The Autosomal Me – The Holy Grail – Identifying Native Genealogy Lines

Posted on May 31, 2013 by Roberta Estes

Sangreal – the Holy Grail. We are finally here, Part 9 and the final article in our series. The entire purpose of The Autosomal Me series has been to use our DNA and the clues it holds to identify minority admixture, in this case, Native American, and by identifying those Native segments, and building chromosomal clusters, to identify the family lines that contributed that Native admixture. Articles 1-8 in the series set the stage, explained the process and walked us through the preparatory steps. In this last article, we apply all of the ingredients, fasten the lid, shake and see what we come up with. Let’s take a minute and look at the steps that got us to this point.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.

Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.

In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In Part 6, “The Autosomal Me – DNA Analysis – Splitting Up” we began the analysis part of the data we’ve been gathering. We looked at how to determine whether minority admixture on specific chromosomes came from which parent.

Part 7, “The Autosomal Me – Start, Stop, Go – Identifying Native Chromosomal Segments” took a deeper dive and focused on the two chromosomes with proven Native heritage and began by comparing those chromosome segments using the 4 GedMatch admixture tools.

Part 8, “The Autosomal Me – Extracting Data Segments and Clustering,” we extract all of the Native and Blended Asian segments in all 22 chromosomes, but only used chromosomes 1 and 2 for illustration purposes. We then clustered the resulting data to look for trends, grouping clusters by either the Strong Native criteria or the Blended Asian criteria.

In this final segment, Part 9, we will be applying the chromosomal information we’ve gathered to our matches and determine which of our lines are the most likely to have Native Ancestry. This, of course, has been the goal all along. So, drum roll…..here we go.

In Part 8, we ended by entering the start and stop locations of both Strong Native and Blended Asian clusters into a table to facilitate easy data entry into the chromosome match spreadsheet downloaded from either 23andMe or Family Tree DNA. If you downloaded it previously, you might want to download it again if you haven’t modified it, or download new matches since you last downloaded the spreadsheet and add them to the master copy.

My goal is to determine which matches and clusters indicate Native ancestry, and how to correlate those matches to lineage. In other words, which family lines in my family were Native or carry Native heritage someplace.

The good news is that my mother’s line has proven Native heritage, so we can use her line as proof of concept. My father’s family has so many unidentified wives, marginalized families and family secrets that the Native line could be almost any of them, or all of them! Let’s see how that tree shakes out.

Finding Matches

So let’s look at a quick example of how this would work. Let’s say I have a match, John, on chromosome 4 in an area where my mother has no Native admixture, but I do. Therefore, since John does not match my mother, then the match came from my father and if we can identify other people who also match both John and I in that same region on that chromosome, they too have Native ancestry. Let’s say that we all also share a common ancestor. It stands to reason at that point, that the common ancestor between us indicates the Native line, because we all match on the Native segment and have the same ancestor. Obviously, this would help immensely in identifying Native families and at least giving pointers in which direction to look. This is a “best case’ example. Some situations, especially where both parents contribute Native heritage to the same chromosome, won’t be this straightforward.

Based on our findings, the maximum range and minimum (least common denominator or “In Common” range is as follows for the strongest Native segments on chromosomes 1 and 2.

	Chromosome 1	Chromosome 2
Largest Range	162,500,000 – 180,000,000	79,000,000 – 105,000,000
Smallest Range	165,658,091 – 171,000,000	90,000,000 – 103,145,425

At GedMatch

At GedMatch, I used a comparison tool to see who matched me on chromosome 1. Only 2 people outside of immediate family members matched, and both from Family Tree DNA. Both matched me on the critical Native segments between about 165-180mg. I was excited. I went to Family Tree DNA and checked to see if these two people also matched my mother, which would confirm the Native connection, but neither did, indicating of course that these two people matched me on my father’s side. That too is valuable information, but it didn’t help identify any common Native heritage with my mother on chromosome 1. It did, however, eliminate them as possibilities which is valuable information as well.

DNAGedcom

I used a new tool, DNAGedcom, compliments of Rob Warthen who has created a website, DNA Tools, at www.dnagedcom.com. This wonderful tool allows you to download all of your autosomal matches at Family Tree DNA and 23andMe along with their chromosomal segment matches. Since my mother’s DNA has only been tested at Family Tree DNA, I’m limiting the download to those results for now, because what I need is to find the people who match both she and I on the critical segments of chromosome 1 or 2.

Working with the Download Spreadsheet

It was disappointing to discover that my mother and I had no common matches that fell into this range on chromosome 1, but chromosome 2 was another matter. Please note that I have redacted match surnames for privacy.

The spreadsheet above shows the comparison of my matches (pink) and Mother’s (white). The Native segment of chromosome 2 where I match Mother is shaded mustard. I shaded the chromosome segments that fell into the “common match” range in green. Of those matches, there is only one person who matches both Mother and I, Emma. The next step, of course, is to contact Emma and see if we can discover our common ancestor, because whoever it is, that is the Native line. As you might imagine, I am chomping at the bit.

There are no segments of chromosome 2 that are unquestionably isolated to my father’s line.

Kicking it up a Notch

Are you wondering about now how something that started out looking so simple got so complex? Well, I am too, you’re not alone. But we’ve come this far, so let’s go that final leg in this journey. My mom always used to say there was no point in doing something at all if you weren’t going to do it right. Sigh….OK Mom.

The easiest way to facilitate a chromosome by chromosome comparison with all of your matches and your Strong Native and Blended Asian segments is to enter all of these segment groups into the match spreadsheet. If you’re groaning and your eyes glaze over right after you do one big ole eye roll, I understand.

But let’s take a look at how this helps us.

On the excerpt from my spreadsheet below, for a segment of chromosome 5, I have labeled the people and how they match to me. The ones labeled “Mom” in the last column are labeled that way because these people match both Mom and I. The ones labeled “Dad” are labeled that way because I know that person is related on my father’s side.

Using the information from the tables created in Step 8, I entered the beginning and end of all matching segment clusters into my spreadsheet. You can see these entries on lines 7, 8, 22, 23 and 24. You then proceed to colorize your matches based on the entry for either Mom or Dad – in other words the blue row or the purple row, line 7, 22 or 24. In this example, actually, line 5 Rex, based on the coloration, should have been half blue and half purple, but we’ll discuss his case in a minute.

The you can then sort either by match name or by chromosome to view data in both ways. Let’s look at an example of how this works.

Legend:

White Rows: Mother’s matches. When Mother and I both match an individual, you’ll see the same matches for me in pink. This double match indicates that the match is to Mother’s side and not Father’s side.
Pink Rows: My matches.
Purple “Mom” labels in last column: The individual matches both me and Mom. This is a genetic match.
Teal “Dad” labels in last column: Genealogically proven to be from my father’s side. This is a genealogical, not a genetic label, since I don’t have Dad’s DNA and can only infer these genetically when they don’t also match Mother.
Dark Pink Rows labeled “Me Amerind Only” are Strong Native or Blended Asian segments from Chromosome Table that I have entered. My segments must come from one of my parents, so I’ve either colored them purple, if the match is someone who matches Mother and I both, or teal, if they don’t match both Mom and I, so by inference they come from my father’s line.
Dark Purple Rows labeled “Mom Amerind Only” are Mom’s segments from the Chromosome Table.
Dark Teal Rows labeled “Dad Amerind Only” are inferred segments belonging to my father based on the fact that Mother and I don’t share them.

Inferred Relationships

This is a good place to talk for just a minute about inferred relationships in this context. Inference gets somewhat tenuous or weak. The inferred matches on my father’s side began with the Native segments in the admix tools. Some inferences are very strong, where Mother has no Native at all in that region. For example, Mom has European and I have Native American. No question, this had to come from my father. But other cases are much less straightforward.

In many cases, categorization may be the issue. Mom has West Asian for example and I have Siberian or Beringian. Is this a categorization issue or is this a real genetic difference, meaning that my Siberian/Beringian is actually Native and came from my father’s side?

Other cases of confusion arise from segment misreads, etc. I’ve actually intentionally included a situation like this below, so we can discuss it. Like all things, some amount of common sense has to enter the picture, and known relationships will also weigh heavily in the equation. How known family members match on other chromosome segments is important too. Do you see a pattern or is this match a one-time occurrence? Patterns are important.

Keep in mind that these entries only reflect STRONG Asian or Native signals, not all signals. So even if Mother doesn’t have a strong signal, it doesn’t mean that she doesn’t have ANY signal in that region. In some cases, start and stop segments for Mom and Dad overlapped due to very long segments on some matches. In this case, we have to rely on the fact that we do have Mother’s actual DNA and assume that if they aren’t also a match to Mother, that what we are seeing is actually Dad’s lines, although this may not in actuality always be true. Why? Because we are dealing with segments below the matching threshold limit at both Family Tree DNA and 23andMe, and both of my parents carry Native heritage. We can also have crossed a transitional boundary where the DNA that is being matched switches from Mom’s side to Dad’s side.

Ugh, you say, now that’s getting messy. Yes, it is, and it has complicated this process immensely.

The Nitty-Gritty Data Itself

Taking a look at this portion of chromosome 5, we have lots going on in this cluster. Most segments will just be boring pink and white (meaning no Native), but this segment is very busy. Mom and I match on a small segment from 52,000,000 to 53,000,000. Indeed, this is a very short segment when compared to the entire chromosome, but it is strongly Native. We both also match Rex, our known cousin. I’ve noted him with yellow in the table. Please note that Mom’s white matches are never shaded. I am focused on determining where my own segments originate, so coloring Mother’s too was only confusing. Yes, I did try it.

You can see that Mother actually shares all or any part of her segment with only me and Rex. This simplifies matters, actually. However, also note that I carry a larger segment in this region than does Mother, so either we have a categorization issue, a misread, or my father also contributed. So, a conundrum. This very probably implies that my father also carried Native DNA in this region.

Let’s see what Rex’s DNA looks like on this same segment of chromosome 5, from 52-53 using Eurogenes. In the graph below, my chromosome is the top bar, Rex’s the middle and the bottom bar shows common DNA with the black nonmatching. Yellow is Native American, red is South Asian, putty is Siberian, lime green is Mediterranean, teal is North Europe, orange is Caucus.

This same comparison is shown to Mother’s DNA (top row) below.

It’s interesting that while Mother doesn’t have a lot of yellow (Native), she does have it throughout the same segment where Rex’s occurs, from about 52 through 53.5.

Does this actually point to a Native ancestor in the common line between Rex, Mom and I, which is the Swiss/German Johann Michael Miller line which does include an unidentified wife stateside, or does this simply indicate a common ancient population long ago in Asia? It’s hard to say and is deserving of more research. I feel that it is most likely Native because of the actual yellow, Native segment. If this was an Asian/European artifact, it would be much less likely to carry the actual yellow segment.

Is Rex also genealogically related to my father? As I’ve worked through this process with all of my chromosomes and matches, I’ve really come to question if one of my father’s dead ends is also an ancestral line of my mother’s.

The key to making sense of these results is clusters.

Clusters vs Singleton Outliers

The work we’ve already done, especially in Step 8, clusters the actual DNA matching segments. We’ve now entered that information into the spreadsheet and colored the segments of those who match. What’s next?

The key is to look for people with clusters. Many matches will have one segment, of say, 10 that match, colored. Unless this is part of a large chromosome cluster, it’s probably simply an outlier. Part of a large chromosome cluster would be like the large Strong Native segments on chromosome 1 or 2, for example. How do we tell if this is a valid match or just an outlier?

Sort the spreadsheet by match name. Take a look at all of the segments.

The example we’ll use is that of my cousin, Rex. If you recall, he matches both me and Mother, is a known first cousin twice removed to me, (genetically equal to a second cousin), and is descended from the Miller line.

In this example, I also colored Mother’s segments because I wanted to see which segments that I did not receive from her were also Native. You can see that there are many segments where we all match and several of those are Native. These also match to other Miller descendants as well, so are strongly indicative of a Native connection someplace in our common line.

If we were only to see one Native segment, we would simply disregard this as an outlier situation. But that’s not the case. We see a cluster of matches on various segments, we match other cousins from the same line on these segments, and reverting back to the original comparison admixture tools verifies these matches are Native for Rex, Mom and me.

Hmmmm…..what is Dad’s blue segment color doing in there? Remember I said that we are only dealing with strong match segments? Well, Mom didn’t have a strong segment at that location and so we inferred that Dad did. But we know positively that this match does come from Mother’s side. I also mentioned that I’ve come to wonder if my Mom and Dad share a common line. It’s the Miller line that’s in question. One of Johann Michael Miller’s children, Lodowick, moved from Pennsylvania to Augusta County, Virginia in the 1700s and his line became Appalachian, winding up in many of the same counties as my father’s family. I’m going to treat this as simply an anomaly for now, but it actually could be, in this case, an small indication that these lines might be related. It also might be a weak “Mom” match, or irrelevant. I see other “double entries” like this in other Miller cousins as well.

What is the pink row on chromosome 12? When I grouped the Strong Native and Asian Clusters, sometimes I had a strong grouping, and Mom had some. The way I determined Dad’s inferred share was to subtract what Mom had in those segments from mine. In a few cases, Mom didn’t have enough segments to be considered a cluster but she had enough to prevent Dad from being considered a cluster either, so those are simply pink, me with no segment coloring for Mom or Dad.

Let’s say I carry Strong Native/Mixed Asian at the following 8 locations:

10, 12, 14, 16, 18, 20, 22, 24

This meets the criteria for 8 of 15 ethno-geographic locations (in the admix tools) within a 2.5 cM distance of each other, so this cluster would be included in the Mixed Asian for me. It could also be a Strong Native cluster if it was found in 3 of 4 individual tools. Regardless of how, it has been included.

Let’s now say that Mom carries Native/Mixed Asian at 10, 12 and 14, but not elsewhere in this cluster.

Mom’s 3 does not qualify her for the 8/15 and it only leaves Dad with 5 inferred segments, which disqualifies him too. So in this case, my cluster would be listed, but not attributable directly to either parent.

What this really says is that both of my parents carry some Native/Blended Asian on this segment and we have to use other tools to extrapolate anything further. The logic steps are the same as for Dad’s blue segment. We’re going to treat that as an outlier. If I really need to know, I can go back to the actual admixture tools and see whether Mom or Dad really match me strongly on which segments and how we compare to Rex as well. In this case, it’s obvious that this is a match to my Mother’s side, so I’m leaving well enough alone.

