The Y chromosome
In humans the Y chromosome is approximately 60 Mb long (million base pairs) long and contains just 78 genes . The SRY gene (sex-determining region Y) located on the Y chromosome encodes a protein that triggers the development of the testes and through an extended hormonal pathway causes a developing foetus to become male . With the exception of two regions, PAR 1 and 2 (PAR = pseudoautosomal region), located at the tips of the chromosome, no recombination occurs during meiosis. The remaining 95% of the Y chromosome is non-recombining, male specific, and is passed from father to son unchanged, except when mutations occur. The lack of recombination may be the reason why there are relatively few genes on the Y chromosome. If there is no chromosome crossing over, mutations within genes have little chance to be repaired or rectified and hence will be passed onto the next generation.
Y chromosome polymorphisms
The Y chromosome contains a large number of polymorphisms including variable number  and short tandem repeats (VNTRs and STRs), insertions, deletions and single nucleotide polymorphisms (SNPs). The first STR locus to be identified on the Y chromosome was DYS19 . Since then hundreds of Y chromosome STR have been described. The development of Y STR typing has mirrored the development of the autosomal STRs, and multiplexes have been developed with increasing numbers of robust and highly discriminating Y STR multiplexes [43-46]. The growth in interest in Y STR loci has led to numerous
population studies to establish allele frequency databases. The ‘Y Chromosome Haplo- type Reference Database’ was established to collate STR haplotypes (www.yhrd.org). To ensure comparability between datasets, minimal and extended haplotypes were defined. Two commercial kits, the PowerPlex® Y (Promega Corporation) and the AmpFISTR® Yfiler® (Applied Biosystems) incorporate all of the extended haplotype loci (Table 13.2).
Forensic applications of Y chromosome polymorphisms
That the Y chromosome is only found in males makes it a valuable tool, in particular for the analysis of male and female mixtures after sexual assaults when differential DNA extraction is not possible; Y STR analysis has been successful with female:male ratios of up to 2000:1 . The presence of male DNA has also been detected when vaginal swabs are analysed, even when no spermatozoa have been detected – either through the assailant being azoospermic (1-2% of rape cases) or through the deterioration of the spermatozoa [44,48]. The Y STRs can also be used to detect the presence of two male profiles – the interpretation of the mixtures depends on the presence of major and minor contributors .
In addition to using Ychromosome testing for the identification of evidential samples, it has also been used for paternity testing and is particularly valuable in deficient cases, where the alleged father is not available for testing. In these cases, any male relative who is paternally related to the alleged father can be used as a reference. An extreme example of where this has been used is the paternity analysis that linked the third US president, Thomas Jefferson to the child of one of his slaves, Sally Hemings . Cases involving human identification have also used the Y chromosome as a tool to link remains to paternal family members, and as with deficient paternity cases the use of the Y chromosome is particularly advantageous when there are no parents or children to use as reference material; it also simplifies the sorting of the material following mass disasters . The mutation rate in Y STR loci is similar to autosomal STRs, at approximately 2.8 × 10−3 [51, 52]. The Y chromosome will accumulate mutations as it is passed through the patrilineal line and direct comparison between males on the same lineage may result in a false exclusion if mutations are not considered. The non-random distribution of the Y chromosome among global populations, due largely to the widespread practice of patrilocality [53, 54] (where the female moves to the male’s birth place/residence after marriage), makes it a useful tool for inferring the geographical origins of biological material recovered from a crime scene and human remains . In some cultures, where the male name is passed onto male children, there is also the potential of attributing surnames to Y profiles [56, 57].
Interpretation and evaluation of Y STR profiles
When the Y chromosome profiles from a reference and an unknown sample match, the significance of the match has to be assessed. The first step is to assess the frequencies of the Y STR haplotypes in the population of interest. The simplest method is to report the frequency of the Y STR haplotype in the population, known as the counting method. The figure quoted is entirely dependent upon the size of the database and is normally based on frequency databases that are constructed for the major ethnic groups represented within individual countries, although comparisons can also be made to the combined data in the yhrd databases with over 40000 haplotypes (representing at least the minimal haplotype). So, for example, a match can be reported as ‘the haplotype has been seen twice in 400 UK Caucasian individuals’. Difficulties arise in the interpretation of the Y chromosome. This is primarily caused by the patrilineal inheritance and clustering of male family members in relatively small geographic areas. This geographical clustering of male relatives coupled with the limited size of the haplotype frequency databases (many haplotypes are seen only once) makes the estimation of profile frequencies hazardous. An alternative method for assessing the significance of a match is to use a likelihood ratio and to incorporate population subdivisions with the increased potential for common co-ancestry . Re- gardless of the method used to calculate the matching frequency, when presenting the results of Y chromosome analysis, as with mtDNA, there is a need clearly to state how the use of Y STR typing varies from that of autosomal markers and that there will be other males in the population with the same Y STR haplotype.
