Y-DNA project help

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Ideogram of the Y chromosome

Newcomers of Y chromosome DNA tests and in Y-DNA projects (Haplogroups, Surname, Geographical) are often overwhelmed by the many technical terms used for testing Y-DNA listed here and in the Genetics Glossary.

Contents

Y chromosome

schematic how SNP mutations create haplogroups (clades) in the Y-tree
The Y chromosome (Y-DNA) is a DNA structure found in the nucleus of a male cell. Humans have 23 pairs of Chromosomes, 22 pair of autosomes and one pair of sex chromosomes, XX for females and XY for males. The Y chromosome is passed on without recombination by a father to his sons.

SNP

A SNP (Single-nucleotide polymorphism) happens when a single place in the genome sequence is altered during the cell formation process and this mutation persists in the progeny. A person has many inherited SNPs that together create a unique DNA pattern for that individual. Snips clarify the branching of a tree-separation of different subhaplogroups and to discover deep ancestry. A terminal SNP is the defining SNP of the latest subclade known by current research. It should be unique (UEP) and constant in time. ISOGG mantains a Y-SNP Index where synonymous names are listed.

Clade

Clade comes from the Greek word Klados = branch. A Clade on the Y chromosome tree is also called a Haplogroup. Subclade describes a sub-clade being downstream (occurring later in time). A Clade includes all the descendants of a single founder (common ancestor).

Ancestral/Upstream, Derived/Downstream

In the Y-tree older nodes (ancestors, toward the root) are Ancestral/Upstream. Younger nodes (descendants, toward the present) are Derived/Downstream.

Haplogroup

A Haplogroup is a branch of the human family tree. All men in the same Y-DNA haplogroup share the same SNP (unique marker in the Y-chromosome) which they have inherited from their common ancestor. The haplogroup is like a name for that common ancestor person. The haplogroup tells about current distribution and the migration patterns of the descendants of the haplogroup founder. The major Eurasian Y-DNA-haplogroups (E1b, G2a, I1, I2, J1, J2, R1a, R1b, etc.) formed over tens of thousands of years. In 2012 for many Y-DNA recent SNPs (under 3,000 years old) are available. These types of SNPs are informative for the historical time and sometimes can allow a connection to genealogical time.

Nomenclature System (YCC)

2002 the Y Chromosome Consortium (YCC) proposed two widely accepted nomenclature systems for Y-DNA haplogroups.[1] Major haplogroups are labeled with large capital letters (A–T). "Paragroups" are distinguished from haplogroups by using the * (star) symbol, which represents chromosomes belonging to a clade but not its subclades. Examples for the haplogroup definded by the SNPs L21/M529/S145 and L459:

  • Hierarchical system: R1b1a2a1a1b4 (FTDNA 2009), R1b1a2a1a1b3 (ISOGG 2012 v7.62), R1b1b2a1a2f (23andMe 2009).
  • Shorthand - SNP system: R-L21, R1b-L21, R-M529, R-S145. This system is more robust to changes in topology but widespread SNPs have often up to three synonymous names. For seldom and new terminal SNPs there is also the risk that they are not unique (recurrent) or not detectable with all lab methods.

Name Versions - Y-Chromosome Phylogenetic Trees

Since 2002 many new ramifications (SNPs) even in basal branches and subclades where found. The YCC [2], other scientific papers, societies and companies published substantial refining and updates to the Y-Chromosome Phylogenetic Tree, where the haplogroup names for deep clades often are different. In Genetic Genealogy the following name versions are important:

Y-STR - DYS values

STR (Short tandem repeat) is a short DNA motif (pattern). Y-STRs occur on the Y-DNA. DYS (DNA Y-Chromosome Segment) numbers show the repeats of an STR on that position. A DYS value tipically mutates with a certain (low) probability to a higher or lower value from generation to generation. By this DYS values are not unique and not constant in time.

Y-DNA - Haplotype

Y-DNA Haplotype is defined as one person's set of values for the DYS locations. A set of DYS values is highly informative for tracing recent ancestry (genealogical time). The quantity of needed DYS values depends on the research goal and the frequency of nearby haplotypes. For surname projects 12 or 25 markers can be enough, while for extended haplotpye studies (lineage distinction, pre surname time, SNP research) and to find more distant matches 37 to 111 markers are used. Modal haplotype is the most commonly occurring haplotype derived from a specific group. It should be near or identical to the common ancestor of that group.