Let’s see what the matches reveal.

Matches

Referring back to the Nitty Gritty Data spreadsheet, Mom’s match to Phyllis on row 15 confirms an Acadian line. This is the known line of Mother’s Native ancestry. This makes sense and they match on Native segments on several other chromosomes as well. In fact, many of my and Mother’s matches have Acadian ancestry.

My match to row 19, Joy, is a known cousin on my father’s side with common Campbell ancestry. This line is short however, because our common ancestor, believed to be Charles Campbell died before 1825 in Hawkins County, TN. He was probably born before 1750, given that his sons were born about 1770 and 1772. Joy and I descend from those 2 sons. Charles wife and parents are unknown, as is his wife.

My match to row 20, inferred through my father’s side, is to a Sizemore, a line with genetically proven Native ancestry. Of course, this needs more research, but it may be a large hint. I also match with several other people who carry Sizemore ancestors. This line appears to have originated near the NC/VA border.

I wanted to mention rows 4 and 17. Using our rules for the spreadsheet, if I match someone and they don’t also match Mother on this segment, I have inferred them to be through my father. These are two instances that this is probably incorrect. I do match these people through Mother, but Mother didn’t carry a strong signal on this segment, so it automatically became inferred to Dad. Remember, I’m only recording the Strong Native or the Blended Asian segments, not all segments. However, I left the inferred teal so that you can see what kinds of judgment calls you’ll have to make. This also illustrates that while Mom’s genetic matches are solid, Dad’s inferred matches are less so and sometimes require interpretation. The proper thing to do in this instance would be to refer back to the original admixture tools themselves for clarification.

Let’s see what that shows.

Using HarrappaWorld, the most pronounced segment is at about 52. Teal is American. You can see that Mother has only a very small trace between 53 and 54, almost negligible. Mother’s admixture at location 52 is two segments of purple, brown and cinnamon which translate to Southwest Asian (lt purple), Mediterranean (dk purple), Caucasian (brown) and Balock (cinnamon), from Pakistan.

Checking Dodecad shows pretty much the same thing, except Mother’s background there is South Asian, which could be the same thing as Caucus and Pakistan, just different categorizations.

In this case, it looks like the admixture is not a categorization issue, but likely did come from my father. Each segment will really be a case by case call, with only the strongest segments across all tools being the most reliable.

It’s times like this that we have to remember that we have two halves of each chromosome and they carry vastly different information from each of our parents. Determining which is which is not always easy. If in doubt, disregard that segment.

Raw Numbers

So, what, really did I figure out after all of this?

First, let’s look at some numbers.

I was working with a total of 292 people who had at least one chromosomal segment that matched me with a Strong Native or Blended Asian segment. Of those, 59 also matched Mom’s DNA. Of those, 18 had segments that matched only Mom. This means that some of them had segments that also matched my father. Keep in mind, again, that we are only using “strong matches” which involves inferring Dad’s segments and that referring back to the original tools can always clarify the situation. There seems to be some specific areas that are hotspots for Native ancestry where it appears that both of my parents passed Native ancestry to me.

Many of my and my mother’s 59 matches have Acadian ancestry which is not surprising as the Acadians intermarried heavily with the Native population as well as within their own ethnic group.

Several also have Miller Ancestry. My Miller ancestor is Johann Michael Miller (1692-1771) who immigrated in the colonial period and settled on the Pennsylvania frontier. His son, Philip Jacob Miller’s (1726-1799) wife was a woman named Magdalena whose last name has been rumored for years to be Rochette, but no trace of a Rochette family has ever been found in the county where they lived, region or Brethren church history…and it’s not for lack of looking. Several matches point to Native Ancestry in this line. This also begs the question of whether this is really Native or whether it is really the Asian heritage of the German people. Further analysis, referring back to the admixture tools, suggests that this is actually Native. It’s also interesting that absolutely none of Mother’s other German or Dutch lines show this type of ancestry.

There is no suggestion of Native ancestry in any of her other lines. Mother’s results are relatively clean. Dad’s are anything but.

Dad’s Messy Matches

My father’s side of the family, however, is another story.

I have 233 matches that don’t also match my mother. There can be some technical issues related to no-calls and such, but by and large, those would not represent many. So we need to accept that most of my matches are from my Father’s side originating in colonial America. This line is much “messier” than my mother’s, genealogically speaking.

Of those 233 matches, only 25 can be definitely assigned to my father. By definitely assigned, I mean the people are my cousins or there is an absolutely solid genealogical match, not a distant match. Why am I not counting distant matches in this total? We all know by virtue of the AncestryDNA saga that just because we match family lines and DNA does NOT mean that the DNA match is the genealogical line we think it is. If you would like to read all about this, please refer to the details in CeCe Moore’s blog where she discussed this phenomenon. The relevant discussion begins just after the third photo in this article where she shows that 3 of 10 matches at Ancestry where they “identify” the common DNA ancestor are incorrect. Of course, they never SAY that the common ancestor is the DNA match, but it’s surely inferred by the DNA match and the “leaf” connecting these 2 people to a common ancestor. It’s only evident to someone who has tested at least one parent and is savvy enough to realize that the individual whose ancestor on Mom’s side that they have highlighted, isn’t a match to Mom too. Oops. Mega-oops!!!

However, because we are dealing in our project, on Dad’s side, with inferences, we’re treading on some of the same ground. Also, because we are dealing with only “strong clustered” segments, not all Native or Asian segments and because it appears that my parents both have Native ancestry. To make matters worse, they may both have Algonquian, Iroquoian or both.

I have also discovered during this process that several of my matches are actually related to both of my parents. I told you this got complex.

Of the people who don’t match Mother, 32 of them have chromosomal matches only to my father, so those would be considered reliable matches, as would the closest ones of the 25 that can be identified genealogically as matching Dad. Many of these 25 are cousins I specifically asked to test, and those people’s results have been indispensable in this process.

In fact, it’s through my close circle of cousins that we have been able to eliminate several lines as having Native ancestry, because it doesn’t’ show as strong and they don’t have it either.

Many of these lines group together when looking at a specific chromosome. There is line after line and cousin after cousin with highlighted data.

Dad’s Native Ancestors

So what has this told me? This information strongly suggests that the following lines on my father’s side carry Native heritage. Note the word “carry.” All we can say at this point is that it’s in the soup – and we can utilize current matches at our testing company and at GedMatch, genealogy research and future matches to further narrow the branches of the tree. Many of these families are intermarried and I have tried to group them by marriage group. Obviously, eventually, their descendants all intermarried because they are all my ancestors on my father’s side. But multiple matches to other people who carry the Native markers but aren’t related to my other lines are what define these as lines carrying Native heritage someplace.

Campbell – Hawkins County, Tn around 1800, missing wife and parents, married into the Dodson family
Dodson – Hawkins County, Tn, Virginia – written record of Lazarus Dodson camping with the Cherokee – missing wife, married into the Campbell and Estes family

Claxton/Clarkson – Russell Co., Va, Claiborne and Hancock Co., Tn – In NC associated with the known Native Hatcher family. Possibly a son-in-law. Missing family entirely.
Cook – Russell Co., Va. – daughter married Claxton/Clarkson – missing wives
Harrold, Harrell, Herrell – Hancock Co., Tn., Wilkes Co., NC – missing wives
McDowell – Hancock Co. Tn, Wilkes Co., NC, Augusta Co., Va – married into the Harrell family, missing wife

McNeil, McNiel – Wilkes Co., NC – missing wives, married into the Vannoy family
Vannoy – Wilkes County – some wives unaccounted for pre-1800
Crumley – Greene County, Tn., Lee Co., Va. – oral history of Native wife, married into the Vannoy family
Brown – Greene County, Tn, Montgomery Co., Va – married into the Crumley family, missing wives

While this looks like a long list, the list of families that don’t have any Native ancestry represented is much longer and effectively serves to eliminate all of those lines. While I don’t have “THE” answer, I certainly know where to focus my research. Maybe there isn’t the one answer. Maybe there are multiple answers, in multiple lines.

The Take Away

Is this complex? Yes! Is it a lot of work? You bet it is! Is everything cast in concrete? Never! You can see that by the differences we’ve found in data interpretation, not to mention issues like no-calls (areas that for some reason in the test don’t read) and cross overs where your inheritance switches from your mom’s side to your dad’s side. Is there any other way to do this? No, not if your minority admixture is down in that weedy area around 1%.

Is it worth it? You’ll have to decide. It guess it depends on how desperately you want to know.

Part of the reason this is difficult is because we are missing tools in critical locations. It’s an intensively laborious manual process. In essence, using various tools, one has to figure out the locations of the Native and Asian chromosome segments and then use that information to infer Native matches by a double match (genetic match at DNA company plus match with Strong Native/Blended Asian segment) with the right parent. It becomes even more complex if neither parent is available for testing, but it is doable although I would think the reliability could drop dramatically.

Tidbits and Trivia

I’ve picked up a number of little interesting tidbits during this process. These may or may not be helpful to you. Just kind of file them away until needed:)

Matches at testing companies come and go….and sometimes just go. At Family Tree DNA, I have some matches that must be trembling on the threshold that come and go periodically. Now you see them, now you don’t. I lost matches moving from the Affy chip to the Illumina chip and lost additional matches between Build 36 and 37. Some reappeared, some haven’t.

The start and stop boundaries changed for some matches between build 36 and build 37. I did not go back and readjust, as most of these, in the larger scheme of things, were minor. Just understand that you are looking for patterns here that indicate Native heritage, not exact measurements. This process is a tool, and unfortunately, not a magic wand:)

The centromere locations change between builds. If you have matches near or crossing the middle of the chromosome, called the centromere, there may be breaks in that region. I enter the centromere start and stop locations in my spreadsheet so that if I notice something odd going on in that region, the centromere addresses are right there to alert me that I’m dealing with that “odd” region. You can find the centromere addresses in the FAQ at Family Tree DNA for their current build.

At 23andMe, when you reach the magic 1000 matches threshold, you start losing matches and the matching criteria is elevated so that you can stay under 1000 matches. For people with colonial American or Jewish heritage, in other words those with high numbers of matches, this is a problem.

Watch for matches that are related to both sides of your family. If your family lived in colonial America, you’re going to have a lot of matches and many are probably related to each other in ways you aren’t aware of.

If your parents are related to each other, this process might simply be too complex and intertwined to provide enough granular data to be useful.

Endogamous groups are impossible to sort through as to where, meaning which ancestor, the DNA came from. This is because the original group founders’ DNA is just getting passed around and around, with little or no new DNA being introduced. The effect of this on downstream generations relative to genetic genealogy is that matches appear to be more closely related than they are because of the amount of matching DNA they carry. For my Brethren and my Acadian groups of people, I just list them by the group name, since, as the saying goes, “if you’re related to one Acadian, you’re related to all Acadians.”

If you’re going to follow this procedure, save one spreadsheet copy with the Strong Native only and then a second one with both the Strong Native and Blended Asian. I’m undecided truthfully whether the Mixed Asian adds enough resolution for the extra work it generates.

When in question, refer back to the original tools. The answer will always be found there.

Unfortunately, tools change. You may want to take screen shots. During this process, FTDNA went from build 36 to 37, match thresholds changed, 23andMe introduced a new user interface (which I find much less intuitive) and GedMatch has made significant changes. The net-net of this is when you decide to undertake this project, commit to it and do it, start to finish. Doing this little by little makes you vulnerable to changes that may make your data incompatible midstream – and you may not even realize it.

This entire process is intensively manual. My spreadsheet is over 5500 rows long. I won’t be doing it again…although I will update my spreadsheet with new matches from time to time. The hard work is already done.

This same technique applies to any minority ancestry, not just Native, although that’s what I’ve been hunting for and one of the most common inquiries I receive.

I am hopeful that in the not too distant future many of these steps and processes will be automated by the group of bright developers that contribute to GedMatch or via other tools like DNAGedcom. HINT – HINT!!!

I would like to follow this same process to identify the source of my African heritage, but I’m thinking I’ll wait for the tools to become automated. The great irony is that it’s very likely in the same lines as my Native ancestors.

If You Want to Test

What does it take to do this for yourself using the tools we have today, as discussed?

If your parents are living, the best gift you can give yourself is to test them, now, while you still can. My mother has been gone for several years, but her DNA archived at Family Tree DNA was still viable. This is not always the case. I was fortunate. Her DNA is one of the best gifts she gave me. Not just by inheritance, but by having hers tested. I thank her every single day, for both! I could not have written this article without her DNA results. The gift that keeps on giving.

If you don’t have a parent to test, you can test several other family members who will provide some information, but clearly won’t carry the same amounts of common DNA with you as your parents. These would include your aunts and uncles, your parents’ siblings and what I’ve referred to as your close cousin circle. Attempt to test at least someone from each line. Yes, it gets expensive, but as one of my cousins said, as she took her third or 4th DNA test. “It’s only money. This is about family.”

You can also test your own siblings as well to obtain more information that you can use to match up to your family lines. Remember, you only receive half of your parents DNA, and your siblings will received some DNA from your parents that you didn’t.

I don’t have any other siblings to test, but I have tested cousins from several lines which have proven invaluable when trying to discern the sources of certain segments. For example, one of these Native segments fell on a common segment with my cousin Joy. Therefore, I know it’s from the Campbell line, and because I have the Campbell paternal Y-DNA which is European, I know immediately the Native admixture would have had to be from a wife.

Much of this puzzle is deductive, but we now have the tools, albeit manual, to do this type of work that was previously impossible. I am somewhat disappointed that I can’t pinpoint the exact family lines, yet, but hopefully as more people test and more matches provide genealogical information, this will improve.

If you want to play in this arena, you need to test at either Family Tree DNA, 23andMe, or both. Right now, the most cost effective way to achieve this is to purchase a $99 kit from 23andMe, test there, then download your results from 23andMe and upload them to Family Tree DNA for $99. That way, you are fishing in both pools. Be aware that less than half of the people who test at either company download results to GedMatch, so your primary match locations are with the testing companies. GedMatch is auxiliary, but critical for this analysis. And the newest tool, DNAGedcom is a Godsend.

