DNA testing initially, and accordingly had delayed testing himself for years. After he saw his results, he was less than completely satisfied with the way they were displayed, and thought that there had to be a better way.

He became involved with a UK-based Facebook group discussing DNA and genealogy, and credits that with helping move his understanding of DNA rapidly past the basic and intermediate stages. He began looking at ways to group and display chromosome mapping and segment sharing more intuitively and visually and, in July 2017, invited just a few people to have a look at what was working on as, essentially, "alpha" testers. Jonny readily admits that if we'd seen the application at that stage, we would not have been impressed.

David Threlkeld
David Threlkeld
(1961–2018)

We've lost a Threlkeld cousin. He passed away February 5, 2018 in his sleep, and evidently peacefully, at the age of 56.

David Threlkeld was my second cousin. We discovered each other only last August. A mutual relative told him of me, and he telephoned on August 29. This was just as Hurricane Harvey began to move north leaving in its wake catastrophic flooding that would come to be ranked as, by far, the most rainfall of any tropical cyclone on record in the United States. And the scammers were already at work: predatory and typically unlicensed contractors, roofers, and "disaster recovery specialists" knocking on doors and calling to try and squeeze money out of those suffering most from the hurricane's aftermath.

This is how I knew within the first several seconds that Dave was a kind and patient man. If he gave his last name when I answered, I didn't hear it. So he got my gruff, unsolicited-sales-call, full-on challenge voice...which on the vocal scale registers as an over-loud Darth Vader.

That didn't faze Dave's friendliness a bit. He explained who his father was and who had given him my number and, as soon as my dim lightbulb sparked, we reset and then talked for almost 45 minutes. He had already tested with AncestryDNA, and was enthusiastic about a Y-chromosome test with Family Tree DNA and joining the Threlkeld DNA Project.

Threlkeld House, Shelbyville
The Threlkeld/Weakley House, Shelbyville, Kentucky

If you happened to visit Google Images today you noticed that, quietly and with no fanfare, Google has removed the "View Image" button from the results of image searches. I know many genealogists—and you may be one of them—who regularly use Google Images to search for new instances of photos depicting geography, structures, and particularly people of interest to you. It's convenient, lets you preview the images, and of course employs the robust Google search engine.

Beginning a few hours ago, though, you no longer have the easy option to click on a button and view an image at full resolution in a new web browser window. That's good for businesses, publishers, and artists that make money from their products; not so good for genealogists who simply want a century-old photo of a great-grandmother to put in a family tree.

There is a rather singular reason for the change which we'll touch on in just a moment, but the result is an implication that people can no longer download an image, or an intention

DNA Central

It's been four weeks to the day since Blaine Bettinger first posted on his blog, The Genetic Genealogist, about the upcoming April launch of DNA Central. Now, April isn't that far away.

I've followed Blaine's Blaine's contributions to the genetic genealogy community for years, and have already told him that I will be the first in line when the doors open. There are a number of "Citizen Scientists" who regularly offer their expertise to the millions who have now taken genealogy-driven DNA tests, and Blaine's one of the best. From his January 25 blog post:

This new subscription-based site will have blog posts about the latest and greatest, how-to content (including a "What Next?" series), short videos (such as the "3-Minute DNA" series), webinars, and forums. We'll also have monthly giveaways and much more. It's everything you need to finally understand and apply the results of your DNA testing!

Visit that blog post to find a link to subscribe to receive DNA Central announcements, or you can click here to go directly to the subscription form There is no cost or obligation to subscribe to the mailing list.