Identification of the Hypothesized African Ancestry of the Wife of Pvt. Henry Windecker Using Genomic Testing of the Autosomes.

Transcription

1 Identification of the Hypothesized African Ancestry of the Wife of Pvt. Henry Windecker Using Genomic Testing of the Autosomes Introduction African Ancestry: The hypothesis, based on considerable circumstantial genealogical evidence, that the wife of Pvt. Henry Windecker was Dorothy Pickert, can be explored using autosomal DNA testing of her descendants. Dorothy would have been the granddaughter of Eve (Classen) Pickert, who frustrated Sir William Johnson by selling liquor to the Indians of Canajoharie. Johnson noted that Eve could speak perfect Mohawk and was a mullato. Thus there may be a small fragment of this African ancestry that is detectable in some of the descendants of this woman via son John Pickert the proposed father of Dorothy Windecker. Hence if those in the Sgt. Daniel Young line (he married Elizabeth Windecker) have an African segment, whereas those of other lines such as that of Lt. John Young do not this will be considered as evidence supporting the hypothesis as to the identity of Windecker s wife Dorothy. The genealogical evidence will be added later. Genetic Testing Both 23andMe and decodeme use over half a million SNP markers with modern chip technology and this represents a major step forward in personal genomics testing for ancestry. Hence the results from the analyses of both companies will be taken as the best option available to date and serious consideration must be given to the outputs here which identify percentage of European, Asian, and African. The reference groups are somewhat restricted and include the HapMap Utah sample for Europeans, the Yoruba Nigerians for Africans, and the Han Chinese for Asians. Thus if a block or segment of a chromosome clusters more with the Yoruba than other groups it will be labeled African and its boundaries defined. To explore the relevant data in relation to the hypothesis that Lt. John Young s wife was Native American, as suggested by the strong genealogical evidence that she was of the Mohawk nation, click here. In the analysis to follow we will explore the autosomal data (22 pairs of autosomes), which experience meiosis (recombination) with each generation. Due to meiosis, any segment that may have survived from Dorothy Windecker s grandmother would be expected to be small less than 10 Mb in length, or 7 cm in genetic distance. 23andMe Testing: Autosomal Data Young Family African Segments on the Autosomes Using the FetchPaint Coding Thomas Nelson 23andMe Segments from Ancestry Painting of 23andMe 1

2 {"intervals": "{\"20\": [[11244, , \"CC\"]], \"21\": [[ , , \"CC\"]], \"22\": [[ , , \"CC\"]], \"1\": [[742429, , \"CC\"]], \"3\": [[38411, , \"CC\"]], \"2\": [[19443, , \"CC\"]], \"5\": [[91139, , \"CC\"]], \"4\": [[63508, , \"CC\"]], \"7\": [[140736, , \"CC\"]], \"6\": [[110391, , \"CC\"]], \"9\": [[36587, , \"CC\"]], \"8\": [[154984, , \"CC\"]], \"11\": [[188510, , \"CC\"]], \"10\": [[103934, , \"CC\"]], \"13\": [[ , , \"CC\"]], \"12\": [[64079, , \"CC\"], [ , , \"AC\"], [ , , \"CC\"]], \"15\": [[ , , \"CC\"]], \"14\": [[ , , \"CC\"]], \"17\": [[51088, , \"CC\"]], \"16\": [[37354, , \"CC\"], [ , , \"AC\"], [ , , \"CC\"], [ , , \"AC\"], [ , , \"CC\"]], \"19\": [[217034, , \"CC\"]], \"18\": [[59836, , \"CC\"]]}", "p1": " a0885c7ab", "popstruct": {"results": [["Europe", ">99%"], ["Asia", "<1%"], ["Africa", "0%"], ["unassigned", "0%"]], "desc": ""}, "function_call": "paint"} Asian segments While the significance of the unrepresented (does not show in Ancestry Painting diagram probably due to break in middle of segment) block on chromosome 16 remains to be assessed. It will be compared to some new testing of David Faux later in this paper. Robert Nelson - African Segment seen via 23andMe Ancestry Painting {"intervals": "{\"20\": [[11244, , \"CC\"]], \"21\": [[ , , \"CC\"]], \"22\": [[ , , \"CC\"]], \"1\": [[742429, , \"CC\"], [ , , \"CY\"]], \"3\": [[38411, , \"CC\"]], \"2\": [[19443, , \"CC\"]], \"5\": [[91139, , \"CC\"]], \"4\": [[63508, , \"CC\"]], \"7\": [[140736, , \"CC\"]], \"6\": [[110391, , \"CC\"]], \"9\": [[36587, , \"CC\"]], \"8\": [[154984, , \"CC\"]], \"11\": [[188510, , \"CC\"]], \"10\": [[103934, , \"CC\"]], \"13\": [[ , , \"CC\"]], \"12\": [[64079, , \"CC\"]], \"15\": [[ , , \"CC\"]], \"14\": [[ , , \"CC\"]], \"17\": [[51088, , \"CC\"]], \"16\": [[37354, , \"CC\"]], \"19\": [[217034, , \"CC\"]], \"18\": [[59836, , \"CC\"]]}", "p1": "02cc9569c55fc7f1", "popstruct": {"results": [["Europe", ">99%"], ["Asia", "0%"], ["Africa", "<1%"], ["unassigned", "0%"]], "desc": ""}, "function_call": "paint"} African segment 2