Also note that transferring your result to Family Tree DNA is NOT the same thing as actually testing there. Why does this matter? If you want a future test at Family Tree DNA, who is the premiere genetic genealogy testing company, offering the most variety and “deepest” commercial tests, they archive your DNA for 25 years, but if you transfer results, they don’t have your DNA to archive, so no future products can be ordered. All I can say is thank Heavens Mom’s DNA was there.

Ancestry.com doesn’t provide any tools such as the chromosome browser or even the basic information of matching segments. All you get is a little leaf that says you’re related, but the questions of which segment or how are not answerable today at Ancestry and as CeCe’s experience proved, its unreliable. It’s possible that you share the same surnames and ancestor, but your genetic connection is not through that family line. Without tools, there is no way to tell. Ancestry released raw data files a few weeks ago and very recently, GedMatch has implemented the ability to upload them so that Ancestry participants can now utilize the additional tools at GedMatch.

Although this has been an extraordinarily long and detailed process, I can’t tell you how happy I am to have developed this new technique to add to my toolbox. My Native and African ancestors have been most elusive. There are no records, they didn’t write and probably didn’t even speak English, certainly not initially. The only clues to their existence, prior to DNA, were scant references and family lore. The only prayer of actually identifying them is though these small segments of our DNA – yep – down in the weeds. Are there false starts perhaps, and challenges and maybe a few snakes down there? Yes, for sure, but so is the DNA of your ancestors.

Happy gardening and rooting around in the weeds. Just think of it as searching for the very best buried treasure! It’s down there, just waiting to be found. Keep digging!

I hope you’ve enjoyed this series and that it leads you to your own personal genealogical treasure trove!

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The Autosomal Me – Extracting Data Segments and Clustering

Posted on April 8, 2013 by Roberta Estes

This is Part 8 of a multi-part series, “The Autosomal Me.”

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets. Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis. In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

Part 7, “The Autosomal Me – Start, Stop, Go – Identifying Native Chromosomal Segments”, took a deeper dive and focused on the two chromosomes with proven Native heritage and began by comparing those chromosome segments using the 4 GedMatch admixture tools.

In this segment, Part 8, we’ll be extracting all of the Native and Blended Asian segments on all 22 chromosomes, but I’ll only be using chromosomes 1 and 2 for illustration purposes. We will then be clustering the resulting data to look for trends. If you’re following along and using this methodology, you’ll be extracting the Native segment start and stop locations from all 22 chromosomes.

I apologize in advance for the length of this article, but there was just no good place to break it into pieces.

So, let’s get started. As a reminder, we are using the admixture tools at www.gedmatch.com.

I experimented with several types of extractions to see which ones best reflected the results found by both 23andMe and Dr. McDonald and confirmed by the start and stop segments in the highly Native segments of chromosomes 1 and 2 in Part 7 of this series. We verified that all 4 tools accurately reflected and corroborated the segments listed as Native, so now we’re going to apply that same methodology to the rest of our chromosomal data.

Initially, I tried to use the information from chromosomes 1 and 2 to extract the Native chromosomes using only the “best” tool, but when I looked at all 4 tools, I quickly realized that there was no single “best” choice. A couple of crucial points came to light.

Some of the geographic colors are almost impossible to tell apart.
None of the tools are universally best.
When looking at all 4 tools, generally a “best 3 out of 4” approach allowed for one of the tools to be wrong, to perhaps reference a slightly different data base that called the segment differently or for the colors to be indistinguishable. In other words, if three called a segment Native and one did not, it’s Native and conversely, if less than 3 call it Native, in this comparison, it’s not.

Unfortunately, this created an awful lot of work. This is probably the best example of where automation tools could and would make a huge difference in this process.

I did two separate extracts. The first one is what I refer to as the “Strong Native” extract and the second is the “Blended Asian.” In part, I did these separately as a check and balance to be sure that my first extraction was accurate.

In the first extract, I selected only one category, the one best fitted to “Native American” for each tool. I used the following categories for each admixture tool:

MDLP – Amerind
Eurogenes – North Amerindian
Dodecad – NE Asian
Harrappaworld – American

I completed this process for every chromosome, but I’m only showing the first two chromosomes in this article.

By way of example, using the first tool, MDLP, North Amerind looks black, but is actually very dark grey. It is, fortunately, distinctive.

On the chromosome painting below, my results for the first part of chromosome 1 are shown in the first band, and mother’s for the same segment are shown as the second band. The bottom band represents common segments and the black is non-matching segments, meaning those I obtained from my father. Sometimes this third band can help you determine what you are really seeing in terms of colors and blending, but it’s not always useful. In this case, trying to spot a small amount of dark gray against black is almost impossible, so not terribly helpful. But if you were looking for red, that would be another story. As you move through this process, remember, it’s not exact and utilizing best 3 of 4 will help you recover from any major errors.

You can see that my grey segments show up from about 12-13 and then again at about 14.5. Sometimes it’s difficult to know how to count something. For example, my Native at 14.5 – it’s actually more like 14.25 -14.5, but I chose not to divide further than half mb segments. As long as you are consistent in whatever methodology you select, it will work out.

Please note that when reading these charts, that the small hash mark is the indicator for the measure. In other words, the small hash mark above 10M means that is the 10M location. It’s obvious here, but on some charts, the hash mark and the location legend look to be 1-off. Again, as long as you’re consistent, it really doesn’t matter.

Mother’s Native segments are more pronounced and obvious. They range from about 8-14. Using the actual tools, you would record this and then continue scrolling to the right until you reach the end of the chromosome. On chromosomes 1 and 2, I found the strong Native segments for the four admixture tools, as shown below.

The boxed numbers show the areas that were found “in common” between 23andMe, Dr. McDonald and the admixture tools, as determined in Part 7 of this series. Highlighted segments show segments where at least 3 of 4 admixture tools reported Native heritage. As you can see, there were clearly additional Native segments not reported by 23andme and Dr. McDonald.

Strong Native Chromosomal Detail Table

Because we have both my and mother’s results, we can infer my father’s contribution. Clearly, some of his will wind up being some amount of “noise” and some IBS segments, but not all, by any means, and this is the only way to get a “read” on Dad. This is one form of phasing data. Phasing refers to various methodologies of figuring out which DNA comes from what source, meaning which parental line.

While the strongest Native segments are the ones individually most likely to indicate Native American ancestry, that really isn’t the whole story. I discovered that many of these Native segments are actually embedded in other segments that are indicative of Native heritage too. In other words, it’s not a line in the sand, yes or no, but more of a sliding scale.

On the chromosome painting below, this one using Eurogenes, with my results shown above and mother’s below, you can see two excellent examples. Regions relevant to Native ancestry include:

Red – South Asian
Brown – Southwest Asian
Yellow – North Amerindian and Arctic
Putty – Siberian
Emerald – East Asian

You can see that while mine is almost universally yellow, or Native, with a little Siberian (putty) mixed in for good measure between 169-170, a hint of East Asian (emerald) plus a little Asian (red), mother’s isn’t. In fact, hers is a mixture of Native American and South Asian (red), with more red than yellow, Siberian (putty) and a large segment of East Asian (emerald green).

While her yellow Native segments alone would be staggered across this entire segment in 7 different pieces, when taken together as a whole, the “blended Asian” segment reaches entirely across the screen with the exception of 1 mb between 161.5-162.5, roughly.

The following Blended Asian Chromosomal Detail Table shows all of the blended Asian segments using all four of the admixture tools for chromosomes 1 and 2.

It’s clear that these regions are not solely “Native American” but reach back in time genetically into Asia, particularly Northeast Asia.

Again, the boxed numbers show the “in common” segments between all tools and the yellow highlighted segments are common between at least three of the four admixture tools.

Please note that there were some issues distinguishing colors, as follows:

For the MDLP comparison, Mesoamerican and Paleo Siberian are both putty colored and indistinguishable on the chart. Also, the apple green for Arctic Amerind is very similar to the Austronesian.

When using Dodecad, Southeast Asian (light green) and South Asian (apple green) are nearly impossible to distinguish from each other on the graphs.

When using HarappaWorld, the apple green for Siberian was very similar to the light forest green for Papua New Guinea and was very difficult to distinguish. The South Asian putty appears often with the other Native markers, and I considered including this group, but it too was difficult to distinguish from other regions so in the end, I opted not to include this category.

If you are colorblind – get help as this is impossible otherwise.

Blended Asian Chromosomal Detail Table

On the blended Asian Chromosome Detail Table, I added yellow highlighting where the same segments show in other Asian geographies that showed in the Strong Native table. In each column, the Strong Native category is the last one at the bottom of the list.

The blue highlighting shows other common segments found that were not included in the Strong Native segments. For a Strong Native yellow segment to be highlighted, it had to be present in 3 of 4 tools, or 75%. In the Blended Asian group, there are a total of 15 categories between the 4 admixture tools, so for a segment to be shaded blue, it must be found in at least 8 of the categories, so just over half. There are many segments that are found in several categories across the tools. For example, segment 192-193 on chromosome 1 is found five times. This isn’t to say you should discount this segment, only that it isn’t one of the strongest, most universal. Surprisingly, there really weren’t too many that were close to the cutoff. Several, but not a majority, were in the 4 or 5 range, only one was at 7.

Clustering

The third step in data extraction is to look at all of the data together. In this step, we are removing the geographic boundaries of Siberian, N. Amerindian, etc. and combining all of our data. I have only combined the data within columns, not between columns, so we can get a feel for which tool or tools performed best or maybe not so well. Each chromosome in each column has its data ordered numerically, and yes, this is a manual cut and paste process. Sorry. I warned you, this is an very manually intensive process.

After I put each column in numerical order, I arranged them so that the numbers were approximately in a line, or a row, with each other. For example, in the first group below, you can clearly see that the first cluster of results is found using all 4 tools. When looked at individually, only the blue results were noted as common (at least 8 of 15 for blue), but when viewed as a cluster, you can see between the tools that the cluster itself runs from about 7.5, with a small break from 8-9, and then to about 14.5. As you would expect the beginning and end points of the cluster trail off and are not uniform between tools, but the main part of the cluster is found in all the tools. This introduces the question of how to measure a cluster. In this case, there is a clean break using all tools between 8 and 9, but that is only 1 mb, rather difficult to measure accurately. You could record this as two distinct clusters but since it’s very closely adjacent the rest of the cluster, I’m inclined to include this as one large cluster and use the starting and ending segments for the cluster as a whole, in other words, the cluster runs from 7.5 through 14.5. The alternate, or more conservative methodology would be to use the “in common” numbers, but in this case, that would be only 10-11.5 and I think you would miss a great deal of useful data. So, for clusters, I’m recording the full extent of the cluster. In some cases, you may need to exercise a judgment call.

Let’s look at the second group of numbers, beginning with 18.5 in Harrappaworld. This grouping runs though about 28. Eurogenes found some blended Asian between 27-28.5 as well in two of the geographies, but over all, of the 15 tools, we don’t see much. This could be a result of a number of things. I could have had problems with the colors, there may be only a very small amount and it may be categorized as something else with the other tools. I would not consider this a cluster, and using our best 3 or 4 methodology eliminates this cluster from consideration. This also holds true for 43-43.5.

However, the next cluster, from 55.5 to 58 is found in the Strong Native comparison, indicated by the yellow highlighting and is found using all 4 tools. This is definitely a cluster.

I’ve synthesized the cluster information into a list. From the clusters above, I’ve created a list that I will be using in the next segment for data input into my spreadsheet of matches. The blended segments below that include Strong Native segments are shown with yellow.

Using the GedMatch admixture applications, we’ve isolated the strongest Native and the Blended Asian segments and clusters in preparation for identifying specific Native family lines within our group of matches.

This process shows that, for the most part, the Strong Native segments picked up the strongest signals, about half of the segments that will be useful in determining Native admixture, although it does miss some.

When we use the clustering technique to view our results across all the admixture tools, we see a somewhat different picture emerge, adding several Blended Asian clusters.

In Part 9 of this series, we will use the highlighted Strong Native segments and the Blended Asian clusters, both of which suggest Native chromosomal “hotspots” to begin our comparison to our genetic matches for genealogical relevance. In other words, using this information, we will determine which genealogical lines carry Native ancestry.

Part 9 may be somewhat delayed. The good news is that Family Tree DNA is finishing work on their Build 36 to Build 37 conversion. The bad news is that it fell right in the middle of writing this series. When they finish Build 37, I’ll finish Part 9 of this series. In the mean time, you can be extracting your minority segments using the tools and techniques that we have covered in Parts 1-8.

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The Autosomal Me – DNA Analysis – Splitting Up

Posted on March 12, 2013 by Roberta Estes

This is Part 6 of a multi-part series.

In this segment, Part 6, “DNA Analysis – Splitting Up” we’re going to focus on specific aspects of those tools and begin our analysis of our minority ancestry.

Analysis. Sounds like I’m climbing on the shrink’s couch. But I’m not, I’m saving all my dollars for DNA kits! Besides, I don’t want to stop! This analysis, we’ll do by putting several pieces of data together and sorting the wheat from the chaff. And yes, we’ll be splitting up…well…splitting our DNA up into pieces contributed by our father and mother.

Let’s start with looking at the DNA segments that mother and I share that are Native.

According to Doug McDonald, we have significant Native matches on chromosomes 1 and 2, with third party tools confirm that finding. Unfortunately, the only company where Mom’s DNA resides is Family Tree DNA whose test did not reveal the Native ancestry. 23andMe did confirm Native segments in my DNA in those locations.

I’ve used several third party tools at GedMatch to see where Mom and I both have Native heritage, where she has it and I don’t, and equally as important, where I have it and she doesn’t? What is that so important? Simple, it means my father had Native heritage too, and tells me on which chromosomes his Native DNA is located This could, when matching people in the future, on particular segments, help to isolate who our common Native ancestor was, or at least which line. That is the ultimate goal we are working towards with this entire process.

In this case, to identify my father’s Native lines, if Mom and I neither or both have Native markers at a particular chromosome location, the values are irrelevant, because the Native lineage came from mother. I did notice in a few cases that I had more than mother, and of course, in that situation, it means that my father contributed some too, or my mother had a misread in that region or a categorization issue exists. For that reason, I am looking for patterns, not single instances. We’ll discuss using patterns in a future segment.