Jobling, M., Hurles, M., and Tyler-Smith, C. (2004) Human Evolutionary Genetics: Origins, Peoples and Disease. Garland Science. Cavalli-Sforza, L.L., Menozzi, P., and Piazza, A. (1996) The History and Geography of Human Genes. Princeton University Press.
The Y Chromosome Haplotype Reference Database: http://www.ystr.org/index.html
EMPOP – Mitochondrial DNA Control Region Database: http://www.empop.org/
1.Giles, R.E., et al. (1980) Maternal inheritance of human mitochondrial-DNA. Proceedings of the National Academy of Sciences of the United States of America-Biological Sciences 77, 6715- 6719.
2.Shitara, H., et al. (1998) Maternal inheritance of mouse mtDNA in interspecific hybrids: segre-gation of the leaked paternal mtDNA followed by the prevention of subsequent paternal leakage. Genetics 148, 851-857.
3.AnkelSimons,F.,andCummins,J.M.(1996)Misconceptionsaboutmitochondriaandmammalian fertilization: implications for theories on human evolution. Proceedings of the National Academy of Sciences of the United States of America 93, 13859-13863.
4.Thompson, W.E., et al. (2003) Ubiquitination of prohibitin in mammalian sperm mitochondria: possible roles in the regulation of mitochondrial inheritance and sperm quality control. Biology of Reproduction 69, 254-260.
5.Schwartz, M., and Vissing, J. (2002) Paternal inheritance of mitochondrial DNA. New England Journal of Medicine 347 (8), 576-580.
6.Garrido, N., et al. (2003) Composition and dynamics of human mitochondrial nucleoids. Molec- ular Biology of the Cell 14, 1583-1596.
7.Cavelier, L., et al. (2000) Analysis of mtDNA copy number and composition of single mitochon- drial particles using flow cytometry and PCR. Experimental Cell Research 259, 79-85.
8.Margineantu, D.H., et al. (2002) Cell cycle dependent morphology changes and associated mi- tochondrial DNA redistribution in mitochondria of human cell lines. Mitochondrion 1, 425-435.
9.Robin, E.D., and Wong, R. (1988) Mitochondrial-DNA molecules and virtual number of mito- chondria per cell in mammalian-cells. Journal of Cellular Physiology 136, 507-513.
10.Bogenhag, D., and Clayton, D.A. (1974) Number of mitochondrial deoxyribonucleic-acidgenomes in mouse L and human Hela cells – quantitative isolation of mitochondrial deoxyri- bonucleic acid. Journal of Biological Chemistry 249, 7991-7995.
11.Anderson, S., et al. (1981) Sequence and organization of the human mitochondrial genome. Nature 290, 457-465.
12.Andrews, R.M., et al. (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nature Genetics 23, 147-147.
13.Dyall, S.D., et al. (2004) Ancient invasions: from endosymbionts to organelles. Science 304, 253-257.
14.Brown, W.M., et al. (1979) Rapid evolution of animal mitochondrial-DNA. Proceedings of the National Academy of Sciences of the United States of America 76, 1967-1971.
15.Hashiguchi, K., et al. (2004) Oxidative stress and mitochondrial DNA repair: implications for NRTIs induced DNA damage. Mitochondrion 4, 215-222.
16.Parsons, T.J., et al. (1997) A high observed substitution rate in the human mitochondrial DNA control region. Nature Genetics 15, 363-368.
17.Forster, L., et al. (2002) Natural radioactivity and human mitochondrial DNA mutations. Pro- ceedings of the National Academy of Sciences of the United States of America 99, 13950-13954.
18.Tamura,K.,andNei,M.(1993)Estimationofthenumberofnucleotidesubstitutionsinthecontrol region of mitochondrial-DNA in humans and chimpanzees. Molecular Biology and Evolution 10,512-526.
19.Meyer, S., et al. (1999) Pattern of nucleotide substitution and rate heterogeneity in the hypervari- able regions I and II of human mtDNA. Genetics 152, 1103-1110.
20.Excoffier, L., and Yang, Z.H. (1999) Substitution rate variation among sites in mitochondrial hypervariable region I of humans and chimpanzees. Molecular Biology and Evolution 16, 1357- 1368.
21.Carracedo, A., et al. (2000) DNA commission of the International Society for Forensic Genetics: guidelines for mitochondrial DNA typing. Forensic Science International 110, 79-85.
22.Melton,T.,andNelson,K.(2001)ForensicmitochondrialDNAanalysis:twoyearsofcommercial casework experience in the United States. Croatian Medical Journal 42, 298-202.
23.Melton, T., et al. (2005) Forensic mitochondrial DNA analysis of 691 casework hairs. Journal of Forensic Sciences 50, 73-80.
24.Hopwood, A.J., et al. (1996) DNA typing from human faeces. International Journal of Legal Medicine 108, 237-243.
