yDNA Haplogroup Q Project - Family Project Website

Background
Introduction to Q
Terminology
SNPs
Historic Phylogenetic Trees
STRs
Published Populations
References

Introduction

yDNA Haplogroups are based on SNPs, Single Nucleotide Polymorphisms, that occur in the non recombining region of the y-Chromosome. Haplogroup Q is one of two clades within the mega-Haplogroup P. It is defined by the SNP M242. This mutation is believed to have occurred 15,000 - 20,000 years ago. Q is found in Asia, the Americas, Europe, and the Middle East.

On May 5, 2008 Karafet 2008 was published in Genome Research. This rolled out the new Y-Chromosome Consortium Tree, YCC, which FamilyTreeDNA has adopted. The new tree has brought many changes to Q. The three prior defining SNPs, M242, P36, and MEH2 have been found to be non redundant.

"Clade Q

Clade Q is defined by the M242 mutation (Supplemental Fig. 15). Within this clade, there are 13 haplogroups marked by 17 SNPs, as well as an unmarked paragroup (Q*). Haplogroup Q is distributed widely in North Eurasia and is found at high frequencies in some Siberian groups (Karafet et al. 2002) and at low frequencies in Europe, East Asia, and the Middle East. It is also the major lineage among the Native Americans, with Q-M3 (Q1a3a) being almost completely restricted to the Americas (Zegura et al. 2004). Undifferentiated paragroup Q* is observed at low frequencies in India and Pakistan.

Major rearrangements

The M242 mutation is positioned upstream of P36.2. MEH2 was not typed in a set of our samples; however, there is evidence that MEH2 is a subset of the Q-P36.2 haplogroup (Peter de Knijff, pers. comm.)."

YCC 2008 Q Tree

P
- P*
- Q {M242}
  - Q*
  - Q1 {P36.2}
    - Q1*
    - Q1a {MEH2}
      - Q1a1 {M120, N14}
      - Q1a2 {M25, M143}
      - Q1a3 {M346}
        Q1a3a {M3}
        Q1a3a*
        Q1a3a1 {M19}
        Q1a3a2 {M194}
        Q1a3a3 {M199, P106, P292}
      - Q1a4 {P48}
      - Q1a5 {P89}
      - Q1a6 {M323}
    - Q1b {M378}
- R

Terminology

DNA

Deoxyribonucleic acid is the storage unit for all living things. It is made up of four bases: adenine (A), cytosine (C), guanine (G) and thymine (T), and is held together by a combination of esthers, phosphates, and sugars. Although DNA contains genes much of it is structural. DNA Genealogy utilizes these structural and non-coding regions.

Mutation

A mutation is any change in one of the base pairs of DNA.

Maximum

This is the upper bound or highest value in a range of results.

Mean

This is the average that most of us use in daily life. It is found by finding the sum of a group of and dividing it by the number in the group.

Median

This form of average gives us the middle score from a group of values.

Minimum

This is the lower bound or lowest value in a range of results.

Mode

This is the third type of average. It tells us, given a sample, what value occurs most often.

Mutation Rate

Mutation rates for STRs and SNP are predictions of how likely a mutation is to happen over a length of time. They should not be considered set or predictable like the ticking of a clock. Individual mutations are unpredictable like the number of times a year one forgets the car keys. They can be plotted over time though to create a backwards dating system with a reliability range. For the first 37 markers the Q Project uses the mutation rates from Chandler 2006.

Locus	Rate	Locus	Rate
DYS393	0.00076	DYS447	0.00264
DYS390	0.00311	DYS437	0.00099
DYS19	0.00151	DYS448	0.00135
DYS391	0.00265	DYS449	0.00838
DYS385*	0.00226	DYS464*	0.00566
DYS426	0.00009	DYS460	0.00402
DYS388	0.00022	Y-GATA-H4	0.00208
DYS439	0.00477	YCAII*	0.00123
DYS389i	0.00186	DYS456	0.00735
DYS392	0.00052	DYS607	0.00411
DYS389ii	0.00242	DYS576	0.01022
DYS458	0.00814	DYS570	0.00790
DYS459*	0.00132	CDY	0.03531
DYS455	0.00016	DYS442	0.00324
DYS454	0.00016	DYS438	0.00055

Please reference that work for confidence intervals and other details.

SNP

A Single Nucleotide Polymorphism is a change to a single position in DNA. That is a point in DNA that had read TTAGATA might now read TTAGACA.

Standard Deviation

Calculated as the square root of the variance, the standard deviation of a population tells us how much the values vary about the mean.

STR

A Short Tandem Repe