Using the MDLP chromosome mapping tool, as MDLP appears to be the most comprehensive, I created a spreadsheet using my results as a base. I then added mother’s values in the spaces where I had no values, and then I highlighted my results in the locations where mother had no value. The essence of this is that the red, bold, underscore values mean Mom had a Native result here, but I didn’t receive it. A yellow highlighted cell means I got the entire amount from my father, because my mother has no percentage showing. In other cases, of course, it’s possible that both mother and father contributed Native ancestry on some adjacent chromosome segments. The MDLP mapping tool with my additions is shown below for chromosomes one through eight. Chromosomes 9-22 are similar, but the chart is too big to display as a whole. This provides an example of how to do this analysis with your own results.

The results were very interesting.

My two primary regions, North-East-Europe and Atlantic-Mediterranean-Neolithic, were represented on every chromosome for both my mother and myself. No surprises there. The other regions would be considered minority admixture.

In 2 categories, North-European-Mesolithic and East Siberian, only my father contributed genetic material on some chromosomes and there were no chromosomes where my mother alone contributed.

In 1 category, Melanesia, only my mother contributed genetic material on some chromosomes and there were no chromosomes where my father alone contributed.

In all other categories, both parents contributed on some chromosomes where the other didn’t. This is important, because it will allow me to associate a match with a particular segment of a chromosome on a particular parent’s side with Native ancestry.

In the minority categories for Native American, Mesoamerican, Arctic-Amerind, South America Amerind and North Amerind, grouped together, both parents contributed on some chromosomes where the other didn’t, and in two categories, on 3 chromosomes, I carry more than my mother, indicating an additional contribution from my father.

This is a repeated occurrence, with Native ancestry for my parents and I combined showing on a total of 42 chromosome locations across 4 geographic/ethnic categories, and in at least three cases, both parents contributed.

In the African categories, South African, Sub-Saharan and Pygmy, I had contributions from both parents on a combined total of 18 chromosome segments. The African admixture, in total, was less than the Native, and they are assuredly below 5% combined. If they were present at higher levels, I wouldn’t need to go through these genetic gyrations to prove or disprove the heritage and which parent contributed, because it would be evident in the testing results of all companies.

In our next segment, Step 7, we will be further scrutinizing Chromosomes 1 and 2 for additional information about Native heritage and assigning specific Native segments that I carry on various chromosomes to either my mother or father’s lineage.

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The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools

Posted on March 3, 2013 by Roberta Estes

This is Part 5 of a series.

Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.” Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works. Part two gave an example of the power of fragmented chromosomal mapping and the beauty of the results. Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets. Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.

In this segment, Part 5, we’re going to look at various third party tools and what they can do for our search for minority admixture. We will use the download files from either 23andMe and Family Tree DNA and utilize third party tools to analyze the raw data. We’ll see how third party developers put those puzzle pieces together, if the results are consistent and what they tell us.

The Weeds

When dealing with testing companies, particularly any individual source (as opposed to multiple testing company results, as I have done), minority admixture, especially less than 1% may not be successfully recognized. One percent equates to between 6 and 7 generations or about to the 1800 threshold in time. However the history of both African and Native admixture in colonial America goes back another 200 years to the Jamestown era.

The social history in the US means that there are many people looking for this admixed heritage as long ago as 1609 when Jamestown was established and the first European/Native marriages took place (although there were “blonde Indians” reported by Jamestown settlers). In round numbers, that’s about 400 years or between 13 and 16 generations. Of course, a minority ancestor drops below the 1% threshold between 7 and 8 generations (with the first generation being the person tested) and by the time you get to the 12th generation, you’re at .048%. At this level, Bennett Greenspan says we’re “rooting around in the weeds,” and he’s right.

However, rooting around in the weeds for those dreaded IBS (Identical by State) segments in genealogy is exactly what we need when looking for small amounts of minority admixture. What’s an IBS segment you ask? It’s a segment that is typically too small to be counted as an IBD, or identical by descent, segment. IBS means that you’re from a common population if you match someone with a very small segment, not necessarily that you share a common ancestor within the past several generations. But how to you tell if a small segment is IBS or IBD?

There is no absolute line in the sand, but often segments smaller than 7cM (centimorgans) or 700 SNPS (some say 5cM and 500 SNPs) fall into the IBS category. This has caused some researchers to discard all segments of this size because they can’t tell the difference. That’s unfortunate, because clearly some of these segments are IBD and the IBS segments can be useful too.

When looking for minority admixture in two people, both of them having these small segments in the same location can provide meaningful information, and can confirm minority heritage. Said another way, if two people have less than 1% Native heritage, both share a common ancestor, and both carry part of their “less than 1%” on the same segment….one might say it’s not likely to be coincidence. Identifying the common segments of your common ancestor can lead to identifying the specific family line those segments came from, especially if you match others as well. This is in essence what Minority Admixture Mapping, or MAP, does. It uses these techniques to look for patterns in these small fragmented pieces that, when taken together, indicate minority heritage. Having said that, some IBS segments will indeed, be simply that, because you share the same base population, but some will be IBD, or more current in time. With the MAP technique, we’re sorting through ways to utilize these small segments, whether they are IBS or IBD.

Using the tools, MDLP, Eurogenes, Dodecad and HarrappaWorld at GedMatch allows us to “root around in the weeds,” to quote Bennett, and find those all-important small IBS/IBD segments that connect us to a particular ethnicity and ultimately, to other relatives who carry these same segments in the same locations.

In general, using these this type of DNA is called BGA, or Biogeographical Ancestry where we use SNPs of autosomal DNA called AIMs, Ancestry Informative Markers. A SNP is a Single Nucleotide Polymorphism, or a mutation that happened in one specific location on a gene. AIMs are generally SNPs, not clusters of markers, found at different frequencies in different populations. We combine all we know about them scientifically with information about population frequencies and then draw inferences about where our ancestors came from based on that information. So a SNP that is useful in determining ancestry is called an AIM.

These SNPs, or AIMs, are the foundation for these BGA tools that we will be using to sort through small segments of minority admixture. So this is a building block process. Scientists identify SNPs found in different populations at different frequencies and identify them as such, then scientists and genetic genealogists create BGA tools that use and combine SNPs/AIMs to suggest populations and ethnicities for those who carry them. Using these tools, majority ancestry is easy to discern. We’re going to use those tools to look at groups of SNPs/AIMs clustered in small, fragmented IBS or IBD segments to do Minority Admixture Mapping (MAP) to confirm our minority admixture and to identify our minority admixed lines, families and perhaps even (in time) our original minority ancestor.

I bet you thought I couldn’t fit all of those acronyms in one paragraph, but I did:) It is a bit like alphabet soup, but when you understand that this is a building process, it’s much easier to grasp as a whole.

Having at least one parents DNA makes this process much easier, because you can immediately tell if your other parent, by inferrence or process of elimination, has contributed any of the minority ancestry, or if it’s all on one side of the tree. Of course, that’s assuming your parents aren’t related to each other. There’s a test for that too at GedMatch. If you don’t have one parent available, you can “make do” with aunts, uncles and cousins, but it’s a much more tedious process.

Third Party Tools

To use any of these BGA tools, you’ll need to download your results from either 23andMe, Family Tree DNA or National Geographic. Currently at GedMatch, the only supported formats are 23andMe or Family Tree DNA, because the National Geographic test is so new. I used my Family Finder (Illumina Build 36) raw data file.

To download your results from 23andMe, sign on to your account, then click on this link and it will take you to the area to download your results.

https://www.23andme.com/you/explorer/

Save the file and do not open it as the act of opening it sometimes causes corruption and you will have a hard time uploading the file. If the upload fails, download a new copy and start over. If you have an older copy on your computer, it’s always a good idea to use a fresh copy to incorporate any changes made by the vendor since your last file download.

To download your results from Family Tree DNA, sign on to your personal page, click on the Family Finder tab and then on “Download Raw Data.” As I write this, Family Tree DNA is in the midst of a conversion from Build 36 to Build 37 for their autosomal files (in order to facilitate the integration of 23andMe results), so you may need to be a bit patient while this process completes. Files may not be available for download at some points. You certainly don’t want to mix comparisons, meaning using one build 36 and one build 37 file for comparison.

If you’re following this process yourself with your own data, please read all the way through this posting before starting your own processing.

Now, let’s look at the third party tools.

Stanford University

This tool is available at Stanford University. Scientists have collaborated to provide this service and I think it’s quite interesting. This tool is not compatible with any browser except Chrome and it requires a download of your autosomal data in a .txt file. If it can’t load your file, the loading task simply never completes. For me, that meant it wasn’t a .txt file I was trying to load.

http://esquilax.stanford.edu/

Load your file and choose Ancestry, then Paintings, then Hap Map 3 (experimental), then Paint my Chromosomes.

Their legend, above, translates to the regions, below.

ASW – African ancestry in Southwest USA

CHD – Chinese in Metropolitan Denver, Colorado

GIH – Gujarati Indians in Houston, Texas

LWK – Luhya in Webuye, Kenya

MEX – Mexican Ancestry in Los Angeles

TSI – Toscani in Italia

Unfortunately, this isn’t terribly useful. Hap Map 3 utilizes additional regions, including Utah, but this tool doesn’t seem to be mapping them, so my closest match region is Italy, which is midleading since none of my family was from Italy. Hap Map 2 is also an option which does include the Utah population, but it’s not as up to date otherwise as Hap Map 3.

David Pike has figured out how to tweak these settings some. You can read about it at this link: https://www.23andme.com/you/community/thread/8062/. David’s posting on June 20^th shows what he did. However, compared to the other tools available, I find this a poor choice and did not spend a lot of time trying to work with it.

However, a second feature that they provide is fun.

Stanford provides a Neanderthal tool that’s a little different than the Nat Geo or 23andMe ones. Click on Explore, Neanderthal, Look Up Exercise. Then enter your primary ethnicity and click on Look Up Exercise again.

Of a possible 84 Neanderthal alleles, I have 9, partially displayed below.

GedMatch

www.Gedmatch.com is a complimentary (voluntary contribution) site created by two genetic genealogists that includes several autosomal analysis tools. One of the areas of this site is “Admix Tools.” On that page one finds several private or proprietary tools, some written by genetic genealogists, some by researchers, and all free. Let’s take a look at each one and their results. If you want to see any of the results more closely than the photos here allow, you can run each of the comparisons using kit F6656 (mine) as the first kit and kit F9141 (my mother) as the second kit.

Each of these tools offers the same functionality, as follows.

We will be utilizing 4 of these functions for each tool.

Admixture Proportions
Admixture Proportions by Chromosome
Chromosome Painting
Paint Differences between 2 kits, 1 chromosome

We select from the tools as follows:

Let’s take a look at what the tools provide.

MDLP World 22

The MDLP software is sponsored by two genetic genealogists. You can read more about the project at http://magnusducatus.blogspot.com/ and http://magnusducatus.blogspot.com/2012/09/behind-curtains-mdlp-world-22-showcase.html.

MDLP shows several populations. I was interested to see if my mother also shared the African percentage. Interestingly, mother does have a South African segment, but it’s .12, so less than mine. Therefore, I would have obtained part of my African heritage from my father. She also has three different categories of Native American heritage, compared to my one. She carried a total of 1.92% and I carry .58%. Otherwise, our results are very similar.

The next feature is ethnicity mapping by chromosome. While the display is too large to see well it’s interesting to note that indeed, both Native American and African were detected on several chromosomes, not just on chromosomes 1 and 2 as reported by 23andMe and Dr. McDonald. Note that DeCode Genetics showed “East Asian” admixture on several chromosomes.

Here’s a portion of the above chart that you can actually see. The highlighted blue regions are your major ethnic regions.

Another feature is chromosome painting, shown below. This shows the first part of my chromosomes 1 and 2 painted by ethnic/regional breakdown. The legend for each tool is different and above their graph.

These tools also provide the ability to compare one chromosome between two people. On the graph below, my chromosome 1 is on the top, and my mother’s is second, with the third band being our common painting. The black represents non-shared regions, meaning those contributed to me by my father. Unfortunately, North American Native American is dark grey, sometimes difficult to distinguish from black.

The graph below shows that while I do share a large piece of Chromosome 1’s Native region (about 160-180mb) with my mother, there are also segments, 169-170 for example, where I have Native genes that she does not, indicating Native heritage in this location from my father’s side.

Eurogenes K9

Eurogenes was created by another genetic genealogist. You can read more about it at http://bga101.blogspot.com.au/2012/04/eurogenes-admixture-utilities-at.html.

Eurogenes calls me primarily North European with .67 Native American and no African in the percentages above, but below, on the individual chromosomes, some African does show, although not on as many chromosomes as MDLP.

In the charts above and below, you can see that Eurogenes detected small amounts of African along with Native American.

Notice that at about 10mb on chromosome 1, on the graph below in the top band, that the North American Indian (yellow) and the South Asian (red) are imbedded with each other. These appear again together at the beginning of chromosome 2, shown as the second band. This hints at how and why it’s sometimes so difficult to determine and filter Native American from Asian. There is no line in the sand, there is a continuum between populations, the only differentiator being 10,000 to 15,000 years spent apart in which time, they, hopefully, developed enough differentiating mutations that we can tell them apart.

On the chart below, the top band shows the chromosome painting of my chromosome, and the second band shows the chromosome 1 Native American segment (about 160-180 mb) of my mother with the third band showing both matching and non-matching regions, painted black. Looking at the segment of chromosome 1, in the graph below, characerized as Native, we can see in mine, top row, that this is categorized as Native American (yellow), but some of the same regions below, in Moms are categorized as South Asian (red), causing a technical non-match, when in reality, It’s likely a categorization issue, not a genetic mismatch. In future analysis, we’ll be using two methods of comparison, one called “Strong Native” that only matches Native to Native and another, the “Blended Asian” method that allows for grouping of similar ancestral types that together likely indicate a Native heritage.

Dodecad V3

Dodecad was created by an anthropologist. You can read more about it at http://dodecad.blogspot.com/ and http://dodecad.blogspot.com/2011/06/design-of-dodecad-v3.html.

Dodecad, unfortunately, does not subdivide into Native American, so the Native will show here as some form of Asian. Northwest Africa shows in the percentages above, but more detailed African heritage shows in the chromosome detail below in regions not shown above.

Above, my chromosome painting for the first part of chromosomes 1 and 2.

Below, the comparison showing the Native segments from about 160-180mb. My Native segment (top) compared to mother’s (middle) with the comparison of the two on the bottom for chromosome 1.

HarappaWorld

HarappaWorld divides results into fewer population groups and is focused on Asia. You can read more about it at http://www.harappadna.org/2012/05/diy-harappaworld/.