25.Goodwin, W., et al. (1999) The use of mitochondrial DNA and short tandem repeat typing in the identification of air crash victims. Electrophoresis 20, 1707-1711.
26.Holland, M.M., et al. (1993) Mitochondrial-DNA sequence-analysis of human skeletal remains- identification of remains from the VietnamWar. Journal of Forensic Sciences 38, 542-553.
27.Gill, P., et al. (1994) Identification of the remains of the Romanov family by DNA Analysis. Nature Genetics 6, 130-135.
28.Stone, A.C., et al. (2001) Mitochondrial DNA analysis of the presumptive remains of Jesse James. Journal of Forensic Sciences 46, 173-176.
29.Ivanov, P.L., et al. (1996) Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II. Nature Genetics 12, 417-420.
30.Stoneking,M.,etal.(1995) Establishing the identity of Anderson Anna Manahan. Nature Genetics 9,9-10.
31.Marchington, D.R., et al. (1998) Evidence from human oocytes for a genetic bottleneck in an mtDNA disease. American Journal of Human Genetics 63, 769-775.
32.Sekiguchi, K., et al. (2003) Inter- and intragenerational transmission of a human mitochondrial DNA heteroplasmy among 13 maternally related individuals and differences between and within tissues in two family members. Mitochondrion 2, 401-414.
33.Chinnery, P.F., et al. (2000) The inheritance of mitochondrial DNA heteroplasmy: random drift, selection or both? Trends in Genetics 16, 500-505.
34.Lagerstrom-Fermer, M., et al. (2001) Heteroplasmy of the human mtDNA control region remains constant during life. American Journal of Human Genetics 68, 1299-1301.
35.Brenner, C.H., and Weir, B.S. (2003) Issues and strategies in the DNA identification of World Trade Center victims. Theoretical Population Biology 63, 173-178.
36.Goodwin, W., et al. (2003) The identification of a US serviceman recovered from the Holy Loch, Scotland. Science and Justice 43, 45-47.
37.Balding, D.J. (2005) Weight-of-evidence for Forensic DNA Profiles, John Wiley & Sons.
38.Buckleton, J., et al. (2005) Forensic DNA Evidence Interpretation, CRC Press.
39.Skaletsky, H., et al. (2003) The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825-U822.
40.Sinclair, A.H., et al. (1990) A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif. Nature 346, 240-244.
41.Jobling, M.A., et al. (1998) Hypervariable digital DNA codes for human paternal lineages: MVR- PCR at the Y-specific minisatellite, MSY1 (DYF155S1). Human Molecular Genetics 7, 643-653.
42.Roewer, L., et al. (1992) Simple repeat sequences on the human Y-chromosome are equally polymorphic as their autosomal counterparts. Human Genetics 89, 389-394.
43.Butler, J.M., et al. (2002) A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers. Forensic Science International 129, 10-24.
44.Gusmao, L., et al. (1999) Y chromosome specific polymorphisms in forensic analysis. Legal Medicine 1, 55-60.
45.Mulero, J.J., et al. (2006) Development and validation of the AmpFlSTR (R) Yfiler (TM) PCR amplification kit: a male specific, single amplification 17 Y-STR multiplex system. Journal of Forensic Sciences 51, 64-75.
46. Krenke, B.E., et al. (2005) Validation of a male-specific, 12-locus fluorescent short tandem repeat (STR) multiplex. Forensic Science International 148, 1-14.
47. Prinz, M., et al. (1997) Multiplexing of Y chromosome specific STRs and performance for mixed samples. Forensic Science International 85, 209-218.
48. Sibille, I., et al. (2002) Y-STR DNA amplification as biological evidence in sexually assaulted female victims with no cytological detection of spermatozoa. Forensic Science International 125, 212-216.
49. Foster, E.A., et al. (1998) Jefferson fathered slave’s last child. Nature 396, 27-28.
50. Corach, D., et al. (2001) Routine Y-STR typing in forensic casework. Forensic Science Interna- tional 118, 131-135.
51. Kayser,M.,etal.(2000) Characteristics and frequency of germline mutations at micro satellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs. American Journal of Human Genetics 66, 1580-1588.
52. Kayser, M., and Sajantila, A. (2001) Mutations at Y-STR loci: implications for paternity testing and forensic analysis. Forensic Science International 118, 116-121.
53. Oota, H., et al. (2001) Human mtDNA and Y-chromosome variation is correlated with matrilocal versus patrilocal residence. Nature Genetics 29, 20-21.
54. Burton, M.L., et al. (1996) Regions based on social structure. Current Anthropology 37, 87-123.
55. Jobling, M.A. (2001) Y-chromosomal SNP haplotype diversity in forensic analysis. Forensic Science International 118, 158-162.
56. Jobling, M.A. (2001) In the name of the father: surnames and genetics. Trends in Genetics 17, 353-357.
57. Sykes, B. and Irven, C. (2000) Surnames and the Y chromosome. American Journal of Human Genetics 66, 1417-1419.