Y-chromosomal STR haplotypes in Pakistani populations
Introduction
Y-chromosomal STRs are proving useful markers in forensic analysis and paternity testing since they allow Y chromosomes to be distinguished [1], and a forensic database has been established [2]. However, the Y chromosome differs from the autosomes in that it is transmitted only from father to son, and escapes recombination over most of its length, so consists largely of a haploid Y-specific region which carries the STRs used for forensic purposes. Because of the lack of recombination, a son carries the same Y-STR haplotype as his father, except when mutations occur. Such mutations are rare: their frequency in the commonly used loci has been measured at approximately 2×10−3 per locus per generation [3], [4]. Thus, even haplotypes consisting of multiple loci can be transmitted intact for many generations and may consequently be shared by large numbers of male-line relatives. Haplotype sharing is exacerbated by the large variance in the number of offspring of males, and high fertility itself can run in families [5]. When coupled with population subdivision, this can lead to gross departures from simple expectations about the distribution of haplotypes in a population. While these considerations are not important when exclusion is observed, they complicate the interpretation of matches.
As a result, it is desirable to use large numbers of highly variable STRs to define as many haplotypes as possible, and to obtain empirical data about haplotype sharing. We have recently identified a set of six additional Y-STRs [6], and now present the haplotypes they identify in the Pakistani population in combination with 10 of the more commonly used STRs. Pakistan has a population of 130 million and is divided into about 18 ethnic groups based up on their origins and, in some cases, language [7]. These groups include the Burushaski language-isolate-speakers from Hunza in northern Pakistan and the Dravidian-speaking Brahuis from Balochistan in the south. Indo-European speakers within Pakistan include the Baloch, Balti, Bhil, Hazara, Kalash, Kashmiri, Makranis, Mohannas, Parsis, Pathans, Punjabis and Sindhis [8]. The Punjabi populations consist of an admixture of indigenous and invading populations and comprise several diverse castes such as the Arains, Gujars, Meos and Rajputs [9].
Section snippets
Populations
Blood samples were collected with informed consent from individuals of known ethnic origin and family history. The populations included in this study are the Baloch (n=60), Balti (n=16), Brahui (n=111), Burusho (n=94), Hazara (n=23), Kalash (n=44), Kashmiri (n=12), Makrani Baloch (n=25), Makrani Negroid (n=33), Parsi (n=90), Pathan (n=94) and Sindhi (n=124). Blood was collected from only those males who were known to be unrelated for at least the last three generations, and a lymphoblastoid
Results
The 16 STRs were typed in 711 males. Some STRs (e.g. DYS388, DYS391, DYS434) showed one common allele with the other alleles occurring at low frequencies (Fig. 1). Other STRs (e.g. DYS19, DYS389b, DYS390) showed a more bell-shaped distribution, with several alleles present at comparable frequencies. The number of alleles found at each locus ranged from 4 (DYS389I, DYS435, DYS436) to 10 (DYS388), a variation of less than three-fold (Fig. 1, Table 1). However, the diversity at the individual loci
Discussion
The dataset presented here, consisting of 711 individuals typed with 16 Y-STRs, allows us to examine some of the properties of the loci, and illustrates the substructuring present in the Pakistani population. DYS434, DYS435 and DYS436 have low diversities and will not be markers of choice for forensic work. In contrast, DYS437, DYS438 and DYS439 have high diversities, equivalent to the commonly used loci, and thus provide a useful addition to those already available.
The finding of haplotypes
Acknowledgements
We thank the DNA donors for making this work possible, Saima Siddiqi and Sadia Rehman for their invaluable help, Mark Thomas for providing details of his multiplex protocols before publication, and Carlo Previderé and Mark A. Jobling for comments on the manuscript. We were supported by a Wellcome Trust CRIG (S.Q.M.), Studentship (T.Z.) and the CRC (C.T.-S).
References (10)
- et al.
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.
(2000) - et al.
The Y chromosome in forensic analysis and paternity testing
Int. J. Legal Med.