In HarrappaWorld, Beringian and American appear to be equivalent to Native American. Like Dodecad and Eurogenes, African does not show in the total percentages, but does on the individual chromosome analysis, although in smaller percentages with this application.

Chromosome painting of my chromosomes 1 and 2 are shown below.

The graphs below show the Native region comparison of chromosome 1 between me, top row, mother, middle row, and the third graph showing the common areas, with black representing areas where there is no match.

For each of these tools and their results, we’ll do further analysis in a future segment of this series.

Tools Summary

Now that we’ve looked at these individual tools, and building on the Test Results Chart created in Parts 3 and 4, let’s compare and see what information these tools add.

Test Results Chart Including Third Party Tools

Test/Company	European	Asian	Native	African	Unknown
Pedigree Analysis	75%	0	~1%	0	24%

Testing Companies
Family Tree DNA – Original	100%[1]	0	0	0
deCodeme	92%	5%	Inferred[2]	3%
deCodeme – X	91%	6%	Inferred	3%
Dr. McDonald	97-99%	1-3%	0.5%	0
23andMe – Original	99%	1%	Inferred[3]	0	0
23andMe – 2012 – Standard	99.2%[4]	0	.5%	0	.3%
23andMe – 2012 – Conservative	98.7%[5]	0	.3%	0	1%
23andMe – 2012 – Speculative	99.3%[6]	0	.5%	0	.2%
Family Tree DNA – 2012	100%[7]
Geno 2.0	79%[8]	18%	0	0	0
Ancestry	92%[9]	0	0	0	8%

Third Party Tools
MDLP	86.68%	12.55%	.58%	.17%	0
Eurogenes	94.83%	4.5%	.67%	0	0
Dodecad	85.47%	13.43%	Inferred	1.09%	0
HarrappaWorld	86.56%	12.80%	.65%	0	0

Of the various chromosomes, the breakdown is as follows. Dodecad does not break the categories in a comparable fashion to these other 3 tools, so their results are omitted in the following chart. Please note that how geographies are categorized can make a significant difference.

Minority by Chromosome Chart

Tool/Chr	MDLP Native	Eurogenes Native	Harrappa Native	MDLP African	Eurogenes African	Harrappa African
1	Y	Y	Y	N	N	N
2	Y	Y	Y	Y	Y	N
3	N	N	N	Y	Y	N
4	Y	N	Y	N	N	N
5	N	N	N	N	N	N
6	Y	Y	Y	Y	N	N
7	N	N	Y	N	N	N
8	Y	Y	Y	Y	N	Y
9	Y	N	N	Y	N	N
10	Y	N	N	Y	N	N
11	Y	N	Y	Y	N	N
12	Y	N	Y	N	N	N
13	Y	N	Y	N	N	N
14	Y	Y	Y	Y	N	N
15	Y	N	N	N	N	Y
16	Y	Y	Y	Y	N	N
17	Y	Y	Y	N	N	N
18	N	N	N	N	N	N
19	Y	Y	Y	Y	N	N
20	Y	Y	Y	Y	N	N
21	Y	N	Y	N	N	N
22	N	N	N	Y	Y	N

From these various tools, it’s obvious that I do have some Native admixture, probably about 1%, and it’s from both parents. I also have some African, but it looks to be an even smaller proportion that Native American.

Join me for Part 6 of this series, where we look at how to analyze and use this information.

[1] 71.5% western European, 28.4% Northeastern European

[2] Inferred that Asian is actually Native in an American with no history of Asian ancestry.

[3] No category, inferred.

[4] 78.6% Northern European, 1.8% Southern European, 18.7% Nonspecific European

[5] 54.6% Northern European, .3% Southern European, 43% Nonspecific European

[6] 91.7% Northern European, 3% Southern European, 3.3% Nonspecific European

[7] 75.18% West Europe (French and Orcadian), 24.82 Europe (Romanian, Russian, Tuscan and Finnish). Note that my mother’s results are almost identical except the Finnish is missing from hers.

[8] 43% North Europe and 36% Mediterranean

[9] 80% British, 12% Scandinavian

______________________________________________________________

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The Autosomal Me – Testing Company Results

Posted on February 24, 2013 by Roberta Estes

This is Part 4 of a multi-part series, The Autosomal Me.

Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.” Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works. Part 2 gave an example of the power of fragmented chromosomal mapping and the raw beauty of the results. Part 3, “The Autosomal Me – Who Am I?,” discussed how to use our pedigree charts to gauge expected results and how autosomal results are grouped into population buckets. We also named this technique, Minority Admixture Mapping, or MAP for short.

In this segment, Part 4, let’s take a look at what the testing company autosomal results look like. The results are presented in timeline order, with the oldest results first and the latest, and presumably most accurate results, last.

23andMe Version 1

23andMe was the first company to offer this type of testing affordably. They initially only offered 3 population groups, and one inferred that Asian was actually Native American. Of course, that wasn’t a valid assumption for everyone, but it was the best that could be done under the circumstances. This was my ethnicity results display at 23andMe until December 2012 went their updated version was released.

DeCode Genetics

DeCode Genetics initially offered autosomal tests for ancestry. Unfortunately, under the pressure of financial issues, they stepped away from the genetic genealogy marketspace and have since been sold.

Their test showed the following ethnic breakdown, picking up both my Native and African heritage:

I particularly like these results because the X chromosome is included, and seeing Native on the X chromosome, which has a unique inheritance path is a very important piece of data.

Family Tree DNA Version 1

Family Tree DNA’s first version of their Family Finder product produced results stating that I am 100% European, split between western and northern, shown below (minus the map.)

Dr. Doug McDonald

Doug McDonald, a retired physical chemistry professor, compiles contributed raw data and compares the raw data locations with both reference populations and the contributor results. This is not a commercial endeavor but a private research project which has been ongoing for years. His analysis of my raw data results from 23andMe and Family Tree DNA showed that they are primarily European. His first analysis was without Middle Eastern populations and the results showed European except for a total of about 3% East Asian, Oceana and American. However, in a second run including the Pakistan and Middle Eastern populations, the results now showed 88% European, about 1% Oceanic and American and the balance Middle Eastern and Pakistani.

A small amount of Middle Eastern heritage is not unexpected since I do have confirmed Turkish ancestors.

Dr. McDonald indicated that this was slightly more, 1-2%, than most Europeans, and that I was generally planted firmly in the middle of the “English” area in his data. His results showed no African.

Standard deviation (statistical noise) is about 1%. He can achieve these low deviation numbers by using such a large number of markers (536,904 to be exact)[1] for his comparison. I am grateful to Dr. McDonald for his contribution, not only to me, but to this field.

The graph below shows that my primary ancestry falls in the English/French region.

The second graph maps these results on my chromosomes. The American, bright green, is found on chromosomes 1 and 2, and the X chromosome shows South Asian.

Doug indicates that the Native American is found at about the .5% level. Interestingly, on my mother’s graphs and charts (below), the Native segments are nearly identical, but my first grey South Asian segment on my X is Mideast on her chart.

It’s also interesting to note that my Native American on chromosome 2 is larger than my mother’s which may well reflect Native heritage on my father’s side. Ironically, the oral history of Native ancestry was on my father’s side, not my mothers.

Doug’s analysis has been updated several times over the years and these results are the most current. The vendors have made upgrades too. In 2012, both 23andMe and Family Tree DNA underwent upgrades to their ethnicity software and the Genographic Project version 2.0 test was released.

23andMe 2012 Updated Version

The new 23andMe software offers different confidence levels.

The standard estimate, or confidence level, shows that I have about .5% Native American. This is consistent with Dr. McDonald’s findings.

A second view is available which paints the chromosomes. A split view is also available if one of your parents has been tested at 23andMe as well. That is not an option for me.

The conservative estimate, below, shows less Native at .2%.

The speculative level below shows the Native back to .5% but adjusts the European regions significantly.

Although 23andMe does not provide participants with the start and stop locations, through alternative means, meaning a very smart friend, Rebekah Canada, who is a Java programmer, start and stop locations can be discerned.

CeCe Moore documented Rebekah’s technique for those who will be following along with their own results through this process.

In a future segment of this series, we’ll look at alternative ways to discern Native segments. Thanks to Rebekah’s technique, I can tell you that 23andMe shows my Native segments as follows:

Chromosome 1 – 165,658,091 to 175,711,116

Chromosome 2 – 86,316,174 to103,145,426

23andMe also provides a Neanderthal percentage. What fun!!!

Family Tree DNA Updated 2012 Version

My mother was deceased before chip based autosomal testing was available, but I ordered the Family Finder test for her as soon as it was available. Thankfully her DNA was stored at Family Tree DNA and was still viable.

Mother’s original results are shown above and her most recent results are shown below. Her results shifted within Europe and her margin of error doubled.

My current results from Family Tree DNA’s updated software are shown below.

National Geographic Genographic 2.0

I was very surprised to see my National Geographic results. They were very unexpected, in particular the high percentages of Mediterranean and Southwest Asian, totaling 54%.

It made more sense when I read the information. It’s true, reading is fundamental.

These results are, in essence, more anthropological in nature.

Of course, one of the fun parts of the Genographic results are the Neanderthal and Denisovan percentages.

These are somewhat different than the 23andMe results, although if you add the Neanderthal and Denisovan values together, the resultant 2.2% is very close to 23andMe’s 2.5%.

Ancestry.com

In 2012, Ancestry introduced an autosomal DNA test as well. What it provides is very limited, with limited tools, but it does provide percentages of ethnicity in addition to matches. Recently, Ancestry announced that the percentages may change over time. They have been severely beaten within the genetic genealogy community for quality issues with this product, including percentages of ethnicity that are highly erroneous. Their stated time reference is 500 years ago.

Recently this new page was added before you can see your detailed results.

Ancestry shows my heritage as only British and Scandinavian.

Ironically, Ancestry has mapped the birth locations of my ancestors in Europe on the map above, based on my family tree submitted. Interesting that Germany doesn’t show in Ancestry’s ethnicity list but many of my family lines originated in Germany and Holland, and none in Scandinavia.

Testing Provider Summary

Where do we stand now?

A summary of the various test results is shown below compared to my pedigree analysis.

Test Results Chart

I have included Dr. McDonald’s analysis here, not because he’s a testing provider in the sense of the testing companies, but because his offering was available in this timeframe, and because he worked with Family Tree DNA to develop their Population Finder code.

You can see that the results are relatively consistent between testing companies. There is certainly no question about majority ancestry, but the minority admixture which hovers someplace near 1%, give or take 5% in either direction, is much less consistent and not always reported. If I were to have tested with only one company and taken the results as gospel, I could certainly have been left believing that I had no Native or African admixture. For many people, it’s this small amount of minority admixture that they are seeking. So in answer to the question of which testing company is “best,” the answer is, if you’re looking for trace amounts of anything, the compendium of all the testing companies (minus Ancestry) would provide the best set of results. We will be using the match information as well in the next sections, so certainly nothing has been “wasted” testing with multiple companies, again, except Ancestry. I am hopeful that Ancestry will in the future release our raw data (which they have promised to do) in a useable format, fix their misleading ethnicity results and add chromosome painting tools so that we can fully utilize our data.

In Part 5 of the series, we’ll take a look at third party tools and how they can continue to refine and add to our knowledge of our admixture.

1. Genealogy-DNA Rootsweb posting by Doug McDonald on 7-26-09 and personal correspondence.

2. 71.5% western European, 28.4% Northeastern European

3. Inferred that Asian is actually Native in an American with no history of Asian ancestry.

4. No category, inferred.

5. 78.6% Northern European, 1.8% Southern European, 18.7% Nonspecific European

6. 54.6% Northern European, .3% Southern European, 43% Nonspecific European

7. 91.7% Northern European, 3% Southern European, 3.3% Nonspecific European

8. 75.18% West Europe (French and Orcadian), 24.82 Europe (Romanian, Russian, Tuscan and Finnish). Note that my mother’s results are almost identical except the Finnish is missing from hers.

9. 43% North Europe and 36% Mediterranean

10. 80% British, 12% Scandinavian

______________________________________________________________

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The Autosomal Me – Who Am I?

Posted on February 13, 2013 by Roberta Estes

This is Part 3 of a multi-part series.

This series focuses on answering the questions of identity through autosomal testing, in particular, for minority ancestry. By minority, I mean any small, elusive amount of any type of ancestry you are seeking to discover in your heritage. In my case, that’s both Native American and African.

This segment, Part 3, focuses on using pedigree charts to gauge expected results, how autosomal ethnic groups are determined and how fragmented minority admixture mapping is different from other techniques. This leads us into Part 4 which shows the various results from different testing companies and how they differ.

Part 5 features third party analysis tools and Part 6 begins the analyses of the data that parts 3, 4 and 5 provide.

Let’s hope that with all of this information, we can answer at least part of the question: Who am I? Who am I really?

A lot of who I am has to do with who my ancestors were, where they lived, what they did, choices they made. Did they fight in the American or French Revolution? On which side? Were they Native? Were they African? Were they slaves? So, who were they?

One of the reasons I began with genetic genealogy more than a decade ago was to confirm or disprove the persistent family history of Native American heritage that I had been unable to resolve using only traditional genealogy tools. I have made inroads with that, in unexpected ways and places, because of and in addition to genetic genealogy. Genetic genealogy and traditional genealogy go hand in hand.

It’s difficult tracking down each line to perform mitochondrial or Yline DNA tests. Sometimes, it’s beyond difficult and it’s impossible. Lines die out, people refuse to test or you simply can’t find the right people. We need other tools.

Enter autosomal genetics. From the beginning, early in genetic genealogy, we had the CODIS type forensic and paternity type tests. I reviewed the results of those early tests relative to my pedigree chart in a paper I wrote, Revealing American Indian and Minority Heritage Using Y-line, Mitochondrial, Autosomal and X Chromosomal Testing Data Combined with Pedigree Analysis published in JoGG in the Fall 2010 Issue. We’ve come a long way since then.

In that article, I dissected my pedigree chart to determine how much of different types of ancestry I carried and how that compared with the testing that had been performed at that time.

Using the end of line ancestors pedigree analysis method described in the paper, which determines the percentage of ethnicity that each end-of-line ancestor contributed to me, my origins totals were as follows:

Geographic Origin Chart

(1) The ethnic heritage of several lines could probably be inferred by surname or ethnicity of marriage partner. However, I have avoided the temptation to make inferences within the United States, as the Native or African ancestry may well lie with one of these ancestors. These are in fact the perfect candidates and to eliminate them from consideration by inferring origins would be a disservice.