3 DeCODEme Testing for Tom Nelson: Note that there is no correspondence between the displays (paintings) of 23andme and DeCODEme for Tom. The Asian segment on Chromosome 12 from 23andMe does not show in the above DeCODEme analysis; and 23andMe does not detect the large Asian blocks on Chromosome 1, and the African block on Chromosome 8 shown in the display via DeCODEme. This inconsistency makes it very difficult to determine which of the two data sources is correct if either. 3

4 Above is a closer look at the large (about 15 Mb) African block of Tom Nelson on Chromsome 8 via the DeCODEme browser. This constitutes strong evidence of some African ancestry. The present author has not seen any blocks of this nature in those without documented or suspected African ancestry. Analysis: Both Tom and his uncle Robert have African segments on Chromosomes 8 and 1 respectively when taking the DeCODEme and 23andMe data into consideration. The DeCODEme output was generated using the latter s algorithm on Tom s data uploaded from 23andMe. Both are descendants of Pvt. Henry Windecker in either one or two branches. 4

5 Decodeme Testing of David Faux: Although somewhat difficult to see in the above display mode, this is the representation of the DeCODEme data for David Faux. In addition to notable Asian segments not found in 23andMe, there is are areas with possibly significant African ancestry shown here, especially on the X chromosome. However, this region around the centromere, although labeled 100% African by decodeme, has been show elsewhere (e.g., new testing developed by Doug McDonald) to be bogus in some way and is considerably more likely to be European in origin. New Tests in Relation to the Autosomes of David Faux: 1) Dr. Doug McDonald s New Segment Test Here follows a diagram generated by Dr. McDonald using a large number of new reference samples, classified into broader categories such as South Asian. 5

6 Although this data was generated with a lower confidence interval than might be warranted, and the East Asian yellow segment did disappear when the criteria was tightened, the block in deep blue (African) situated not far from the telomere (in the region of 3 Mb to 10 Mb) may have some significance since it is cross validated with new testing by the Eurogenes Project. 2) Eurogenes: Test of Heterozygosticity markers and Regions not Typically Found in Northwestern Europeans: 6

7 The developer of the Eurogenes Project indicated that he was dissatisfied with the program ADMIXTURE in that it could not differentiate between ancient matches (identical by state) and those more recent (identical by descent), nor does it pick up significant smaller segments, nor does it place the minority ancestry on a map of the chromosomes. Thus a white American who obtained zero of a category such as Sub- Saharan African using admixture tests, may have undetected recent ancestry from this group. To address this issue the author used a tool called RHHCounter/RHHMapper and used the following data source: I put together a data set of over 350 samples that showed less than 2% West Eurasian influence in ADMIXTURE analyses, and clustered in or very near Europe on MDS plots. I then let RHHcounter search these samples for genotypes with less than 0.005% frequency amongst them. The samples 7

8 originating from North of the Alps and Carpathians scored 5-15 heterozygote hits each, usually widely dispersed around the genome. However, in a few Americans of North European descent, the heterozygotes took the form of small segments. His rationale is supported by the new study of McGinnis et al., The average northwestern European will have from 5 to 8 little hash marks scattered about the genome. What becomes more significant if they begin to cluster, and then it may indicate a segment from a non - western European source (most probably African, but not necessarily so). Here is the display of David Faux: A close cluster of two hash marks can be seen here. A genetic genealogist on the 23andMe blog developed a program to specify the location of the marks. Here they are situated between position and Mb from the telomere of the p end of 8

9 chromosome 16. The identifying rs numbers and the population data from the dbsnp database is: Rs (position Mb) = David s genotype here is A/G (rare). 100% of Europeans and Asians have the A allele, and 16% of Africans have the G allele. Hence only Africans in this database have a G allele in desnp. Rs (position Mb) = David s genotype is C/T. 100% of Europeans have the C allele. Only 6% of Asians and 40% of Africans have the T allele. Thus the probability here says that David s T allele came from an African source, but Asian is also possible. Gene Position SNP Versions Genotypes A2BP rs A or G AG David Faux AA Lilly Mendel (Mom) AA Greg Mendel (Dad) As seen above, for the allele G for SNP rs , only Africans have been shown to have this version. This motif comes from the author s mother s side of the family (as would be required to support the above hypothesis) since his Uncle Dale matches him on the block between to Mb on chromosome 16, and he has the same two heterozygous non - western European alleles. Clearly, however, Tom Nelson does not have the same motif. He does not match the author or the author s uncle on that part of chromosome 16 using 23andMe s Family Inheritance, or the other databases of Jim McMillan and Leon Kull who look at smaller matches. In addition, Tom s allele motif is AA, the standard European and Asian version. What would be very unusual is that the same region may have come from the Young family, but Tom got the Asian part of chromosome 16 from Catharine Brant- Hill via ancestor Lt. John Young. However, David Faux and his uncle Dale Williamson 9

10 may have received virtually the same block, but from John s brother Sgt. Daniel Young s wife Dorothy Windecker. Note that there are no Native Americans included in the HapMap database from which this data is obtained. Hence the segment in which these markers are embedded could come from any non European source (confirmed by the separate Eurogenes methodology). Conclusion: The fact that Robert Nelson (chromosome 1), Thomas Nelson (chromosome 8), and David Faux (chromosome 16) each have an African segment found in three different testing motifs, but none of the descendant s of Lt. John Young have any African indicators, suggests that the African may have come down from Dorothy Windecker (who is a double ancestor for David Faux and perhaps the Nelsons). Hence it is tentatively concluded that Dorothy Windecker s grandmother is, as the circumstantial evidence suggests, Eva Pickert, a mullato woman of Canajoharie. David K. Faux 23 November 2010 Caledonia Ontario and Seal Beach California Copyrighted material. 10