What is Y-chromosome Analysis

&

How is it Useful in Genealogy?

The study of Y-chromosomes is similar to the study of male surnames — Y-chromosomes are passed down from biological fathers to their sons. Sons inherit one Y-chromosome from their biological father and sons inherit one X-chromosome from their mother at the time of conception. In contrast, daughters inherit one X-chromosome from their biological father and one X-chromosome from their mother. Males have a Y-chromosome, females do not.

So, the study of Y-chromosomes is the study of the history of Y-chromosomes over time as they are passed from biological father to son to grandson to great-grandson, along an unbroken line of biological fathers and sons.

In many western societies, the surname of the male parent is passed from the father to the son by social custom. So in any many ways in many western societies, the study of Y-chromosomes is similar to the study of male surnames, with some important possible differences.

Y-chromosome analysis can be used to confirm or rule out a close biological relationship among males who do not have traditional paper proofs to establish their genealogy. A good application of Y-chromosome analysis is assisting families that immigrated from one country to another during the past 300 years and the trail of paper proofs is difficult to find or they no longer exist. This analysis can also be used to establish biological family groups of individuals in a single county that are unaware they are closely related because of spelling differences in the surname, etc.

Females who can prove a biological relationship to a living male whose Y-chromosome can be matched with other closely related males can benefit from a Y-chromosome study. Females can't be DNA sources in the project because they don't have a Y-chromosome.

Y-chromosomes change gradually over time in most cases — The process of copying Y-chromosomes (and other chromosomes) from one generation to the next is mostly an error-free process. If the copying process made a lot of mistakes in each generation, it would be disastrous for the offspring and for the whole human race; we would not exist as a species. Although the process of copying the Y-chromosome from one generation to the next is mostly error-free, some errors do occur from time to time, and these errors in copying the Y-chromosome can be passed down from fathers to sons.

The rate at which errors, also called mutations, occur while copying Y-chromosomes is important. If the errors are extremely rare (say one mutation every 500,000 years for example), it would be impossible to make meaningful comparisons between Y-chromosomes from two males because all Y-chromosomes would look pretty much alike. If, on the other hand, mutations occur at a fairly high rate (say one mutation in each generation) it would be difficult to compare Y-chromosomes and group them together as being related because all the Y-chromosomes would have many differences. In other words, it would be hard to see the pattern of inheritance from one generation to the next if the mutation rate is fairly high.

Fortunately, there are a number of locations on the Y-chromosome where mutations occur at about the right rate (about one mutation in every 15 to 50 generations), to be useful in comparing Y-chromosomes passed down from fathers to sons to grandsons, etc. By analyzing 10 or more locations, also called loci (loci is plural of locus; from Latin meaning place) by scientists, on the Y-chromosome, it is possible to group Y-chromosomes together based on their descent from a common ancestor. The more loci that are compared, the more information can be decerned for individuals in an extended family lineage.

The names of the loci that are examined during the analysis of the Y-chromosome by have long names, with short abbreviations. These loci names begin with the letters DYS. There are other loci on the Y-chromosome that can be examined and they go by other names.

Y-DNA12 Test

In the table above, the numbers in columns under the name of each DYS locus represent the physical length of repeated DNA found at that locus. DYS loci consist of short segments of repeated DNA. Each row in the table above represents a male who has had these loci sequence.

Sometimes when a Y-chromosome is copied and passed on to a male child, the cellular machinery makes a mistake when copying DYS DNA: (1) sometimes adding an additional repeat; (2) sometimes deleting a repeat, and more rarely, (3) adding two repeats or deleting two repeats.

It is important to know that Y-chromosome markers like the DYS loci are inherited by a male as a single block. Because males have only one Y-chromosome per cell, scientist use the term haploid to describe this condition. In contrast other chromosomes a male has in his cells are present in pairs, a condition called diploid. A particular combination of Y-chromosome loci, all of the markers in a single row in the table above, are referred to as a haplotype.

In the table above, individual #2 is much more closely related to individual #1 and individual #3 than he is to individual #4. The light green shaded area in the table is a group of closely related indiviuals. The yellow cells in the table indicate differences found in relation to individual #2. Individual #4 belongs to a different family group.

Based on the statistics of comparing these ten DYS loci, individuals that differ by only one or two changes, or mutational events, are considered closely related. More than two differences indicates a much more distant relationship that is not useful for genealogy. By extending the analysis to 25 or 37 DYS loci much more can be descerned about the relationship of individuals 1, 2 and 3 in the above table.

Individual #4 differs from all the others by at least three loci (and by 4 or 5 mutational events compared to #2), and is considered to be only distantly related.

How much you can learn from Y-chromosome analysis depends on:

1. Choosing how many loci to compare between Y-chromosomes—Bruce Walsh at the University of Arizona in his paper in the scientific journal Genetics 158: 897-912 (June 2001) titled Estimating the Time to the Most Recent Common Ancestor for the Y chromosome or Mitochondrial DNA for a Pair of Individuals, outlines the statistical basis for determining how many markers are needed to group Y-chromosomes into biological family groups. The minimum number of markers appears to be 10. The more markers analyzed, the more precisely lineages can be examined. As Y-chromosome mapping becomes more prevelant, we should expect the cost per maker to decline and the number of markers that can be analyzed to increase.
2. Choosing the right loci to look for mutations on the Y-chromosome. Loci mutate at different rates, so choosing the right loci is important. Kayser et. al. [this is a pdf file] in their paper titled Characteristics and Frequency of Germline Mutations at Microsatellite Loci from the Human Y Chromosome, as Revealed by Direct Observation in Father/Son Pairs, Am. J. Hum. Genet. 66:1580 - 1588, 2000 established direct experimental evidence to support mutation rates at Y-chromosome loci in father-son pairs.
3. The number of individuals participating in a Y-chomosome project is important to establish the halpotype of a family group. The more individuals that participate, the more confident we can be of grouping individuals together as family groups.

Return to project home page.

Return to Jim Sims home page.

Inquires regarding the information on this page should be directed to Jim Sims. This page was last updated on Monday, 14 February, 2005 10:38 PM , Central Time, USA.