Y-DNA - Matches

Y-DNA Matches are other kits (tested males) that have the same or similar numbers for the DYS values. While the same values usually are only probable in near relatives (father, son, brother, grandfather, cousins), step mutations can show a relation until many generations ago. In major european haplogroups (R1b-U106, R1b-U152, R1b-L21, I1-M255, E1b-M78, J2a-L26, G2a-L30, I2-M223, etc.) many subclades have overlapping haplotypes. In this cases only by high DYS coverage and positive testing of a recent terminal SNP the recent common ancestor is proven.

Cluster

A group of kits all together near by haplotype (Y-DNA matches) and having no discovered unique SNP defining a haplogroup is called Cluster. The given name is only temporary defined and usually only used within the project. It is interesting for members of a Cluster to work together for discovery of new SNPs (WTY, Y-Sequencing, Deep Clade test) and test funding of interesting and informative low coverage samples.

Y-STR testing

See Y-DNA STR testing chart, Y chromosome DNA tests

FTDNA Y-STR DYS Upgrade (Y-Refine)

  • Login to FTDNA (MyFTDNA) > Order an Upgrade > Order a Standard Test > Select A Product
  • Select your desired Upgrade:
    • 12 Marker kits: Y-Refine12to25 ($49), Y-Refine12to37 ($99), Y-Refine12to67 ($189);
    • 25 Marker kits: Y-Refine25to37 ($49), Y-Refine25to67 ($148);
    • 37 Marker kits: Y-Refine37to67 ($99), Y-Refine37to111 ($200);
    • 67 Marker kits: Y-Refine67to111 ($129)
  • Make your order clicking on Next, etc.

Y-SNP testing

Predominant Y-DNA-haplogroups in Europe

See Y-DNA SNP testing chart, SNP testing

If a terminal SNP can be predicted with high probability or not is depending on the haplotype frequency and number of DYS values. For a strong prediction, usually possible for seldom haplotypes with enough matches and kits with 67 or 111 markers, the testing of single SNPs is often the better choice. If a kit has low DYS coverage (12 to 37 markers), has no SNPs tested and matches to a huge haplotype cluster from different subclades a SNP test covering many SNPs at once is often the smarter solution. SNP chips provide a good value for the money, while Y-sequencing is the method providing deepest results down to "family haplogroups".

Genographic Project: Geno 2.0 SNP chip

Geno 2.0 test is available for $199.95 at the Genographic Project page and tests for over 12,000 Y-SNPs. It includes SNP results for mtDNA, auDNA and X-DNA. This chip-based test is since then promoted by FTDNA as replacement of the very solid Sanger-sequencing based FTDNA Deep Clade test ($129) with much less tested Y-SNPs, despite having failure on many well known Y-SNPs and some volatile results.

  • If you have received your results please transfer your data from Genographic Project Geno 2 (in Profile / Expert Options) for free to Family Tree DNA. Only by doing this Y-SNP results will be available in FTDNA projects.
  • Download also your raw data and submit it to haplogroup researchers.

BritainsDNA Chromo 2 Raw Y-DNA SNP chip

BritainsDNA and its associated companies for $199 (£129 or €160) look at over 15,000 Y-SNPs including all the SNPs on the ISOGG Y-SNP tree and additional SNPs not yet in the public domain. Only around 4200 of the Chromo 2 Y-SNPs overlap with the SNPs on the Geno 2.0 chip. This test is assumed to bring good results for haplogroups common in British Isles like R1b-L21.

23andMe SNP chip

23andMe v3 for $99 provides only a basic Y-haplogroup level covering 1,766 variants. It includes SNP results for mtDNA, auDNA and X-DNA.

FTDNA Single SNP test - Order an Advanced Test

  • Login to FTDNA (MyFTDNA) > Order an Upgrade > Order an Advanced Test > Select Filter Test Type SNP
  • Search for recommended SNP (for example L123) and Add it to the cart. Repeat the last step for additional SNPs.
  • Make your order clicking on Next, etc.

