Estimating Y Chromosome Specific Microsatellite Mutation Frequencies using Deep Rooting Pedigrees

Heyer, Évelyne; Puymirat, Jack; Dieltjes, Patrick; Bakker, Egbert; Knijff, Peter de

doi:10.1093/hmg/6.5.799

Cited by 227 publications

(198 citation statements)

References 16 publications

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“…In the literature, a discrepancy of average mutation rates at Y-chromosome markers is reported, depending on whether the estimate is pedigree based or phylogeny based. By direct count in deep-rooted pedigrees, a mutation rate of 2Â10 À3 per generation has been estimated, 40 and by studying father/son pairs, a similar average mutation rate of 3.17Â10 À3 per locus per generation was estimated. 37 A recent study analyzed 17 microsatellite markers for 18 earlier published studies in combination with a new dataset of father/son pairs (135 212 meiotic transfers in total) and found a median mutation rate of 2.2Â10 À3 .…”

Section: Studies Of Y-chromosome Dnamentioning

confidence: 99%

Drawing the history of the Hutterite population on a genetic landscape: inference from Y-chromosome and mtDNA genotypes

et al. 2009

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Although the North American Hutterites trace their origins to South Tyrol, no attempts have been made to examine the genetic migration history of the Hutterites before emigrating to the United States in the 1870s. To investigate this, we studied 9 microsatellite loci and 11 unique event polymorphism (UEP) markers on the Y-chromosome, the hypervariable region I (HVRI) of the mitochondrial DNA (mtDNA), as well as the complete mtDNA genome of Hutterite and South Tyrolean samples. Only 6 out of 14 Y-chromosome UEP+microsatellite haplotypes and 3 out of 11 mitochondrial haplotypes that were present in the Hutterites were also present in the South Tyrolean population. The phylogenetic relationships inferred from Y-chromosome and mtDNA databases show that the Hutterites have a unique genetic background related to a similar extent to central and eastern European populations. An admixture analysis indicates, however, a relatively high genetic contribution of central European populations to the Hutterite gene pool. These results are consistent with historical records on Hutterite migrations and demographic history. In addition, our data reveal similar numbers of Y and mitochondrial haplotypes in Hutterite male and female founders, respectively. The Hutterite male and female gene pools are similar with respect to genetic diversity and genetic distance measures and comparable with respect to their origins, suggesting a similar evolutionary history.

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Section: Studies Of Y-chromosome Dnamentioning

confidence: 99%

Drawing the history of the Hutterite population on a genetic landscape: inference from Y-chromosome and mtDNA genotypes

et al. 2009

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“…10 However, relative mutation rate estimates have limited utility for dating evolutionary events or calculating forensic probabilities. Absolute mutation rate estimates can be obtained by the analysis of allele transmissions in pedigrees (eg, Heyer et al and Gusmão et al 11,12 ). The proportion of allele mismatches in father-son transmissions is currently the most widely used approach to obtain estimates of mutation rates for Y-STRs.…”

Section: Introductionmentioning

confidence: 99%

Mutation rate estimates for 110 Y-chromosome STRs combining population and father–son pair data

Burgarella

Navascués

2010

Eur J Hum Genet

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Y-chromosome microsatellites (Y-STRs) are typically used for kinship analysis and forensic identification, as well as for inferences on population history and evolution. All applications would greatly benefit from reliable locus-specific mutation rates, to improve forensic probability calculations and interpretations of diversity data. However, estimates of mutation rate from father-son transmissions are available for few loci and have large confidence intervals, because of the small number of meiosis usually observed. By contrast, population data exist for many more Y-STRs, holding unused information about their mutation rates. To incorporate single locus diversity information into Y-STR mutation rate estimation, we performed a meta-analysis using pedigree data for 80 loci and individual haplotypes for 110 loci, from 29 and 93 published studies, respectively. By means of logistic regression we found that relative genetic diversity, motif size and repeat structure explain the variance of observed rates of mutations from meiosis. This model allowed us to predict locus-specific mutation rates (mean predicted mutation rate 2.12Â10 À3 , SD¼1.58Â10 À3 ), including estimates for 30 loci lacking meiosis observations and 41 with a previous estimate of zero. These estimates are more accurate than meiosis-based estimates when a small number of meiosis is available. We argue that our methodological approach, by taking into account locus diversity, could be also adapted to estimate population or lineage-specific mutation rates. Such adjusted estimates would represent valuable information for selecting the most reliable markers for a wide range of applications.

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“…In humans or in macroscopic laboratory organisms, it may be possible to restrict attention to a limited set of individuals, for which genetic history is known over one or a few generations. For example, mutation rates are sometimes obtained by counting the number of mutations that have occurred in simple pedigrees (Mukai and Cockerham, 1977;Heyer et al, 1997).…”

Section: Introductionmentioning

confidence: 99%

Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis

Rosenberg

Tsolaki

Tanaka

2003

Theoretical Population Biology

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In infectious disease epidemiology, it is useful to know how quickly genetic markers of pathogenic agents evolve while inside hosts. We propose a modular framework with which these genotype change rates can be estimated. The estimation scheme requires a model of the underlying process of genetic change, a detection scheme that filters this process into observable quantities, and a monitoring scheme that describes the timing of observations. We study a linear ''birth-shift-death'' model for change in transposable element genotypes, obtaining maximum-likelihood estimators for various detection and monitoring schemes. The method is applied to serial genotypes of the transposon IS6110 in Mycobacterium tuberculosis. The estimated birth rate of 0.0161 (events per copy of the transposon per year) and death rate of 0.0108 are both significantly larger than the estimated shift rate of 0.0018. The sum of these estimates, which corresponds to a ''half-life'' of 2.4 years for a typical strain that has 10 copies of the element, substantially exceeds a previous estimate of 0.0135 total changes per copy per year. We consider experimental design issues that enable the precision of estimates to be improved. We also discuss extensions to other markers and implications for molecular epidemiology. r

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Estimating Y Chromosome Specific Microsatellite Mutation Frequencies using Deep Rooting Pedigrees

Cited by 227 publications

References 16 publications

Drawing the history of the Hutterite population on a genetic landscape: inference from Y-chromosome and mtDNA genotypes

Drawing the history of the Hutterite population on a genetic landscape: inference from Y-chromosome and mtDNA genotypes

Mutation rate estimates for 110 Y-chromosome STRs combining population and father–son pair data

Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis

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