In broader categories, and combining those that are similar, we find:

This is a useful exercize, not just for minority admixture, but to help evaluate the results you receive from the various testing companies. For example, you might notice that there is no Scandinavian showing in my pedigree chart, which makes Ancestry’s 80% British and 12% Scandinavian suspect right off the bat. It also makes results as high as 25% Native American reported in one of the earlier tests impossible. This pedigree analysis tool helps you understand what is reasonable to expect in terms of ethnicity breakdown.

Now that we know what the majority ancestry looks like and any minority ancestry that we are aware of, let’s take a look at the various types of autosomal testing available.

Tests and Population Markers

In the paper, I reviewed the older results from companies using either CODIS or proprietary markers. These low resolution tests are out of date now (although many are still being sold) and have been replaced by the much more thorough wide spectrum tests using chip based technology, allowing hundreds of thousands of DNA locations to be tested and evaluated. Of course, the word evaluated is the loose cannon in that sentence, because the quality of the evaluation is key here. And the evaluation is dependent upon accurate and widespread data bases to compare DNA results against to determine which populations have higher and lower frequencies of specific alleles (markers) occurring in their populations.

For example, let’s compare a population in Siberia that shows 100% of a specific marker value, let’s say a value of 10 at marker location ZZZ. Now let’s compare that result to a population from Africa at that same marker location, but with a value never found in Siberia, let’s say a value of 7. Each of thousands of markers are evaluated this way, creating patterns. Now, you have a tester who doesn’t know where their ancestors are from, whose results at marker location ZZZ have a value of 10. Would you say they are more likely to have ancestry in Siberia or Africa?

This participant’s marker results for ZZZ go in the “very strongly Siberia” bucket. Of course, other markers they carry might indicate Africa, or Europe, or elsewhere, because we are a Heinz 57 mix of all of our ancestors. But this is, in essence, how our ethnicity is determined by autosomal DNA testing. Needless to say, you can be a lot more accurate with thousands of markers than with the 15 or 21 CODIS markers, or even the 300+ in some of the proprietary tests.

BGA Testing

Using autosomal results to determine ethnicity is called BGA testing, or Biogeographical Ancestry testing. It has been used for years to determine percentages of ethnicity. So, how is what I’m doing different and what makes it unique and new to genetic genealogy?

1. Traditional BGA testing deals in percentages of ethnicity, meaning generally 1% or more. Small amounts are difficult to track in the best of circumstances. When dealing with small amounts of admixture, not all tests will be able to identify the minority ethnicity in question. We’re using these tests, plus additional BGA chromosomal painting tools combined with some spreadsheet comparison techniques to cross that 1% threshold.

2. The prevailing winds in this industry have been that anything smaller than 1% was undetectable, and that any amount of admixture less than 7cM, 5cM or 3.5cM (depending on the source) was usless. While this is relatively accurate (but not always) when determining a genealogical relationship within the past few generations, it’s not true when looking beyond the accepted 6 to 7 generation threshold where the 1% ethnicity issue comes into play. At that point, we know we can’t identify the minority ancestor genealogically, so we have to identify them by their membership in a minority population group. I am using a variety of tools and techniques to reach across that threshold.

3. Instead of using these various tools to try to establish a genealogical relationship with another tester (such as we share a common great-grandfather), I am using these tools to attempt to identify which line or lines carry minority admixture. If you already know who in your family tree contributes that admixture, you don’t need this technique. If you are looking to confirm minority admixture below 1%, searching for the minority admixture contributing line, or trying to figure out which of your known ancestors contributed minority admixture, then this technique is for you.

Typically these tools have been used to track segments from known ancestors, like a Jewish grandmother, for example. These segments are large and evident. That’s not the case with small amounts of minority admixture. Using several BGA tools together helps to eliminate the possibility of one tool picking up on these small segments and another one missing it. We are bringing all of the resources from various camps together to bear on the situation. This is the ultimate form of recycling, using the shreds that were left on the cutting room floor and deemed to be usless when in actuality, they are diamonds in the rough. We’re reassembling them and looking at them from a different perspective. It’s a new kind of quilting!

A New Name

As I’ve worked through this process, it seems that Minority Admixture Mapping best suits what we are doing, so MAP it is. It makes sense and you can say it.

I still want to know who I am, so in Part 4, we begin our data analysis by looking at the autosomal ethnicity results of the various testing companies and how they compare.

______________________________________________________________

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The Autosomal Me – The Ancestors Speak

Posted on February 10, 2013 by Roberta Estes

This is Part 2 in the series, “The Autosomal Me.” Part 1 was “The Autosomal Me – UnRaveling Minority Admixture.”

Every Sunday, I write something called a Sunday Story. I’ve done this for years. I send them to my kids and I delude myself into thinking they read them. I’m really writing them for my grandkids someday and hopefully, some as yet unborn descendants I’ll have that will care about finding out about the life and times of their a-few-greats grandmother who lived along with the dinosaurs in the last half of the 1900s and first half of the 2000s. I know, I’m optimistic.

I decided that perhaps I would share this weeks Sunday story with all of you. This way, I know that at least someone will read it. Actually, aside from my husband, it’s my daughter-in-law who comments the most often. So welcome to my Sunday Story! You are all honorary cousins!

**********

I know that a great deal of what I do with genetics is lost on my friends and family members. That’s OK, because it’s very specialized. However, I wanted to take a little bit of time to share with you an aspect of the genetics I work with that I think is very beautiful in both a literal and a spiritual way.

The point of genetic genealogy, of course, is to learn about our ancestors, who they were and our connection to them. There are various ways to do this, but most of the time it’s through various matches to other people who share a common ancestor either recently or perhaps further back in time.

Of course, therein lies the rub – how long ago are two people related and who was their common ancestor? Some people who carry minority ancestry are at a distinct disadvantage, because the testing that provides matches and ethnicity generally relies on amounts in excess of 1%, which equates to about 6 or 7 generations. While many of us know that we carry minority ancestry, we would be hard pressed to say that our “pure” Native (or other minority) ancestor fell into that 6 or 7 generation bracket. Six or 7 generations equates to about 150-175 years before our birth, or about 1775-1800 for most of us. By then, many Native people were already admixed and many already lived outside of a traditional tribal unit. Some people carry Native heritage from multiple lines, but since it comes from multiple ancestors, it too is often quite fragmented, so it doesn’t really improve the situation much unless some of those fragments happen to fall together to make larger segments.

Therefore, we are looking for very small amounts of admixture that often don’t show on traditional tests, or if they do, it’s in miniscule amounts.

Enter chromosome painting.

Without going in to boring detail, I’ve recently been working with a new methodology of identifying these fragmented and very small segments. I am using several chromosome painting tools. I’ll be blogging soon enough about how all of this is done, but I just wanted to share with you a couple of beautiful pieces of DNA, through which our ancestors are speaking, and we can see them, in a manner of speaking.

On the graph below, which is my chromosome painting of one a small part of one of my chromosomes on the top, and my mother’s showing the exact same segment on the bottom, the various types of ethnicity are colored, or painted. You can see that both of us have a primary ethnicity of North European, shown by the teal.

The grid shows location 120 on the chromosome. Think of this number as a house number on a street. It’s numbered so we can keep track of where we are on the chromosome. For genealogy purposes, the smallest segment normally considered as relevant is 7 mb or marker segments long. Each tick mark equals one segment or address, so a segment 7 mb long would be from 120-127 which takes you right over to the legend. As you can see, the primary ethnicity has no problem reaching way beyond the contiguous 7 threshold, but the minority ethnicity would not be counted because it’s too small.

However, by the very definition of what minority ancestry is, these small segments are not only present, providing critical information, they are essential in our search and very informative. Let’s see what they are saying to us.

First, let’s talk for a minute about ancestry. There is no line in the sand very often between populations. There are generally only degrees of difference. So in the case of Native American, which is yellow on this chart, we also expect to see it “drift back in time” by being found in conjunction with Siberian (putty), South Asian (red) and East Asian (emerald green). Native Americans were not dropped from alien spaceships, they evolved over time from these other Asian populations, so we would expect to see some of their genetics in Native American people.

So let’s take a look at what we do actually see in the DNA.

The first brightly colored segment in the top band is mine. It includes Native American (yellow), South Asian (red), a big chunk of East Asian (emerald Green), a little bit from the Caucus (ginger) which is the Middle East area, and a piece of West African (light green).

There are two messages from the ancestors in this piece of DNA. First, this segment absolutely, positively does NOT come from mother. We can see this clearly because she has nothing but North European (teal) in that section of her DNA. So, this little gem came from Dad.

The second piece of information is that the ancestor who provided this DNA to Dad was very likely admixed, Native and African.

Of course, if you’re thinking ahead at this point, you’ll be asking, “Which one of your Dad’s other relatives has this same segment?” because, yes, that’s exactly how we will tell which of his lines contributed the Native ancestry. But you’re getting ahead of the story, and well, that is a story for another time. This story today, is about the direct messages of the ancestors and the beauty of our DNA itself.

Let’s look at the next segment of minority DNA. It starts about location 123. Mom’s is much more pronounced than mine and much richer. This tells us that I didn’t receive much of Mom’s. Instead I received mostly North European (teal), along with some East Asian (emerald).

Mom has almost a perfect Native segment here. By perfect, I mean we find a progression from Native back through time through all 4 categories I would expect to find. I consider this entire segment “Native” because it indicates Native heritage. You can see the emerald green (East Asian), putty (Siberian), red (South Asian) and yellow (North American Indian and Arctic) nestled together with no other minority ancestry in close proximity. This means it’s not part of a different kind of Asian segment. Remember, part of Europe was settled by the Mongol Hordes and the Huns, so we do see Asian and western Asian DNA in Europe, along with DNA from the Caucus, but we don’t see isolated segments like this, with just eastern Asian DNA and Native American. So this little beauty is the perfect Native indicator, positively, even though it is only about 4 segments long.

Now take a look at my DNA in that same region in the top row. It’s kind of hard to see the emerald green against the teal, but I only inherited the East Asian (emerald) segments from Mom. Of note, however, is that I also have an East Asian (green) segment that Mom doesn’t have. My East Asian starts about 122 where hers doesn’t begin until 123. So good old Dad contributed a bit here as well. Again, we know this because Mom only has North European at that segment.

And now of course for the kicker. Your DNA looks this same way. How boringly teal it is, or how beautifully rainbow multi-colored depends on how much minority ancestry you have, from how many different lines, and which of your parents you received it from.

I hope you can see why I’m so excited to be developing this new technique to work with highly fragmented DNA to find our ancestors. They are there, they have a voice, and they are speaking to us. All we have to do is figure out how to listen.

I am simply in awe of the beauty of this technique, literally as well as figuratively. While I certainly understand and appreciate logically that matching other people means we’re related, there is something awe-inspiring and tangible about being able to see the painted graphs and view the layers of ancestry nestled together, life forces reaching through time, protecting that DNA with its precious message for us over many generations. All this time, just waiting for us to be able to understand the most personal message from our ancestors, delivered, from them, in our genes, to each of us. This is the voice of our ancestors.

______________________________________________________________

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The Autosomal Me – Unraveling Minority Admixture

Posted on February 6, 2013 by Roberta Estes

You’re invited to come along with me on a journey. It’s an epic event, a journey into the deepest recesses of our cells, into the smallest pieces of our DNA, into the part previously thought to be useless because it’s so tiny. It’s the journey to find minority admixture. Minority in this case means small amounts of admixture. In my personal situation, this means both Native American and African.

People who have larger amounts of admixture don’t necessarily have to do this, although it can still provide useful information. If your autosomal percentages are uniformly recognized and reported by most or all of the testing companies, meaning over 1%, you probably know which of your relatives contributed your minority heritage and you don’t need to look for that proverbial needle in a haystack. Not everyone is that fortunate. I’m not. I know of Native heritage through my mother’s Acadian ancestors, but the ones in my father’s side have consistently eluded identification. It’s there, but where? It’s haystack time for me!

This past year or two, genetic genealogy has been hallmarked by advances in autosomal DNA and the supporting technologies using tools like 23andMe and Family Tree DNA’s Family Finder tests. In order to figure out how people are related to you, what level of cousins they are, and which genealogical line they come from, we’ve been using independent tools like phasing, where you compare your DNA to that of your parents or other close known relatives to see who gave you which pieces, or segments, of DNA. Then, when someone matches you on that segment, you can tell which side of yoru family it came from, and sometimes which genealogical line it came from. This sets the stage for one day being able to have this conversation with someone:

“Hi John, I see that we are 117^th cousins and we have a match at location 17,387,426 on chromosome 3.” Beth

“Hi Beth, why yes, we are indeed cousins, but we’re actually 115^th cousins, 11 times removed instead of 117^th cousins. Our match is through Attilla the Hun’s 37^th concubine.” John

Ok, so maybe I’m dreaming a bit…but this conversation is not just a possibility, it’s a certainty 10 years from now, but perhaps with less dramatic cousinships:)

To date, the rule of thumb for finding ancestors has been that small matches should be disregarded because they are probably identical by state (IBS), not identical by descent (IBD), meaning not useful genealogically.

What’s IBS you ask? It’s a segment that is typically too small to be counted as an IBD, or identical by descent, segment. This means that you and the person you match on this small segment descend from a common population, not necessarily that you share a common ancestor within the past several generations. Genealgoically relevant segments are recognizable because they are larger. To understand why and how this works, refer to my article, “Autosomal Results, the Basics.”

There is no absolute line in the sand, but generally segments smaller than 7cM (centimorgans) or 700 SNPs (some say 5cM and 500 SNPs) fall into this category. Dr. Tim Janzen, the genealogical “father of phasing” discards all matches in his spreadsheets less than 3.5cM. That’s because he’s looking for positive genealogical matches and does not want the data to be cluttered up by possible IBS matches.

However, when you have small amounts of minority ancestry, it stands to reason that these small tidbits could be very useful in identifying which of your genealogical lines produced these small amounts of admixture. If you can identify which lines provided this minority admixture, then you’re well on the way to identifying which ancestor contributed the minority admixture.

