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

Abstract

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.

The Greeks in the West: genetic signatures of the Hellenic colonisation in southern Italy and Sicily

“…Briefly, TMRCA Bayesian posterior distributions were calculated for pairs of chromosomes separated by 0 to 2k mutational steps (where k is equal to the number of loci), assuming haplotypes composed by the set of 20 selected Y-STR loci (see above), a strict stepwise mutational model, a mutation rate of 3.09 × 10 − 3 per locus per generation (averaged values from Burgarella et al 35 and Ballantyne et al 36 ) and a lambda value of 0.0002 (1/N, where N = effective population size; here we used N = 5000 in accordance with the study by Hammer 37 ). For each k, we explored the likelihood distribution at 102 (GC scenario;~2750 years ago using 27 years per generation) and 300 (neolithic scenario;~7500 years ago using 25 years per generation) generations (Supplementary Table S5).…”

“…Accordingly, we choose six loci: DYS393, DYS445, DYS456, DYS460, DYS461 and GATA-A10. The selected panel included loci characterised by tetrameric regular repeats, high and comparable estimated mutation rates (between 2.5 and 3.3 x10 -3 mutations per generation according to Burgarella et al 35 and Ballantyne et al 36 ) and no incomplete alleles. As maternally inherited molecular markers we used 360 bp hypervariable region I sequences, whose divergence, as measured by DHS, increases linearly over 300 generations (Supplementary Figure S2).…”

Neolithic patrilineal signals indicate that the Armenian plateau was repopulated by agriculturalists

“…In addition, the dates generated from this analysis appear to agree with late to early Neolithic expansions for R1b-M343 across the four Armenian collections and most reference populations. However, owing to the contentions associated with the current calibrations of the Y-STR mutation rates, 32,34,35,41 as well as the limitations of the assumptions utilized by the methodologies for time estimations, the absolute dates generated in this study should only be taken as rough estimates of upper bounds.…”

New Advances Reconstructing the Y Chromosome Haplotype of Napoleon the First Based on Three of his Living Descendants

“…Only one of them (CDY.a) is palindromic. The mutation rates, when known (Burgarella & Navascués, 2011), of these differential alleles are in the 10 -3 range (except for DYS447). These rates are impossible to evaluate for the palindromic STR CDY.…”