YSEQ Single SNP test (Sanger Sequencing)

Thomas and Astrid Krahn since November 2013 over YSEQ offer a menu of single SNPs to order. They charge $35 per SNP and new SNPs (so far discovered only through SNP chips or Y-sequencing) can be requested.

FTDNA Paternal Ancestor Info

For every Y-DNA project it is very informative and sometimes important if the oldest paternal line (biological father of the father of the father etc.) information is given completely. This setting can be entered/changed in myFTDNA > My Account > Most Distant Ancestors: Direct Paternal:

  • Country of Origin: enter the oldest known or strongly suspected country of origin of your Y-DNA. For example: "Germany". Otherwise enter "Unknown Origin".
  • Name: enter name, year born/dead, municipality/city/town/village, province/county/region; example: "John Schmid, 1788-1852, Augsburg, Swabia". If only one date is known add informations like "b. 1788", "d. 1852", the place information should be the oldest known (usually birth, then marriage or other records and then dead). If there was a known Non-paternity event (surname change) and the biological father is unknown please indicate the latest known male ancestor and his mother ("Martin son of Maria Miller, b. 1822, Augsburg, Swabia"). It is a common error that the paternal ancestor of Maria is indicated ("Georg Miller, 1730, Swabia") because this ancestor is not the genealogical Y-DNA ancestor (strict paternal line).
  • Ancestral Location Direct Paternal: enter the full location information: house/place/street, municipality/city, ZIP, province/county/region, country. For example: "Hauptmarktplatz, Hoher Weg, Augsburg, Swabia, Bavaria, Germany". Enter the coordinates: Latitude and Longitude

GEDCOM/Family Tree

For surname projects or when your paternal ancestors did often change location (region, countries) the uploading of a GEDCOM file (see Genealogy software) with all the paternal ancestors included will greatly help research and the finding of new connections. You help especially adoptees or unknown male offspring to find the possible generation of connection.

Y-Sequencing

An (almost) complete sequence (readout) of the Y-DNA and analysis of the data is the best available option to get all virtually available information on the Y-chromosome. If the coverage is good enough, all known SNPs can be checked and additionally new SNPs will be found. Since 2013 this service is available DTC (Direct To Consumer). For a good comparison see Y-DNA SNP testing chart.

Family Tree DNA Big Y

Y-DNA Sequencing is offered by Family Tree DNA for $695. It has been confirmed that the raw data will be available. Other information yet unknown (public results not yet available, expected in Feb. 2014).

FGC Comprehensive Y-Chromosome Sequencing

Y-DNA Sequencing including SNP and STR Reports is offered by Full Genomes Corporation for $1,250. Key information:

  • Raw data (BAM file): Read length 100 base pairs, Coverage 50x, 20-25 million bases are called from the ca. 58 million Y-chr bases (centromere and the huge q12 region not included), 12-16 mb are mappable.
  • SNP Reports: check for known Y-SNPs, Y haplogroup assignment, Report of private new SNPs (typically 25-40), approx. 1000 SNPs reported in total
  • STR Report: 300+ Y chromosome STRs (Markers)

YFull interpretation Y-Chromosome sequence

YFull offers analysis of Y-DNA sequences (raw data) for free (public samples for researcher and interpretation). Technical requirements raw files: Alignment BAM file, Coverage min 30X, Read length min 100 bp.

  • Haplogroup and SNPs: Your Y-haplogroup prediction and all known SNPs (over 30k without synonyms)
  • STR results: All known (over 440) Short Tandem Repeats extracted from Y-Chromosome (over 100 new)
  • Private SNP results: SNPs found only in your sample (comparison is done automatically and with all 1000 Genomes samples)
  • and other services

References

  1. Y Chromosome Consortium (2002-02). "A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups". Genome Research. doi:10.1101/gr.217602. http://genome.cshlp.org/content/12/2/339.full. Retrieved 2012-04-12. 
  2. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (2008-05). "New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree". Genome Research. doi:10.1101/gr.7172008. http://genome.cshlp.org/content/18/5/830. Retrieved 2012-04-12. 
  3. Let's All Start Using Terminal SNP Labels Instead of Y Haplogroup Subclade Names, Okay? http://www.yourgeneticgenealogist.com/2012/09/lets-all-start-using-terminal-snp.html

See also