Y-chromosomal haplogroup R1a - PART ONE.

Y-chromosomal haplogroup R1a - PART ONE.

Some of you have probably wondered why it is named like that and how the “fun” has started. In other words – what’s the genesis behind an R1a as an abstract relationship of letters and number. It will need a necessary review of background before final move to the point. 

Most of us have already met the developed form, to put it like that. We are tested using at least 12(+2) Y-STRs (Y-37 is a standard) and given prediction or genotyped using custom chip. Some of us even had a pleasure to undergo a full genome research or form of sequencing reserved for Y-Chromosome. Genetic industry is literally developing before our eyes. But…it had to begin someday.

It shouldn’t be especially difficult to explain, because timeline of genetic genealogy from perspective of Y-Chromosome is relatively brief. Do you want to hear some history? Here we go.

Y-Chromosome. It doesn't look so pretty in reality ;)

         Y-Chromosome is an inherent element of a male genetics and since it was discovered in 1905¹, it’s role has always been within a scope of interest of many people from scientific world. We had to wait few decades until new perspectives were opened after discovery of DNA. It turned out that DNA located on Y-Chromosome (aside pseudo-autosomal region of 3Mbp length²) doesn’t recombine and therefore, may be used for research on paternity. And soon, scientists started to seek for relatedness of males, this time using microsatellite polymorphisms. Polymorphism needs to be explained.  Let’s use a definition made by Cavalli-Sforza and Bodmer (1971). Genetic polymorphism is the occurrence in the same population of two or more alleles at one locus, each with appreciable frequency"(minimum - 1%³). Basically speaking, POLYMORPHISM means an existence of differences in the DNA of population. We can distinguish two types of polymorphisms, which are of our use – microsatellite and single-nucleotide ones (SNPs).  There were two reasons that prevailed in the initial success of microsatellite polymorphisms. First – microsatellite polymorphism can be read by simple measuring its length, counted in base pairs. Second reason was probably the most decisive one - one small set of chromosome locations can be measured ACROSS ALL MEN REGARDLESS OF HAPLOGROUPS. It is clear, isn’t it?

 Why it is called “micro”, then? DNA fragments looked for are really short (2-5 base pairs) and they are repeated, typically from 5 to 50 times⁴. They occur at various locations in human genome and aren’t limited to Y-Chromosome. Term “satellite”, on the other hand, originates from experiments with centrifugation of genomic DNA in a test tube – this process resulted with separating layer of bulk DNA from accompanying (thus: “satellite”) layers of repetitive DNA.

Microsatellite polymorphism when located on Y-Chromosome, is called Y-STR (STR - short tandem repeat, a term typically used by forensic geneticists). It took a lot of effort to find and select Y-STRs that were valuable enough for genetic genealogy. That’s because there is a lot of variance between them – with some microsatellites mutating too fast/too slow or with generally unstable character. It wasn’t easy to fish out the most worthy ones.
First was DYS19 (Roewer et al 1992⁵), in the next row came YCAII a/b (Mathias et al 1994⁶), DYS389 I/II, DYS390, DYS391, DYS392, DYS393 (Roewer et al 1996⁷). In the year of 2000 and 2002 many useful markers from DYS4XX series were found.

After about 8 years from the first discovery, list of solid Y-STR markers was complete enough to sell it as a commercial product. Who was first? An American company Family Tree DNA (FTDNA) located in Houston, Texas. It was available for anyone who offered enough $. Do some of you still remember introductory prices?

Years have passed, number of testable markers grown and hence the accuracy – also the costs have lowered considerably over time.  Y-STRs generally allow to form clusters consisting of related males - especially in macro-scale, by which I mean a distant relationship.  Higher number of shared Y-STRs, particularly “innovations” (rare values not found elsewhere or combinations of such values) may indicate a close relationship between the tested. The problem begins when we want to evaluate loose relationship between totally random people or when we have a significant amount of data. Data that is coming from population study, for instance. The relevant question is -how to test hundreds of people and don’t get overwhelmed with results? Such huge amount of genetic data has to be orderly and Y-SNPs came here with support. This process resulted later with the division into named Y-haplogroups, like R1a, E, I1 etc. It will be explained at the second part of an entry, because it started to be quite lengthy.

We shouldn't be serious all the time...

 See you soon!

Sources: 

1. Brush, S G (Jun 1978). “Nettie M. Stevens and the discovery of sex determination by chromosomes". Isis; an international review devoted to the history of science and its cultural influences (United States) 69 (247):163–72. doi:10.1086/352001. ISSN 0021-1753. PMID 389882.

2. Mangs H, Morris. “The Human Pseudoautosomal Region (PAR): Origin, Function and Future”. Curr Genomics. 2007 Apr; 8(2): 129–136. PMCID: PMC2435358

3. Philip Hedrick. Genetics of Populations. Jones & Bartlett Learning. pp. 104–
 ISBN 978-0-7637-5737-3

4. Turnpenny P, Ellard S (2005). Emery's Elements of Medical Genetics, 12th. ed. London: Elsevier.

5. Roewer L, Arnemann J, Spurr NK, Grzeschik KH and Epplen JT (1992). Simple repeat sequences on the human Y chromosome are equally polymorphic as their autosomal counterparts. Hum Genet 89: 389–394

6. Mathias N, Bayes M, Tyler-Smith C (1994) Highly informative compound haplotypes for the human Y chromosome. Hum Mol Genet 3: 115–123

7.  L Roewer, M Kayser, P Dieltjes, M Nagy, E Bakker, M Krawczak, P de Knijff. Analysis of molecular variance (AMOVA) of Y-chromosome-specific microsatellites in two closely related human populations. Hum Mol Genet, 5 (1996), pp. 1029–1033