When looking for minority admixture in two related people, finding these small segments in the same location should provide meaningful information and confirm minority heritage. Said another way, if you both have less than 1% Native heritage, both share a common ancestor, and both carry your less than 1% on the same segment….one might say it’s not likely to be coincidence, especially if there is a pattern across multiple chromosomes/segments. Identifying the common segments of your common ancestor can lead to identifying the specific family line, especially if you match others as well. In essence, this is the genetic equivalent of “surround and conquer.”

Let me give a very short example here.

Let’s say I match my mother on part of chromosome 1 that is Native.

Then let’s say I match her first cousin (my first cousin once removed) on mother’s mother’s side on a smaller piece of that same segment. This immediately tells me that this particular bit of Native heritage is not from mother’s father’s side.

Another match to a more distant Hill cousin further defines the path of Native ancestry, showing that the Native heritage came through mother’s grandfather’s mother’s line. You can see how we track this ancestry and whittle down the possible sources.

So, I’ve set out to test this minority ancestry tracking theory. Because we are dealing with such small segments of DNA, “rooting around in the weeds,” as Bennett Greenspan so aptly put it, and have no mechanized tools, this journey is long, tiresome and tedious. It’s also thrilling.

As with all experiments, I have wondered many times if I was wasting my time. I’ve completed steps and then redone them a different way when I realized there was a better or more revealing method. More than once. That comes with the territory.

I debated about how to share this new technique. In the past, I would have published this as an academic paper, but with the delays surrounding the publication of JoGG, and the fact that the last paper through JoGG took 18 months to get out the door, much of this information would be stale by then. I thought about publishing as an e-book as well, but I finally settled on my blog. I feel that I can reach more people in a much more timely fashion this way. I also really like the blog because I can write in a more relaxed fashion than I could in any other venue and it gives you the opportunity to interact as well.

I also don’t know what to call this new methodology. I have just been referring to it as the weeds method, but that’s not very scientific. I considered the APM technique – Ancestry Population Mapping. Sounds too nonspecific. The PTM – Personal Torture Method – nah – puts people off even if it is true. MAT – Minority Ancestry Tracking – that’s a possibility but isn’t very specific. Fragmented Chromosome Mapping, FCM, has possibilities. So, I’m open to suggestions. If at the end of this series, it’s still the weeds method….well, then weeds it is.

Over the next few weeks, I’ll be writing about this journey, my discoveries, and sharing techniques with step by step instructions so that you can use the same tools. Join me for the multi-part series, “The Autosomal Me.”

______________________________________________________________

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2012 Top 10 Genetic Genealogy Happenings

Posted on December 28, 2012 by Roberta Estes

2012 has been a very busy year for genetic genealogists. There have been lots of discoveries and announcements that affect everyone, now and in the future. The watchwords for 2012 would be “churn” and “explosive growth.” Let’s take a look at the 10 most important events, why they are important and what they mean for the future of genetic genealogy.

These items are in what I think are relatively good order, ranked by their importance, although I had a very difficult time deciding between number 1 and 2.

1. The New Root – Haplogroup A00

At the Family Tree DNA conference in November, Michael Hammer, Bonnie Schrack and Thomas Krahn announced that they had made a monumental discovery in the age of modern man known as Y-line Adam. The discovery of Haplogroup A00 pushes the “birth” of mankind back from about 140,000 years ago to an amazing 338,000 years ago. Utterly amazing. The DNA came from an American family from South Carolina. This discovery highlights the importance of citizen science. Bonnie is a haplogroup administrator who recognized the potential importance of one of her participants’ DNA. Thomas Krahn of course is with Family Tree DNA and ran the WTY test, and Michael Hammer is at the University of Arizona. So you have the perfect blend here of participant, citizen scientist, commercial lab and academia. What was never thought possible a decade or so ago is not only working, it’s working well and changing the face of both science and humanity.

http://dna-explained.com/2012/11/16/the-new-root-haplogroup-a00/

http://www.haplogroup-a.com./

2. Geno 2.0

Geno 2.0 is the Nickname for the National Geographic Society’s Genographic Project version 2.0. That mouthful is why it has a nickname.

This amazing project has leveraged the results of the past 7 years of research from the original Genographic project into a new groundbreaking product. Geno 2.0, utilizing the GenoChip, a sequencing chip created specifically for Nat Geo, offers the most complete Y tree in the world today, expanding the SNP tree from just over 800 SNPs to over 12,000. They are in essence redrawing the Y chromosome tree as I write this. In addition, the person who purchases Geno 2.0 will receive a mitochondrial DNA haplogroup assignment. Over 3300 new mitochondrial mutations were discovered. A brand new anthropological “percentages of ethnicity” report is featured based on over 75,000 Ancestry Informative Markers, many only recently discovered by the Genographic project. Additionally, participants will receive their percentage of both Neanderthal and Denisovan ancestry based on 30,000 SNPs identified that signal interbreeding between the hominids. A new website will also facilitate social networking and uploading information to Family Tree DNA.

The wonderful news is that there is a massive amount of new information here that will change the landscape of genetic genealogy. The difficulty is that we are struggling a bit under the load of that massive amount of information that is just beginning to descend upon us. It’s a great problem to have!

http://dna-explained.com/2012/07/25/national-geographic-geno-2-0-announcement-the-human-story/

http://dna-explained.com/2012/07/26/geno-2-0-qa-with-bennett-greenspan/

http://dna-explained.com/2012/07/30/geno-2-0-answers-from-spencer-wells/

http://dna-explained.com/2012/07/31/geno-2-0-wty-mtdna-full-sequence-participants-and-more/

http://dna-explained.com/2012/10/14/what-to-order-geno-2-0-vs-family-tree-dna-products/

http://dna-explained.com/2012/10/16/geno-2-0-the-kit-arrives/

http://dna-explained.com/2012/12/11/geno-2-0-results-first-peek/

http://dna-explained.com/2012/12/12/geno-2-0-results-kicking-the-tires/

3. Reconstructed Sapiens Reference Sequence (RSRS)

In July, Family Tree DNA implemented the RSRS that in effect reconstructs the genetic profile of Mitochondrial Eve and bases the comparison of our DNA today against the RSRS sequence as opposed to the Cambridge Reference Sequence (rCRS) created in 1981 that is or was the current standard. The RSRS is a result of the watershed paper published in April 2012 by Dr. Doron Behar and 8 other authors titled “A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root.” A complementary research website, www.mtdnacommunity.org, accompanies the paper.

http://dna-explained.com/2012/07/14/what-happened-to-my-mitochondrial-dna/

http://dna-explained.com/2012/07/15/the-crs-and-the-rsrs/

http://dna-explained.com/2012/07/16/the-mtdna-community/

http://dna-explained.com/2012/12/02/little-a-big-a-mitochondrial-dna/

4. Full Genome and Exome Sequence Offered Commercially by Gene by Gene

It was announced at the November DNA conference that Gene by Gene, the parent company of Family Tree DNA, through their division titled DNA DTC is offering full genomic sequencing for the amazing price of $5495 for the full genome and $695 for the exome. This is a first in the consumer marketspace. Today, this doesn’t have a lot of application for genetic genealogy, but as the price continues to drop, and utilities are built to process the full genomic data, certainly a market and applications will emerge. This is an important step forward in the industry with a product that still cost 3 million dollars in 2007.

http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/

5. Neanderthal and Denisovan DNA

It’s official – they did it. Yep, they interbred and well, they are not them anymore, they are us. Given that everyone in Asia and Europe carries a part of them, but not people from Africa, it would appear that two populations admixed rather thoroughly in Eurasia and/or the populations were small. The amount of Neanderthal and Denisovan DNA will continue at approximately the proportions seen today in Europe (2% Neanderthal) and Asia unless a significant amount of admixture from a population (Africa) that does not carry this admixture is introduced. So if you’re European, you carry both Neanderthal and Denisovan DNA. They are your ancestors. The good news is that you can find how much of each through the Geno 2.0 test. 23andMe results give you the percentage of Neanderthal, but not Denisovan.

http://dna-explained.com/2012/08/31/denisovan-dna-tells-a-story/

http://dna-explained.com/2012/12/12/geno-2-0-results-kicking-the-tires/

6. Ancestral Genome Reconstruction Begins, Led by Falling Autosomal Prices and the Ability to Fish in Multiple Ponds

2012 has been the year of autosomal testing price reductions and a great deal of churn in this marketspace. Companies are playing leap-frog with one another. However, sometimes things are not all that they seem.

Initially, 23andMe opted for an initial payment plus monthly subscription model, which they abandoned for a one time payment price of $299 in early 2012. Family Tree DNA was slightly less, at $289.

Ancestry led the price war by giving away kits, then selling them for $99, then $129 plus a subscription as an entrance into this market. However, looking at the Ancestry consent form hints at possible reasons why they were selling below the cost of the tests. You are in essence giving them permission to sell your DNA and associated information. In addition, to gain full access to your results and matches, you must maintain some level of subscription to Ancestry.com, increasing the total effective price.

Next came Family Tree DNA’s sale where they dropped their autosomal price to $199, but they were shortly upstaged by 23andMe whose price has now dropped to $99 permanently, apparently, a result of a 50 million dollar investment in order to reach 1 million customers. They currently have about 180,000. 23andMe has always been in the medical/health business, so their clients have always understood what they were consenting to and for.

Not to be outdone, Family Tree DNA introduced the ability earlier in 2012 to upload your data files from 23andMe to FamilyTree DNA for $89, far less than a second test, which allows you to fish in a second pond where genealogists live for matches. The challenge at 23andMe is that most of their clients test for the health traits and either don’t answer inquiries or match requests, or know little about their genealogy if they do. At Family Tree DNA, matches don’t have to answer and allow a match, testers are automatically matched with all participants who take the Family Finder test (or upload their 23andMe results) and testers are provided with their matches’ e-mail address.

Of course, Geno 2.0 was also introduced in the midst of this, in July, for $199 with the additional lollipop of new SNPS, lots of them, that others simply don’t have access to yet.

The good news is that consumers have benefitted from this leapfrogging, I think. Let’s hope that the subsidized tests at Ancestry and 23andMe don’t serve long term to water down the demand to the point where unsubsidized companies (who don’t selling participants genetic results to others) have problems remaining viable.

Personally, I’ve tested at all of these companies. I’ll be evaluating the results shortly in detail on my blog at www.dna-explained.com.

The tools provided by most testing companies, plus GedMatch, and multiple ponds to fish in are allowing the serious genetic genealogist to “reconstruct” their genome, attributing segments to specific ancestors. Conversely, we will also be able to “reconstruct” specific ancestral family lines as well by identifying autosomal segments in multiple descendants. This new vision of autosomal genetic genealogy will allow much more accurate ancestral line matching, and ancestor identification in the not-so-distant future.

http://www.yourgeneticgenealogist.com/2012/01/family-tree-dna-now-accepting-23andme.html

http://www.yourgeneticgenealogist.com/2012/05/23andme-eliminates-subscription-model.html

http://www.yourgeneticgenealogist.com/2012/10/clarification-of-what-is-available-to.html

http://www.yourgeneticgenealogist.com/2012/12/23andme-receives-50-million-and-drops.html

http://www.thegeneticgenealogist.com/2012/12/26/23andme-and-labcorp-sued-for-patent-infringement/

7. Ethnicity Tests Mature – Minus 1

The good news is that the various ethnicity tests (known as BGA or biogeographical ancestry tests) that provide participants with their percentages of various world populations are improving. The bad news is that there is currently one bad apple in the card with very misleading percentages – and that is Ancestry.com.

23andMe introduced a new version of their ethnicity product in December, expanding from only 3 geographic categories to several. The Geno 2.0 test results are just beginning to be returned which include ethnicity predictions and references to several base populations.

Family Tree DNA finally has some competition in this arena where for years they have been the only serious player, although opinions differ widely about which of these three organizations results are the most accurate. All four are Illumina chip based, using hundreds of thousands of locations, as compared with the previous CODIS type tests which used between 15 and 300 markers and are now outdated. All companies use different reference populations which, of course, provide somewhat different results to participants. All companies, except Ancestry, have documented and shared their reference population information.

Outside of these companies, Doug McDonald offers a private analysis and Gedmatch offers a series of BGA comparisons written by third parties.

While this industry continues to grow and mature, I’m thinking about just averaging the autosomal ethnic results and calling it good:)

http://dna-explained.com/2012/07/21/ethnicity-finders/

http://dna-explained.com/2012/10/24/ancestrys-mythical-admixture-percentages/

http://dna-explained.com/2012/12/07/new-worldview-at-23andme/

http://dna-explained.com/2012/09/09/doug-mcdonald-on-biogeograpical-analysis/

http://dna-explained.com/2012/12/11/geno-2-0-results-first-peek/

http://www.yourgeneticgenealogist.com/2012_12_01_archive.html

8. Finding Your Roots PBS Series with Henry Louis Gates

PBS sponsored a wonderful series in the spring of 2012 hosted by Henry Louis “Skip” Gates, the chair of African American Studies at Harvard. This series followed a lesser known 2010 series. The 2012 inspirational series reached tens of thousands of people and increased awareness of genetic genealogy as well as sparked an interest in genealogy itself, especially for mixed race and African American people. I was disappointed that the series did not pursue the Native American results unexpectedly obtained for one participant. It seemed like a missed opportunity. Series like this bring DNA testing for genealogy into the mainstream, making it less “strange” and frightening and more desirable for the average person. These stories were both inspirational and heartwarming. I hope we can look forward to similar programs in the future.

http://en.wikipedia.org/wiki/Finding_Your_Roots

CeCe Moore covered this series in March and April on her blog.

http://www.yourgeneticgenealogist.com/2012/03/finding-your-roots-with-henry-louis.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_09.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_16.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_23.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_30.html

9. Ancestry, GeneTree and Sorenson

GeneTree, a for profit company and Sorenson, a non-profit company were both purchased by Ancestry.com. This was about the same time as Ancestry introduced their autosomal AncestryDNA product. Speculation was that the autosomal results at Sorenson might be the foundation for the new autosomal test comparisons, although there has been no subsequent evidence of this.

Ancestry initially gave away several thousand kits in order to build their data base, then sold thousands more for $99 before raising the price to what appears to be a normalized price of $129 plus an annual ancestry subscription.

