Sunday, October 22, 2017

Guide to Building Your Family Haplotree

I've been working on a pet project to supplement my genealogical research, and in this deep dive I'm going to share it with you as follows:

I. Mitochodrial-DNA & Y-DNA Testing Options 
II. Intro to Family HaploTree Building
III. Constructing Your Family HaploTree
IV. Proving Family Anecdote with HaploTree Building

As a genetic genealogist I'm keen to know if there are haplogroups in my pedigree that are rare, newly discovered or only found in specific populations and biogeographical regions. I'm also looking to use haplogroups for ancient ancestral research, to help me trace family surnames that have disappeared in the bowels of the Trans-Atlantic slave trade as well as the migration paths of my immigrant forebears from their homelands to the Americas. 

Since learning about my own Maternal (or mitochondrial DNA) and Paternal (or Y-chromosome DNA) Haplogroups, I'm naturally inquisitive about the ones that I DIDN'T inherit from my parents and other direct pedigree relatives (grandparents, great-grandparents, 2nd-great-grandparents, 3rd-great-grandparents, etc).

Based on the unique inheritance patterns of human Mitochondrial DNA (Mt-DNA) and Y-chromosome DNA (Y-DNA), a child only inherits their mother's mt-DNA haplogroup through a direct matrilineal line (ie from his/her mother, her mother, her mother, etc), and if male his father's Y-DNA haplogroup through a direct patrilineal line (ie from his father, his father, his father, etc). 

This means a child (me) never inherits their father's maternal haplogroup nor from their mother's father. Going to the next generation [my 4 grandparents] this leaves four more haplogroups (3 mt-DNA and 1 Y-DNA) that I wouldn't inherit. And even more in the next generation [from my 8 great-grandparents]. 

Yet these are my direct forebears and even though I didn't inherit their haplogroups directly it means that by extension I biologically descend from an ancestor bearing the haplogroup. So it becomes genetically and genealogically relevant for me. [Be sure to read Section IV to learn about an intriguing haplogroup discovery in my family pedigree.]

Ultimately I want to identify, document and trace all of my other direct fore-parents' haplogroups back to their root populations to reveal what stories they tell. 

I. Mt-DNA & Y-DNA Testing Options

In this first section I discuss mtDNA and Y-DNA testing options. You will need these tests to find out about these other haplogroups in your family. It'a also important to take the right kinds of DNA tests for this project.  

The testing options listed below focus on mtDNA and Y-DNA, including stand-alone products (separate mtDNA and Y-DNA tests), packaged products (mtDNA, Y-DNA, autosomal-DNA for one price), and whole genomic sequencing options. I recommend taking a high resolution mtDNA and Y-DNA test, but as you test more relatives it may be economical to choose a basic test for them.
  • Reminder: For this project, I highly recommend each of your relatives first do an autosomal DNA test to confirm the relationship between you and your shared fore-parent. 
23andMe ($99 US) — offers basic haplogroup assignment predictions based on low coverage mtDNA and Y-DNA, included with its autosomal DNA test product. Haplogroup assignment generally accurate, but may not be as specific because 23andMe utilizes the outdated Build 7 platform.
Noteworthy: If you're watching your budget 23andMe is the most economical option to test learn about the basic (low res) haplogroups of your direct relatives. 

Nebula Genomics ($299 US + subscription*) — offers whole genomic sequence testing (30x or 100x, priced higher) testing. Primarily a health testing site, Nebula is joining the genetic genealogy world. COMING SOON (4Q2020) "Deep Genetic Ancestry" testing with full Y-DNA and mitochondrial-DNA haplogroup reporting via partnership with FamilyTreeDNA. 
Noteworthy: Most economical Whole Genomic Sequence test on the market to date. FREE access to your raw data (BAM, FASTQ) files for upload to third-party sites that interpret Y-DNA and mtDNA data. *Subscription options are for customers who want continuous updates and new reports. 

FamilyTreeDNA (price varies) — offers a range of mtDNA, Y-DNA, and autosomal DNA testing, but I recommended only the Full Mitochondrial Sequence test ($199 US) and Big Y 700 ($449* US). FTDNA's mtDNA and Y-DNA tests are separate products so testing can get pricey.
Noteworthy: FTDNA has the largest database of mtDNA and Y-DNA testers; largest Y-DNA phylotree, and offers haplogroup projects you can join. 

Full Genomes Corp — offers an array of whole genome sequencing (from $675) and Y-DNA products, including the high resolution Y-Elite test ($425, Y-DNA only). Interpretation services included in the cost of some products but offered as stand-alone product as well (from $75).
Noteworthy: Full Genome Corp. offers a payment plan option to help defray costs. Has highest quality results of competitive Y-DNA and WGS 30x tests. 

YSEQ — offers whole genome sequencing tests (from $740), and an array Y-DNA STR and SNP panels (from $18.00). Includes deep sequencing for mt-DNA and Y-DNA with whole genome sequencing product. Interpretation services included. 
Noteworthy: YSEQ helped discover the oldest Y-DNA haplogroup ever found to date, changing what we know about Y-DNA phylogeny. [Read my A00 Cameroon story here].

Dante Labs (starting $599) — offers whole genomic sequence testing (30x) and a range of other products. Primarily a health testing site, whole genomic sequence test is good quality
Free access to your raw data files (BAM, FASTA) for upload to third-party sites that interpret Y-DNA and mtDNA data.
Noteworthy: Dante Labs on sale can be as low as $199 for a WGS 30x test.

King Genome's Tips:
  • James Lick's excellent mtDNA Haplogroup Analysis tool. When you upload your mt-DNA raw data files from AncestryDNA, 23andMe and FamilyTreeDNA (FASTA), it will be conformed to the new build. This could lead to a better mt-DNA haplogroup prediction.
  • For males taking high-resolution Y-DNA tests and both sexes taking full mitochondrial DNA testings, you can upload your raw data file (BAM or vcf) to YFull ($49 US), an interpretation service for next generation sequencing products. Please read Linda Thompson Jonas's excellent blogs here and here to learn more about the importance of deep Y-DNA testing.
II. Intro to Family HaploTree Building
Source: National Genographic screenshot