Mutation rates at Y chromosome specific microsatellites

Gusmão, Leonor; Sánchez-Diz, Paula; Calafell, Francesc; Martı́n, Pablo; Alonso, Carlos Alberto; Álvarez-Fernández, F.; Alves, Cı́ntia; Borjas-Fajardo, Lisbeth; Bozzo, W.R.; Bravo, M.L.J.; Builes, J.J.; Capilla, Javier; Carvalho, M.; Castillo, Carlos; Catanesi, Cecilia Inés; Corach, Daniel; Lonardo, A.M. Di; Espinheira, R.; Carvalho, E.F.; Farfán, M.J.; Figueiredo, Helder Pereira de; Gomes, Iva; Lojo, María Mercedes; Marino, Miguel; Pinheiro, M.F.; Pontes, Manuela; Prieto, Victoria; Ramos-Luis, Eva; Riancho, José A.; Góes, Andréa Carla de Souza; Santapá, O.A.; Sumita, Denilce R.; Vallejo, G.; Rioja, L. Vidal; Vide, M.C.; Silva, Claúdia Vieira da; Whittle, M.R.; Zabala, William; Zarrabeitia, Marı́a T.; Alonso, Antonio; Carracedo, Ángel; Amorim, António

doi:10.1002/humu.20254

Cited by 137 publications

(111 citation statements)

References 30 publications

(51 reference statements)

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“…21 Lower mutability of shorter alleles compared with longer ones has been observed several times. 32,33,12,34 Accordingly, our results show that the variation in meiosis mutation rates could be significantly explained by mean repeat count (Supplementary Tables S5 and S6). Furthermore, when no diversity variable is included in the model, both repeat count and repeat motif contribute independently to explain the mutation rate variability (ie, model m3, Supplementary Table S5).…”

Section: Mutation Rate Estimates For Y-strsmentioning

confidence: 57%

“…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%

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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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Section: Mutation Rate Estimates For Y-strsmentioning

confidence: 57%

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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“…STRs (short tandem repeats) are multiallelic markers and most have a mutation rate of 10 − 3 -10 − 4 per generation. 3 Mutation diversifies Y-chromosome haplotypes associated with a specific surname. However, SNP mutation rates are low enough not to be represented in the timescale of surname inheritance systematization (surnames appeared 500-1000 years ago).…”

Section: Introductionmentioning

confidence: 99%

Y-chromosome diversity in Catalan surname samples: insights into surname origin and frequency

et al. 2015

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The biological behavior of the Y chromosome, which is paternally inherited, implies that males sharing the same surname may also share a similar Y chromosome. However, socio-cultural factors, such as polyphyletism, non-paternity, adoption, or matrilineal surname transmission, may prevent the joint transmission of the surname and the Y chromosome. By genotyping 17 Y-STRs and 68 SNPs in~2500 male samples that each carried one of the 50 selected Catalan surnames, we could determine sets of descendants of a common ancestor, the population of origin of the common ancestor, and the date when such a common ancestor lived. Haplotype diversity was positively correlated with surname frequency, that is, rarer surnames showed the strongest signals of coancestry. Introgression rates of Y chromosomes into a surname by non-paternity, adoption, and transmission of the maternal surname were estimated at 1.5 − 2.6% per generation, with some local variation. Average ages for the founders of the surnames were estimated at~500 years, suggesting a delay between the origin of surnames (twelfth and thirteenth centuries) and the systematization of their paternal transmission. We have found that, in general, a foreign etymology for a surname does not often result in a non-indigenous origin of surname founders; however, bearers of some surnames with an Arabic etymology show an excess of North African haplotypes. Finally, we estimate that surname prediction from a Y-chromosome haplotype, which may have interesting forensic applications, has a~60% sensitivity but a 17% false discovery rate.

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“…13 The selected method is based on the infinite alleles model, a reasonable approximation when few mutations are expected to occur, as in the temporal framework evaluated here. So, considering 9 loci and 40 generations (approximately 1200 years ago with a 31-year generation length 14 ), either 0 or 1 mutational difference is the most likely consequence.…”

Section: Identification Of Recently Introgressed Nw African Haplotypesmentioning

confidence: 99%

Moors and Saracens in Europe: estimating the medieval North African male legacy in southern Europe

et al. 2009

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To investigate the male genetic legacy of the Arab rule in southern Europe during medieval times, we focused on specific Northwest African haplogroups and identified evolutionary close STR-defined haplotypes in Iberia, Sicily and the Italian peninsula. Our results point to a higher recent Northwest African contribution in Iberia and Sicily in agreement with historical data. southern Italian regions known to have experienced long-term Arab presence also show an enrichment of Northwest African types. The forensic and genomic implications of these findings are discussed.

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Mutation rates at Y chromosome specific microsatellites

Cited by 137 publications

References 30 publications

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

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

Y-chromosome diversity in Catalan surname samples: insights into surname origin and frequency

Moors and Saracens in Europe: estimating the medieval North African male legacy in southern Europe

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