Saturday, July 18, 2015

Looking At Ethnicity And Inheritance On The X Chromosome


The chromosome view at 23andMe's Ancestry Composition is very interesting. It's especially interesting if you have an ethnically mixed background. It's difficult to separate the various European ethnic groups. If you're 100% European it isn't as useful. If you're wondering whether you have Jewish, Native American, African, Asian, etc. ancestry it is very helpful.

In my case my Grandmother was from Nicaragua, a place with a great deal of ethnic mixing. Most Nicaraguans are either more than half European, Native American, or African. I believe my Grandmother was a little more than half European. She was probably around a quarter Native American, based on my Mom's DNA results at AncestryDNA. I've been finding the X data at 23andMe to be informative regarding the ethnic mix on our maternal grandmother's side. I'm also beginning to understand the way the X recombines, or doesn't. Sounds like the X is more resistant to recombining than the other chromosomes. So it's possible that an unrecombined X could be passed on, as may be the case with a male cousin, and myself. I looked at the X sharing chromosome inheritance charts. I assumed that I could have inherited X DNA from most of the close lines. Looking at my X DNA I see that I didn't inherit DNA on the X from all close ancestors who could have contributed to my X. Instead I received a majority of the DNA on my X from my maternal Great-Grandmother and Great-Grandfather, based on the Native American, very little if any from anyone else. At least I'm unaware of my Maternal Grandfather having any Native American blood? I plan on testing my Mom to get a better idea of exactly who contributed the most to my X. If my chromosome is completely Native American and Southern European I may have gotten an entire X chromosome from my Nicaraguan Grandmother.

My X chromosomes. Orange is Native American, Purple African, Blue European.
However, looking at maternal cousins results the Southern European may be Northern European? In that case I probably did inherit some X DNA from my Maternal Grandfather. My brother and sister cousins also share segments on in my European region on the X. However one of my female cousin's shared regions is identified as Northern European while the same segment is Southern European according to her brother and a sister's results. The cousins with the Native American and Southern European results look more like my own, overall. You can see from the last X chart that brother and younger sister share half identical DNA across nearly the entire X chromosome (as shown by the green bar).

Orange is Native American, Purple African, Blue European. Brother and younger and sister

His results and the younger sisters results are starkly different than their oldest sister whose maternal and paternal X is practically completely Northern European. Unless some of her Northern European is actually Southern? It's 3 to 1 that our shared European DNA is Southern European. 

Differences when comparing two sisters
You can see by green bar they share DNA across the X

I noticed when I compared the female cousins to their brother the European and Native American lined up very well, when comparing side by side, looking at the share regions. When I compared the two sisters I was surprised the sisters matched all the way across the chromosome, but didn't share the same ethnicity predictions. I forgot that females received identical X chromosomes from their father. Fathers pass on their one X chromosome, unchanged, to their daughters. It appears they match across the chromosome; but, in reality its combined DNA from different lines. An expert on the subject of the X chromosome inheritance, Dr. Kathy Johnson, advised using either GEDmatch or 23andMe's Family Traits chromosome browser to see the half identical and fully identical regions (see ISOGG Wiki for examples of half identical and fully identical segments shared by relatives on the X). The fully identical regions mean  DNA is shared on both the Maternal and Paternal X. The sisters only share half identical regions with their bother because males have only one X and can't be fully identical with sisters. The first fully identical region is in a place where they don't match their brother (see blue chromosome below). The two sisters and brother share DNA where the sisters have their second fully identical segment. The half identical region for the two sisters, not shared by their brother comes from their father. We know this because this is a half identical region for the two sisters, which the brother doesn't share (remember the brother and younger sister do match there. So the older sister inherited more X DNA from her maternal grandfather who was Scots-Irish and German. The younger sister and brother inherited more X from their maternal grandmother who was Nicaraguan). Looking at half identical and fully identical regions is a great way to find out where siblings DNA is inherited from, since this is not shown in the advanced inheritance chromosome browser at 23andMe. 
This is from Family Traits Browser at 23andMe
Showing full identical dark Blue and half identical light blue

Here is a chart Dr. Kathy Johnson made for us.