(1997) - L. Roewer, M. Kayser, K. Anslinger, C. Augustin, A. Caglia, D. Corach, S. Furedi, G. Geserick, L. Henke, M. Hidding,...
- et al.
Estimating Y chromosome specific microsatellite mutation frequencies using deep rooting pedigrees
Hum. Mol. Genet.
(1997) - et al.
Social transmission of reproductive behavior increases frequency of inherited disorders in a young-expanding population
Proc. Natl. Acad. Sci. U.S.A.
(1998)
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Analysis of 24 y chromosomal STR haplotypes in a Chinese Han population sample from Henan Province, Central China
2015, Forensic Science International: GeneticsCitation Excerpt :The improvement achieved by DYS449 was followed by improvements with DYS527a/b, DYS444, DYS522 and DYS447, but did not change by the addition of DYS388. The low diversity of DYS388 in other populations have also been reported in previous reports [4,5]. The combination of these 7 Y-STRs with Yfiler loci in the Henan Han samples which were not greatly improved in terms of discriminatory capacity (DC) and haplotype diversity (HD), indicating that the discrimination power of 24 Y-STR haplotypes in Henan Han is low for forensic and kinship casework.
Analysis of 22 y chromosomal STR haplotypes and y haplogroup distribution in Pathans of Pakistan
2014, Forensic Science International: GeneticsCitation Excerpt :Y-STR haplotypes obtained from many studies are accessible through an online database, YHRD (Y chromosome haplotype reference database: http://www.yhrd.org), which has reported 71,235 Yfiler haplotypes as of December, 2013 (Release 46) [7]. The database shows that Yfiler haplotype diversities may vary according to the genetic features of a population; many populations have relatively high haplotype diversity, but some populations that underwent a strong male bottleneck in their history have low haplotype diversity [8–10]. Pathans are an Iranian-speaking Afghan ethnic group with a widespread geographic distribution in southern and eastern parts of Afghanistan and in north-west Khyber Pakhtunkhwa and Baluchistan province of Pakistan [11,12].
Y-STR haplotype diversity in Punjabi population of Pakistan
2014, Forensic Science International: GeneticsY-chromosomal STR analysis in the Pashtun population of Southern Afghanistan
2012, Forensic Science International: GeneticsCitation Excerpt :We used the website www.yhrd.org/Analyse to perform AMOVA variance analysis (Φst statistics taking the single step-mutation model into account) including significance tests for all pairwise comparisons. The Pashtun (Pathan) population from this study was compared to the North and South Afghanistan Pashtuns (YHRD accession numbers YA003702 and YA003703 published in [4]), Pathans from Pakistan (YA003218 published in [5]) and Afridi Pathans from Uttar Pradesh in India (YA003686 submitted to YHRD by the Central Forensic Science Laboratory, Kolkata, India). In addition full population sets were used for AMOVA, i.e. 1885 haplotypes from India, 444 from Iran and 718 from Pakistan.
A new future of forensic Y-chromosome analysis: Rapidly mutating Y-STRs for differentiating male relatives and paternal lineages
2012, Forensic Science International: GeneticsImproving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms
2009, Forensic Science International: GeneticsCitation Excerpt :Also, at a more local level, higher frequencies of indistinguishable Y-chromosomes can sometimes be found due to members of the same male lineage living in the same geographic region, a phenomenon usually referred to as (male) population substructure. It has been observed that 7–16 highly polymorphic Y-STRs are insufficient for differentiating male lineages when applied to populations that underwent a strong (male) bottleneck in their history: for example, identical Y-STR haplotypes were found in two populations from Pakistan with a frequency of 14% (16 Y-STRs) [10], in Finns at 13% (16 Y-STRs) [11], or even over entire geographic regions such as Polynesia at 16% (7 Y-STRs) [12]. Reduced Y-STR diversity leading to a large number of indistinguishable Y-STR haplotypes can also be caused by cultural effects such as patrilocal residence pattern and polygyny as previously observed in New Guinea [13], or by strongly biased male expansion due to male occupation history and privilege as in Central and Eastern Asia [14,15].