While GeneTree was never a major player in the DNA testing marketspace, Sorenson Molecular Genealogical Foundation played an important role for many years as a nonprofit research institute. There was significant distress in the genetic genealogy community related to the DNA contributed to Sorenson for research being absorbed by Ancestry as a “for profit” company. Ancestry is maintaining the www.smgf.org website, but no additional results will be added. Sorenson has been entirely shuttered. Many of the Sorenson/GeneTree employees appear to have moved over to Ancestry.

The initial AncestryDNA autosomal product offering is poor, lacks tools and the ethnicity portion has significant issues. It’s strength is that many people who test are already Ancestry subscribers and have attached their trees. So you can’t see how you connect genetically to your matches (lack of tools), but you can see the trees, if they are attached and not marked as private, of those with whom you match. Ancestry provides “hints” relative to matching individuals or surnames.

Eventually, if Ancestry improves its products, provides tools and releases the raw data to consumers, this may be a good thing. It’s an important event in 2012 because of the massive size of Ancestry, but the product is mediocre at best. Ancestry seems unwilling to acknowledge issues unless their feet are held to the fire publicly as illustrated with a “lab error” erroneous match for an adoptee caught by the consuming public and ignored by Ancestry until CeCe Moore exposed them in her blog. Whether Ancestry ultimately helps or hurts the genetic genealogy industry is a story yet to be told. There is very little positive press in the genetic genealogy community surrounding the Ancestry product, but with their captive audience, they are clearly going to be a player.

http://www.yourgeneticgenealogist.com/2012/05/ancestrycom-buys-genetree-and-launches.html

http://dna-explained.com/2012/07/12/did-you-test-at-genetree/

http://dna-explained.com/2012/08/30/is-history-repeating-itself-at-ancestry/

http://dna-explained.com/2012/07/18/the-trouble-with-ancestry-com-matches/

http://dna-explained.com/2012/08/14/y-dna-family-tree-dna-vs-ancestry/

http://dna-explained.com/2012/08/16/ancestrys-consent-form-for-ancestrydna-autosomal-test/

http://dna-explained.com/2012/09/10/ancestry-autosomal-results-are-back/

http://dna-explained.com/2012/10/15/ancestrys-dna-survey/

http://dna-explained.com/2012/10/23/ancestry-to-release-array-data-in-2013/

http://dna-explained.com/2012/10/24/ancestrys-mythical-admixture-percentages/

http://www.thegeneticgenealogist.com/2012/06/19/problems-with-ancestrydnas-genetic-ethnicity-prediction/

http://www.yourgeneticgenealogist.com/2012/08/ancestrydna-confusing-relationship.html

http://www.yourgeneticgenealogist.com/2012/08/follow-up-on-ancestrydna-and-adoptees.html

http://www.yourgeneticgenealogist.com/2012/09/23andme-says-no-match-for-adoptees.html

10. GedMatch

GedMatch, www.gedmatch.com, created by John Olson and Curtis Rogers, isn’t new in 2012, but it’s maturing into a tool that is becoming the defacto workhorse of the serious autosomal community. People who test at either 23andMe or Family Tree DNA download their raw results and other match information and then use a variety of tools at GedMatch to look at results in different ways and using different thresholds. GedMatch is currently working to accept the newly arriving Geno 2.0 data files. Ancestry does not at this time allow their customers access to their raw data files, so there is nothing to upload. The bad news is that not everyone downloads/uploads their information. Only the most savvy users, and the download/upload is not always a smooth process, often necessitating several attempts, a magic wand and some fairy dust for luck.

GedMatch is a volunteer effort funded by donations on the GedMatch site. The magnitude of this project came to light when they needed new servers this year because the amount of traffic disabled their internet service provider. It may be a volunteer effort, but it has mainstream requirements. Therefore, while occasionally frustrating, it’s easy to understand why it’s light on documentation and one has to poke around a bit to figure things out. I would actually prefer that they make it a subscription site, clean up the bugs, add the documentation and take it to the next level. It would also be very nice if they could arrange something with the major players in terms of a seamless data transfer for clients. All told, it’s an amazing contribution as a volunteer site. Hats off to Curtis and John for their ongoing contribution to genetic genealogists!!!

www.gedmatch.com

http://www.legalgenealogist.com/blog/2012/08/12/gedmatch-a-dna-geeks-dream-site/

______________________________________________________________

Disclosure

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

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I’m Adopted and I Don’t Know Where to Start

Posted on December 17, 2012 by Roberta Estes

This is one of the two most common querys that I receive.

I’ve addressed some of the adoptee resources in a previous blog, but in this one, I’m going to be very specific about which tests do what, what to expect, how to use them, where to purchase the tests and how much they cost in general terms. Remember when reading this, it’s meant as a guideline and you should always check current products and prices before purchasing.

We all begin with genetic genealogy to answer questions, but adoptees have a special circumstance wherein they generally know nothing at all about their birth parents. Today’s query told me that her birth certificate doesn’t even include a race.

First, all adoptees need to read my post on Adoptee Resources. I’m not an expert on how to deal with all of the bureaucratic and paperwork nightmares involved, which of course vary by state, but there are people who specialize in this and they have groups to help. Take advantage of them. Also, throughout the rest of this blog, be sure to click on the links. I’m not restating things that I’ve already covered elsewhere.

Now, let’s look at the 3 kinds of DNA testing that can benefit adoptees and just how they might use the results.

There are three kinds of DNA testing that you can do.

Mitochondrial for your direct maternal line.
Y-line for your direct paternal line – if you are a male. Sorry ladies.
Autosomal to test your ethnic mix and to find cousins related to you on any line.

On a pedigree chart, these genealogical lines look like this:

You can see the path that the Y chromosome takes down the paternal line to the brother and the path the mitochondrial DNA takes down the maternal line to both the brother and the sister. Autosomal tests the DNA of all of the 16 ancestral lines shown here, but in a different sort of way.

Let’s look at each one separately.

Y-Line DNA – For Paternal Line Testing for Males

The Y-line testing tests the Y chromosome which is passed intact from father to son with no DNA from the mother. This is the blue square on the pedigree chart. In this way, it remains the same in each generation, allowing us to compare it to others with a similar surname to see if we are from the same “Smith” family, for example, or to others with different surnames, in the case of adoption. Small mutations do take place and accumulate over time, and we depend on those so that we don’t all “look alike.”

The good news is that using comparison tools, we can determine a genetic surname in about one third of the cases. That’s pretty good odds for someone who started with no information at all.

Looking at the Estes surname project as an example, you can see in this colorized version that there are mutations shown, in color, even within family groups.

You can test at 12, 25, 37, 67 or 111 marker “locations” on the Y chromosome. In order to look for strong results you’re going to need to test at a minimum of 37 markers, preferably 67 or 111. At Family Tree DNA, which is where I recommend that you test, you can always upgrade later, but it’s less expensive in total to test more initially, plus you may well need the information to know who you match at the highest levels. Right now, 37 markers cost $119 and 67 markers are $199, but a sale is currently underway. You can also join the adoptee project to obtain the best pricing by joining a project.

Family Tree DNA also provides significant tools for Y-line DNA as well as Mitochondrial DNA as well. You can see both Family Tree and Ancestry results compared on this blog, which shows you how to use both companies’ tools. At Family Tree DNA, for all their tests, you are provided with the e-mail addresses of your matches. At Ancestry and 23andMe, you contact matches through thier internal message system. My experience has been that direct e-mails have a better response rate.

You can also order a DNA Report from my company, DNAeXplain, or directly from your personal page at Family Tree DNA, if you need assistance understanding either Y-line or mitochondrial DNA results and wringing every possible tidbit from the available tools.

Obviously, the Y-line test is only for males. Ladies, I feel your pain. However, these next tests are for both sexes.

Mitochondrial DNA – For Direct Maternal Line Testing for Both Sexes

Mitochondrial DNA is inherited by all children from their mother only, with no admixture from the father. Women obtain their mitochondrial DNA from their mother, who got it from their mother, on up the line into infinity. This is the red circle on the right hand side of the pedigree chart. Like Y-line DNA, mitochondrial DNA is passed intact from one generation to the next, except for an occasional mutation that allows us to identify family members and family lines.

Unfortunately, it does not follow any surname. In fact the surname changes with every generation when women marry. This makes it more challenging to work with genealogically, but certainly not impossible. Because of the surname changes in every generation, there are no “surname” projects for mitochondrial DNA, but the Mothers of Acadia project is using mitochondrial DNA to reconstruct the Acadian families.

There are three levels of testing you can take for mitochondrial DNA at Family Tree DNA, which is where I recommend that you test. The mtDNA, the mtDNAPlus and the Full Sequence. The mtDNA test is a starter test that will only leave adoptees needing more. I strongly recommend the full sequence test, but if the budget just won’t allow that, then the mtDNAPlus will do until you can afford to upgrade. Family Tree DNA is the only major lab that tests the full sequence region, plus, they have the largest matching data base in the industry.

To put this in perspective for you, the mtDNA and the mtDNAPlus tests both test about 10% of your mitochondrial DNA and the full sequence test tests all of your 16,569 mitochondrial locations. You can then compare them with other people who have taken any of those 3 tests. For adoptees, you’ll need the power of the full sequence test. Pricing for the mtDNAPlus is currently $139 and the full sequence is $199.

After you receive your results, you can enter the mtDNA and mtDNAPlus portions into public data bases. There are no public data bases for the full sequence segment because there may be medical implications in some of those mutations, so they are not displayed publicly although they are compared privately within the Family Tree DNA data base. You will want to enter your data and check for matches at www.mitosearch.org (upload directly from your matches page at Family Tree DNA), www.smgf.org and www.ancestry.com, although beware of Ancestry’s accuracy issues.

Update: Please note that as of 2019, Family Tree DNA is the only company providing mitochondrial DNA testing and matching. The rest are now obsolete.

If you match someone on either the Y-line or mitochondrial DNA, you may want to do some additional testing to see if you are closely related or if you are related back in time many generations. The good news is that autosomal testing is what you need and there are three autosomal pools to swim in, increasing your chances of a “hit.”

Autosomal Testing – The Rest of the Story – For Both Sexes

If there was a DNA test created for adoptees, this is it. This test can be used alone or in conjunction with the Y-line or mitochondrial DNA testing at Family Tree DNA. They are the only lab to have this advanced matching capability.

Autosomal DNA testing tests all of your 23 pairs of chromosomes that you inherit from both of your parents. You get half of each chromosome from each parent. You can see this pattern on the pedigree chart, represented by all of the 16 genealogical lines. Therefore, as you move up that tree, you should have inherited about 25% of your DNA from each grandparent, about 12.5% of your DNA from each great-grandparent, as have all of their other great-grandchildren.

So, if you were to take an autosomal test, and another one of your grandparents grandchildren tested, you would match them at some predictable percentage of your DNA. You can see the “cheat-sheet” we use below, courtesy of the ISOGG wiki.

You can see that your grandparents other grandchildren are your first cousins, and you share approximately 12.5% of your autosomal DNA with them. Therefore, if you match someone at 12.5%, you are either first cousins, great-grandchildren/great-grandparents or another relative with 12.5 in their “box” below, as compared to you.

For an adoptee, this is the literal Holy Grail. You can match someone at the 25% level, or even the 50% level. Yes, siblings have found each other this way, although not to misset your expectations, it’s rare. Much more common are matches at smaller percentages, but even so, if you match someone who is cooperative, it’s not too difficult to work with their pedigree chart to get some idea who your parents might be. And even if you can’t figure that out, you know you are biologically related to them, something most adoptees have never experienced before aside from their own children.

The adoptee group and others are working on tools and standard procedures for adoptees, as there are ways to work with this information. I have also blogged about the basics of what autosomal DNA gives you, and how to use it.

There are three testing companies that sell autosomal DNA testing. I strongly suggest that you use all three of them, plus download your results to www.gedmatch.com and learn to use those tools, or work with someone on your behalf.

Family Tree DNA sells the Family Finder test. Right now it is priced at $199 or bundled with attractive pricing with either the Y-line or mitochondrial DNA tests. For adoptees, I often like to use this tool in conjunction with the Y-line and mitochondrial DNA tests to see, if you match someone closely, whether you are actually related to them in a recent timeframe or if it is further back. Autosomal testing will pick up relationships reliably back to about the 6^th or 7^th generations, and sporadically beyond that. In addition to a list of matches, you will receive your breakdown of ethnicity, by percent. The admixture portions are improving, but just use them as a guideline, especially for percentages below 10%, and that goes for all three companies, in general.

Another company that sells autosomal testing is www.23andme.com. In addition to a list of cousins, you also receive admixture percentages, and their specialty, health traits. For adoptees, this may be particularly important as well. Be aware that while people who test at Family Tree DNA are interested in genealogy, the typical person at 23andMe tested for the health portion, not the genealogy portion, and may not answer contact requests or may know very little about their family history. However, that doesn’t negate the possibility that you may find a very close match and you’ll never know if you don’t test. Right now, their test is $99, and you can download your results and upload them to Family Tree DNA for an additional $89, making the total price similar to the Family Tree DNA test. However, you need to be somewhat technically savvy to complete the download/upload process.

The third company is www.ancestry.com. Compared to either Family Tree DNA or 23andMe, their tools are sorely lacking, but they too offer a list of matches and ethnicity. I suggest that you simply ignore their ethnicity calculations at this point in time as they are quite misleading. The good news about Ancestry subscribers, which is who you’ll be matching, is that they too are quite interested in genealogy. Unfortunately, you don’t have the data tools you’ll need to see how you match. Again, that does not negate the importance of a close match, so I recommend fishing in this pool even though it certainly doesn’t stand up to either of the other two companies. Their price fluctuates but is floating someplace around $129. Also be aware to access the full feature set of matches including trees, you will need to subscribe to Ancestry as well in some capacity, so the test price is not the only cost involved. Be sure to read their fine print first.

After you obtain your results from either Family Tree DNA or 23andMe, you’ll want to download your raw data results and then upload the file to www.gedmatch.com. This is “donation” site, meaning there is no subscription or fee to use the tools, but they do appreciate donations. Ancestry does not provide your raw data, but has stated that they will sometime in 2013.

While this suite of tools does not replace that missing information locked away in a file someplace, or worse, it does provide adoptees with hope where none may have existed before. Various kinds of DNA testing can provide answers, and relatives, both close and distant. You can also work with these tools with other adoptees and those who specialize in genetic genealogy to unlock those doors.

Remember, the longest journey begins with a single step. Bon Voyage!

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