Chart shows my 2 female and one male cousins ethnicity results
From Family Traits and the Ancestry Composition chromosome views 23andMe

 I have a few more distant cousins who match me on the X. One of them is also Nicaraguan and confirms that that region of the X is Nicaraguan. I have a couple matches on my father's side also. One is a 3rd cousin. Since fathers don't pass down their X to their sons we know this DNA doesn't come from our shared French Canadian line.  
The X is very useful when you have a question involving the X lines of inheritance. My X DNA has confirmed what the other tests seem suggest regarding Nicaraguan marriage patterns. It looks like males with European direct Y lines often married either Native American or African females. Seems like it was more acceptable, and probably because of the smaller female European population, males often married outside their own ethnic group. European females didn't marry out of their own ethnic population as frequently as males. The European males were probably financially better, off making them more attractive marriage partners.
I'm attempting to test my Mom with 23andMe. She is very advanced in age, and in failing health. Not sure if her test will pass? Keeping my fingers crossed that the test will pass. It would be great to phase my results with hers. I could then get a better picture regarding the ethnicity on my maternal X. Curious to see if I've inherited any DNA from my maternal Grandfather or is it all from my Maternal Grandmother? I also see a small bit of Native American on the chromosome which represents my father. Looking at the X lines on my father's side I am unaware of any family tradition regarding Native American in those lines? Another question I would like to find an answer for? I mailed my Mom's kit in yesterday. I'm following its course through the mail using USPS tracking.

X inheritance

Sunday, July 5, 2015

How Do AncestryDNA cM Numbers Compare?

With the mirrors to the other world at AncestryDNA finally cracking open a little some comparison between their results and those from Family Tree DNA, 23andMe, and GEDmatch can be made (if you've been watching the BBC series Strange and Norrell you'll understand that reference).

 I only counted segments 5 cMs and over when comparing.

Starting the comparison with a double 5th cousin who has tested with all 3 companies:
This cousin has results at the 3 major companies plus GEDmatch. In this case AncestryDNA seems to have removed the 9 cM segment on Chromosome 6. This same segment was removed from two other relatives of this match, also. From totals around 24 cMs with GEDmatch and the other two companies we go down to a total of 13.404 at AncestryDNA.

AncestryDNA total shared 13.399 cM Total

Family Tree DNA 23.41 cM Total

GEDmatch cM Total 25.2
23andMe cM Total 24.3

Moving on to this match who has tested with the 3 major companies:
In this case AncestryDNA cut the cM total from 25 to 26 cM's to 6.748. This would mean, if Ancestry is right, this may not be a true cousin match. I haven't established a relationship in this, case so far. So they may be right in this case?

AncestryDNA Total 6.748
Family Tree DNA Total 25.27

23andMe Total 26.2
Moving on to a 4th Cousin:
The particular match is a known, confirmed, 4th cousin. AncestryDNA predicts he is a 5th to 8th cousin. AncestryDNA totals are much smaller with only 6.748 total, while 23andMe says we share 32 cMs. I tend to believe the higher number.
AncestryDNA 4th cousin match total 6.748 cMs
23andMe 4th cousin match total 32 cM's
I've compared a couple more matches, which basically follow along these same lines. I haven't found any cM totals predicted to be closer than 8 cM's, when comparing with AncestryDNA. Some comparisons are 20 cMs different. I've made notes for all of the matches I've been able to identify at AncestryDNA. Looking at the totals for some of these matches I'm surprised at how low the cM totals are. I believe if we compared elsewhere the totals would be higher. I don't know about how the phasing and filtering is working for anyone else? It's not working well for me. I believe the best approach to matching is to provide testers with unphased, unfiltered matches who share a 7 cM segment or more, and with at least 700 SNPs. I don't feel the current matching system is helpful enough in eliminating bad matches, because there are many matches sharing cM totals under 7 (many sharing only 5 cMs total). AncestryDNA's system also tends to remove some good matches. Losing good matches, and having close cousins downgraded, in order to eliminate a few bad matches isn't worth the trade off.