Monday, May 4, 2015

Ethnicity Chromosome Mapping & Determining "Ethnicity" of shared DNA segments between related individuals

>>>>> Savvy genealogists use autosomal DNA tests to explore their genetic ancestry along with such genetic tools (chromosome paintings and browsers, triangulation) to help them learn more about their relationships with genetic relatives by exploring specific DNA markers or segments shared with them. According to ISOGG, commonly used methods for this are "complementary" techniques known as  chromosome mapping ("determining which DNA segments came from which ancestor") and triangulation ("comparing matching DNA segments to determine which ancestor donated which particular segment"). However we also know that our genetic ancestry (colloquially known as "ethnicity") is more than just shared DNA segments. We often descend from numerous ancestries and thus have inherited DNA contributions from multiple biogeographical populations, often challenging our preconceived perceptions and assumptions about our genetic inheritance. For example "white" Americans with small amounts of "Sub Saharan African" DNA are likely to share only "European" admixture with their "black" American genetic relatives. People with multiple ancestries (ie Latinos, South Africans) or similar ancestries (ie Bulgarians) may share ethnic components contrary to what they might expect (ie Latinos sharing "Ashkenazi Jewish" DNA instead of Native American DNA, or Bulgarians sharing "South Asian" DNA segments due to Romani introgression). What's more adoptees and those with an unknown parent may not know anything about their ancestry. Therefore it's reasonable to assume that knowing the "ethnicity" of shared DNA segments between related individuals is an important consideration when doing genealogical research. Simply put, ethnicity matters! 
But how do we determine the "ETHNICITY" of these shared DNA segments? In this deep dive my objective is to discuss an underutilized (it's not new) method -- I'll coin this process Ethnicity Chromosome Mapping* (ECM) -- that can be used in conjunction with chromosome browsing, mapping and triangulation to determine the ethnicity of shared DNA segments as outlined here:

SECTION I.  Instructions (4 steps) for using ECM to find "Ethnicity" of shared DNA segments
-- STEP 1. Identify location and size of potential shared DNA segments using chromosome browsing and mapping tools (CBaMt)
-- STEP 2. Identify potential "ethnicity" of shared DNA segments using CBaMt
-- STEP 3. Find “START POINTS” AND “END POINTS” of shared DNA segments using CBaMt
-- STEP 4. Confirm “ethnicity” of shared DNA segments using Gedmatch's "Paint the Difference Between 2 Kits, 1 chromosome" tool
SECTION II. ECM Pitfalls and Technical Notes
-- (a) What happens when the "ethnicity" of shared IBD DNA segment does NOT match?
-- (b) Technical notes about Chromosome Paintings
-- (c) Technical notes about Gedmatch's "Paint the Differences..." tool

Your results and access to 23andMe, FamilyTreeDNAAncestryDNAand third-party site For optimal results, ECM works best under these conditions: 
*Disclaimer: The ECM methods presented herein are experimental, the term"ethnicity" has no legal meaning and is subject to DNA companies interpretation, so be careful about drawing conclusions. The term "Ethnicity Chromosome Mapping" is of my own invention and has not been endorsed by genetic genealogy organizations nor has it been adopted into genetic genealogy lexicon. You may also contact me with any comments or questions here:
Instructions (4 steps) for using ECM to find "ETHNICITY" of shared DNA Segments 
STEP 1. Identifying location and size of potential shared DNA segments 
(a) Firstly, I would like to introduce you to my sibling JR; my cousin ID; and my new genetic matches CF and sibling RF. I've invited them to help me demonstrate ECM, and you'll see them again as we go along. To initiate ECM whenever you get a genetic match (after taking an autosomal DNA test) or a newly tested relative's results come in, you need to learn some specifics about shared DNA segments. This includes SIZE (aka Genetic Distance, indicating the length of DNA segment in centimorgans); LOCATION on the chromosomes (aka Chromosome mapping; see Kitty Kooper's tool here), and IN COMMON WITH RELATIVES sharing mutual DNA segments [aka Triangulation; see various methods @  Kitty Kooper's chromosome mapper tool, Kelly Wheaton's Lesson 11, & Blaine Bettinger's Visual Phasing]. For ECM these tasks are easily achieved using your DNA company's in-house tools and third-party sites with such chromosome browsing, chromosome mapping and triangulation capabilities as:
  • 23andMe's Family Inheritance: Advanced (FIA) & DNA Relatives Triangulation tool (note: Countries of Ancestry tool is now defunct);
  • FTNDA's Family Finder - Chromosome Browser;
  • One to One tool (for AncestryDNA, 23andMe, FTDNA)