I've been going over the ethnicity result phasing at 23andMe again. My ethnicity results were phased with my mother's because we both tested at 23andMe. These results are also phased even if a parent hasn't tested. Phasing without a parent is done using haplotypes to attempt to separate each chromosome into two parts, one representing each parent. Ancestry also phases results but not for ethnicity. Ancestry phases for the matching process. They use the same haplotype process, however, but don't use parents at all.Haplotypes are picked out using computer programs that look for strings of matching alleles in your raw data results. These strings are learned through looking at genomes of those who have tested previously. This is 23andMe's explanation, "The technical term for determining which alleles reside on the same chromosome together is phasing. DNA data like our raw data is called unphased."
Looking at our families 23andMe phased ethnicity results it becomes apparent right away that results phased with at least one parent are much more accurate. Half of the genome can be correctly matched with one parent and anything left over can be attributed to the other parent.
The breakdown of my ethnicity estimates by parent, below, is correct (they do reflect my documentation and family knowledge. My father's ancestry is about 100% European, whereas my mother had a European father and a mixed heritage Nicaraguan mother). If a parent tests with 23andMe and you connect with them you can get a chart like the one below.
Below is the 23andMe X chromosome after my mother tested. The color scheme for Native American has changed and is yellow. The X chromosome I received from my father is now completely British and Irish, which would be correct based on what I know from his X maternal tree. The Native American disappeared. The X chromosome I received from my mother now appears to be nearly completely Native American, which would make sense because more Spanish men originally settled my maternal grandmother's place of origin Nicaragua than women. The chromosomes I received from my mother all moved to the top line of each chromosome which always happens if you phase with a parent.
Correct Phasing When Phased with ParentLooking at the Chromosome Painting maps ethnicity results it becomes very apparent that it's phased correctly 99.9% of the time when a parent tests.
Phasing Errors When a Parent hasn't tested
We begin to see problems with phased results that are statistical only with no parent testing. Looking at my cousins' and mother's results who haven't had a parent test you can see phasing errors.
Below is the 23andMe chart showing my mother's phased ethnicity Chromosome Painting results. You can see where phasing errors occurred. My mother's father was of British Isles and German ancestry with no Native American or Sub Saharan African ancestry. This has been confirmed with both documentation and DNA testing. A paternal first cousin of my mother has DNA tested and has zero Native American or Sub Saharan African. Several of my mother's paternal 1st cousins once removed have also DNA tested and have zero percentages of those admixtures also. There should be no Native American or Sub Saharan segments on my mother's father's chromosomes. Mixing of Native American and British Isles on the same chromosome such as on chromosome 4, chart below, is definitely wrong. The Native American and Sub Saharan are all from my mother's Nicaraguan mother. Nicaraguans are descendants of the Spanish, Native American, and African Slaves that settled the country.
Below I circled the chromosomes where phasing errors apparently resulted in Native American and African segments to be placed on my mother's father's chromosomes in error. My mother's father's chromosomes can be identified by long stretches of Northern European or British Isles segments. Often my mother's mother's chromosomes are the ones on top, but a few times they have flipped to the bottom one (this has occurred because without a parent testing there is no way to tell for certain which side the chromosome represents). Only 5 chromosomes appear to have phasing errors.
It appears that some Native American and Sub Saharan African on these chromosomes should either move up to the top or down to the bottom of the chromosome.
Below is chromosome 4. The top chromosome definitely looks like it would have been from my Nicaraguan grandmother with a couple of stretches of Spanish DNA. So the yellowish Native American should be moved up to the top chromosome, and a chunk of blue broadly European and Spanish should move down.
My own Native American Chromosome Paint chart has the chromosomes accurately phased because my results are not statistically phased but are parentally phased. Only two tiny segments end up on my paternal side chromosomes. This could represent actual very distant Native American ancestry on my father's side? One of his ancestors was an Indian trader in Pennsylvania who did have a Native wife although I'm not sure if we are descended from her? It's also possible that these tiny Native American segments are false positives? In any case the phasing has been at least 98% accurate. My Sub Saharan segments are 100% correct and are all on my Mother's chromosome.