A Short Tandem Repeat–Based Phylogeny for the Human Y Chromosome

Forster, Peter; Röhl, Arne; Lünnemann, Petra; Brinkmann, C.; Zerjal, Tatiana; Tyler‐Smith, Chris; Brinkmann, B.

doi:10.1086/302953

Cited by 125 publications

(113 citation statements)

References 40 publications

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“…An input file for the MJ algorithm was obtained by the RM algorithm of the program (Bandelt et al, 1995(Bandelt et al, , 1999. By this approach, phylogenetically unrealistic cycles within the network were reduced as suggested by Forster et al (2000). A weighting scheme was used to compensate for genetic variance differences at the five microsatellites so that loci with the highest variances were given the lowest weights.…”

Section: Statistical Analysesmentioning

confidence: 99%

Maternal and paternal genealogy of Eurasian taurine cattle (Bos taurus)

et al. 2009

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Maternally inherited mitochondrial DNA (mtDNA) has been used extensively to determine origin and diversity of taurine cattle (Bos taurus) but global surveys of paternally inherited Ychromosome diversity are lacking. Here, we provide mtDNA information on previously uncharacterised Eurasian breeds and present the most comprehensive Y-chromosomal microsatellite data on domestic cattle to date. The mitochondrial haplogroup T3 was the most frequent, whereas T4 was detected only in the Yakutian cattle from Siberia. The mtDNA data indicates that the Ukrainian and Central Asian regions are zones where hybrids between taurine and zebu (B. indicus) cattle have existed. This zebu influence appears to have subsequently spread into southern and southeastern European breeds. The most common Y-chromosomal microsatellite haplotype, termed here as H11, showed an elevated frequency in the Eurasian sample set compared with that detected in Near Eastern and Anatolian breeds. The taurine Ychromosomal microsatellite haplotypes were found to be structured in a network according to the Y-haplogroups Y1 and Y2. These data do not support the recent hypothesis on the origin of Y1 from the local European hybridization of cattle with male aurochsen. Compared with mtDNA, the intensive culling of breeding males and male-mediated crossbreeding of locally raised native breeds has accelerated loss of Ychromosomal variation in domestic cattle, and affected the contribution of genetic drift to diversity. In conclusion, to maintain diversity, breeds showing rare Y-haplotypes should be prioritised in the conservation of cattle genetic resources.

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Section: Statistical Analysesmentioning

confidence: 99%

Maternal and paternal genealogy of Eurasian taurine cattle (Bos taurus)

et al. 2009

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“…To avoid reticulation, a reduced median algorithm (Bandelt et al, 1995) was used to generate a .rmf file, and the median joining network method (Bandelt et al, 1999) was applied to this file. Following the authors recommendations (Forster et al, 2000), the 'frequency 41' option was applied to discard singly occurring Y types. Same weights were assigned to each haplotype.…”

Section: Statistical Analysesmentioning

confidence: 99%

“…As IMMs are defined as dominant markers, they should most probably be considered as slowly mutating markers. Therefore, we computed divergence times using the mutation rate (0.00018 per generation) reported by Forster et al (2000) for slowly mutating Y-chromosome markers. The generation interval was fitted to 4.84 years.…”

Section: Statistical Analysesmentioning

confidence: 99%

Multiple paternal origins of domestic cattle revealed by Y-specific interspersed multilocus microsatellites

et al. 2010

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In this study, we show how Y-specific interspersed multilocus microsatellites, which are loci that yield several amplified bands differing in size from the same male individual and PCR reaction, are a powerful source of information for tracing the history of cattle. Our results confirm the existence of three main groups of sires, which are separated by evolutionary time and clearly predate domestication. These three groups are consistent with the haplogroups previously identified by Göther-ström et al. (2005) using five Y-specific segregating sites: Y1 and Y2 in taurine (Bos taurus) cattle and Y3 in zebu (Bos indicus) cattle. The zebu cattle cluster clearly originates from a domestication process that was geographically and temporally separated from that of taurine clusters. Our analyses further suggest that: (i) introgression of wild sire genetic material into domesticated herds may have a significant role in the formation of modern cattle, including the formation of the Y1 haplogroup; (ii) a putative domestication event in Africa probably included local Y2-like wild sires; (iii) the West African zebu cattle Ychromosome may have partially originated from an ancient introgression of humped cattle into Africa; and (iv) the high genetic similarity among Asian zebu sires is consistent with a single domestication process.

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“…14,15 Additionally, another widely used microsatellite, DYS392, has recently been demonstrated to deviate from the SMM. 16 In the present study, both microsatellite loci were analysed in a large pooled sample of six Middle Eastern populations.…”

Section: Introductionmentioning

confidence: 99%

Haplogroup-specific deviation from the stepwise mutation model at the microsatellite loci DYS388 and DYS392

et al. 2001

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Deviation from the stepwise mutation model (SMM) at specific human microsatellite loci has implications for population genetic and forensic investigations. In the present study, data on six Y chromosome-specific microsatellites were pooled for 455 paternally unrelated males from six Middle Eastern populations. All chromosomes were assigned to three haplogroups defined by six binary polymorphisms. Two of the microsatellite loci tested, DYS388 and DYS392, displayed marked haplogroup-specific differences in their allele variability. A bimodal distribution of short and long alleles was observed for DYS388 in haplogroup 1 and for DYS392 in haplogroups 1 and 2. Further investigation showed that the short/long alleles segregated almost completely between genealogically distinct haplogroups defined by additional binary markers. Thus, these two loci have a discriminatory power similar to a binary polymorphism. DYS388 was characterised by an extremely low mutation rate in haplogroups 2 and 3, as was DYS392 in haplogroup 3. Sequence analysis of the repeat regions at the two loci revealed no irregularities, indicating that the triplet expansion in these loci is not controlled by sequence variation at the repeat level. A high frequency of long DYS388 alleles has, so far, been found only in populations originating in the Middle East, suggesting that this microsatellite is useful as a region-specific marker. European Journal of Human Genetics (2001) 9, 22-26.

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A Short Tandem Repeat–Based Phylogeny for the Human Y Chromosome

Cited by 125 publications

References 40 publications

Maternal and paternal genealogy of Eurasian taurine cattle (Bos taurus)

Maternal and paternal genealogy of Eurasian taurine cattle (Bos taurus)

Multiple paternal origins of domestic cattle revealed by Y-specific interspersed multilocus microsatellites

Haplogroup-specific deviation from the stepwise mutation model at the microsatellite loci DYS388 and DYS392

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