Thursday, March 5, 2015

Breaking Through the Autosomal DNA Generation Barrier: Connecting to Distant Ancestors

   There has been much debate over the use of small autosomal DNA segments.  It is important to understand where they come from and how they can be used for genetic genealogy.  Small segments are considered noise and false matches.  There are too many small matches to make sense out of, but they are not necessarily false matches.  These segments have been in the population for longer than we thought.  When I match someone at 2 cM it is very likely that they are a 12th cousin, not a 5th cousin.  There is no reason for us to look for small segment matches until we understand where these segments originated.

   When we talk about autosomal DNA, we often over simplify the process of genetic inheritance.  The simple answer is that we inherit half of our DNA from dad and half from mom.  The common message is that with every generation the DNA contribution from an ancestor is randomized and reduced until it is insignificant.  Genetic inheritance is actually much more complex than that.  Complex in a great way.  There is a tremendous amount of ancestral information that we are just beginning to tap into.

   We inherit DNA from our parents and their ancestors in large sections.  Take a look at the graphic below.  Each example is the comparison of a grandchild to a set of paternal grandparents.  You can see in the first example that the grandchild inherited over two-thirds of their grandfather’s first chromosome intact (blue bars).  The remaining section of the first chromosome is from their grandmother.  In the third example, the grandchild has inherited the entire chromosome 14 from their grandmother.  It is physically possible that this grandchild could someday give one of their children the grandmother’s complete chromosome 14.  


In an effort not to over simplify, this is just half the story.  That grandchild has an equal contribution from their maternal grandparents. 

   In the examples above, we can visualize what happens when DNA recombines.  The first example shows where one section of the grandfather’s DNA swapped places with the grandmother’s DNA before it was inherited by the grandchild.  This is called crossover.  In the examples, a) is a single crossover, b) is a double crossover and c) has no crossover.  On average, each of our chromosomes experienced 2 or 3 crossovers before we inherited them.

   Where DNA crossover takes place on a chromosome is not random.  There are approximate locations where the chromosome is more likely to split.  These locations are cleavage sites. 


These locations exist because there are groups of genes along a chromosome that have a tendency to stay together.  These groups are part of gene linkage.  These linked genes only allow for chromosome splits at either end of their linked section.  In my research, the minimum size for one of these gene-linked sections is about 2.5 cM.  These small segments then travel in larger groups.


   In the graphic above, the blue bar represents about a 60 cM match.  The intersection between the black and orange ovals is about 2.5 cM and represents a minimum segment.  In this crossover recombination, the large segment actually split to the right of the minimum segment.  In a future crossover, the chromosome could split on the left side of the minimum segment, giving a large segment bound by the orange oval.

   Why are these minimum segments important?  My research shows that these segments stay in the gene pool for dozens of generations.  Over time, naturally occurring SNP mutations take place.  These minimum inherited segments (MIS) can be differentiated into family groups.

   In my research, I started with 28 well known US colonial surnames and 393 autosomal kits.  For each surname, the associated kits were triangulated.  If three or more kits match on the same segment, you can deduce that it came from a common ancestor.  Each of the surnames investigated had 6 to 13 distinct triangulated segments.  Taken together, these triangulated ancestral segments represent an autosomal haplotype that can be used to identify a descendant’s genetic connection to an ancestor.  Across all of the surnames, these distinct segments appear at recurring locations on each chromosome.  I have listed 21 of these ancestral loci in my paper.

   Not all ancestral segments are the same type.  The segments can be categorized into three groups.  The first category is Common to All.  The surnames in this study are predominantly European.  One segment has been identified on chromosome 2 that triangulates across all surnames.  This segment correlates to a Western Atlantic ethnicity and I call it the Western Atlantic Autosomal Haplotype (WAAH).  The Western Atlantic Autosomal Haplotype should not be confused with ancestry informative markers (AIMs).  The WAAH is composed of about 800 SNPs and there are only about 100 AIMs SNPs in that same stretch of chromosome 2.

   The next category is Shared.  Some segments can be attributed to two or more surnames.  There was considerable intermarriage between US colonial families.  That period was a bottleneck genealogically and genetically.  As two major families married, their combined DNA segments entered the gene pool and were reinforced as their descendants intermarried. 

   The third category is Unique.  These shared segments cannot be attributed to intermarriage of families.  Yet the resulting familial autosomal haplotypes are not composed of a single surname.  In the case of Benjamin Franklin, the genetic proximity to his wife, Deborah Read and his mother, Abiah Folger, may make it impossible to distinguish between Folger, Franklin and Read DNA.  Therefore, the haplotype represents the combined inheritance.  

   Here is one of my case studies.   Augustine Bearse was born in England in 1618 and died in Barnstable, MA before 1697.  The Bearse family was chosen due to my familiarity with the genealogy and the debate surrounding Augustine’s wife.  His wife Mary was supposedly the granddaughter of the Chief of the Cape Cod Native American tribes.  The goal was twofold;  to identify the autosomal haplotype for the Bearse family and determine whether any of the ancestral segments had Native American ethnicity.

   The Bearse study was composed of 48 autosomal samples.  These samples were collected based on claimed genealogical connections.  The triangulated samples generated 8 ancestral loci and indicated an additional 5 loci that had the potential to triangulate with more samples.  The resulting Bearse autosomal haplotype is found below.

Bearse Autosomal Haplotype

   The Bearse haplotype contains the Western Atlantic Autosomal Haplotype (chromosome 2) which is common to all haplotypes in the study.  The other 12 loci are more valuable for genealogical validation.  One of the Bearse descendants triangulates on six of the ancestral segments.  It is highly unlikely that a descendant would match on all of the segments.  Although ancestral segments survive over the generations, the randomness of their distribution makes it difficult for any one person to have received them all.  Yet, triangulating on just one segment unique to Bearse is enough to indicate and validate a relationship.  Lack of a match could mean that an ancestral segment was not inherited or that a non-familial event (adoption, infidelity, etc.) has occurred and the individual’s family tree is incorrect.

   In order to investigate the origins of Augustine’s wife Mary, each ancestry segment from the haplotype was evaluated for ethnicity.  Only the segment on chromosome six at location 55850885 had any Native American ethnicity.  This ancestral segment had not fully triangulated, yet a few of the samples match exactly on Native American SNPs.  With additional samples, the segment could triangulate.  Once validated, the segment might be shared across multiple surnames or unique to Bearse, indicating Native American genes in the Bearse descendants.

   While the amount of autosomal DNA received by each successive generation is only half from each parent, that does not mean that given enough generations a distant ancestor’s genetic contribution will become negligible.  Through genetic linkage, portions of DNA are inherited intact.  Naturally occurring cleavage sites allow for ancestral segments averaging 2.5 cM to be passed from generation to generation as a minimum inherited segment (MIS). 

   Ancestral segment analysis is invaluable for the identification of distant ancestors.  All of the triangulated ancestral locations combine to become a Familial Autosomal Haplotype (FAH) that can be used to validate family history.

   Since finishing my initial research, I have gone on to identify over 50 ancestral loci and over 700 autosomal haplotypes for US colonial ancestors.  Stay tuned for further advances in autosomal research.

References:

Maglio, MR (2015) Minimum Inherited DNA Segment Size and the Introduction of Familial Autosomal Haplotypes (Link)

Website:

© 2015 Michael Maglio and OriginsConnector.  All Rights Reserved.


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