Abstract
Eleven Y-STR loci were applied to 417 confirmed father-son pairs. Seven mutations that comprise single step were observed in a total of 2532 allelic transfers, in locus DYS385, DYS390, DYS391, DYS392, and DYS389II. The total mutation rate estimated in this study was 2.8 × 10−3 (95% CI, 1.1 × 10−3 to 5.7 × 10−3); this result is similar to other populations. Q haplogroup lineage was more frequent than others in this study. These results will contribute the forensic and paternity areas database in Ecuador.
Keywords
1. Introduction
A main characteristic of the Y chromosome haplotypes is that they are transmitted from fathers to sons without change. Therefore, the variation depends on the mutation rate [
[1]
]. The lack of variability of the Y chromosome together with SNP polimorphisms, Alu elements, and microsatellites have been very useful in the analysis and reconstruction of events that led to the recent human evolution []. Mutations have a great influence in the analysis of forensic kinship calculations and in genealogical relationships studies [[3]
]. Mutations rates have been analyzed in different aspects: in multigeneration pedigrees, in father-son pairs, in locus-specific, and allele-specific sites [3
, 4
, 5
, 6
]. They allow to track historical events using a molecular clock, since they leave a trail of human migration events which are important at the time to define new haplotypes [[7]
]. In this study we analyzed the mutation rate in 11 Y-STR loci in a group of Ecuadorian individuals.2. Methods
This study included 206 father-son pairs individuals. Their haplotypes were reported in a previous study [
[8]
]. Blood samples supported on FTA™ cards were obtained from unrelated male donors and their sons, whose paternity cases were previously confirmed by Powerplex 16 and/or AmpFLSTR®Identifiler® PCR Amplification Kit. A written informed consent, for genetics population's studies, was signed by all of the participants.DNA was extracted according to FTA® cards guide recommendations. PCR amplification was performed using PowerPlex® Y System following the protocol provided by the manufacturer. This study included the following STR loci: DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, and DYS439.The allele sizing was carried by GeneMapper® ID V 3.2. using an ABI PRISM® 3100-Avant Genetic Analyzer.
The Y-STR mutation rate and their confidence intervals, at each locus, were calculated using the exact binomial probability distribution (see http://statpages.org./confint.html). Prediction of haplogroup was determined with the Haplogroup predictor software (see http://www.hprg.com/hapest5/).
3. Results and discussion
In this study, seven mutations that comprise single step (gain or loss), were observed in a total of 2532 allelic transfers, in locus DYS385, DYS390, DYS391, DYS392, and DYS389II (Table S1). Mutations were confirmed with Yfiler kit. The total mutation rate estimated in this study was 2.8 × 10−3 (95% CI, 1.1 × 10−3 to 5.7 × 10−3) (Table S2). This result is higher than the reported in a study of Texas population with an average mutation rate of 2.1 × 10−3 per locus (95% CI, 1.7 × 10−3 to 2.5 × 10−3) which also included an analysis of an Hispanic group that showed a data of 1.5 × 10−3 (95% CI, 1.0 × 10−3 to 2.2 × 10−3) [
[6]
]. Other studies on Texas subpopulations reported an average mutation rate of 1.57 × 10−3 [[9]
], 2.3 × 10−3 in the South China Han population [[10]
], and 2.12 × 10−3 in another investigation that analysed 93 published works [[11]
]. Factors like the sample size, the number of STRs applied for the study, and the composition of specific population, could influence the average of mutation rate obtained in this study. Some authors have stated that variation on mutation rates depends on motif size and the complexity of STRs structure [5
, 6
, 12
, 13
]. All of these mutations occur singly in different father-son pairs, 4 mutations were a gain in the sons and 3 resulted in a loss of a repeat (Table S1). There was no correlation between mutation rates and the length of the alleles, or for DYS385b loci with gain type of 2 mutations either, which also showed higher gene diversity (0.9427) in a previous study performed in the same population [[8]
]. Same result was observed in locus DYS391 (Table S2). Similar results have been observed in other studies, where they did not find relationship between mutation rate and motif size [5
, 6
]. The large confidence intervals found in this study could be due to the small number of observed meiosis; corroborated by Burgarella and Navascués (2011) who reported that data of mutation rate, in comparisons to father and son, [[11]
]. Father's age, at the time of the son's birth, was further analyzed; the average age between fathers without mutation was of 29.07 (±9.93) years and with mutations was of 31 (±6.07) years (Table S3). Similar results were published by Ballantyne et al. (2010) where the average father's age was 32.42 (±10.97) years in the group with mutations [[14]
].Although the previous reported frequency for Q haplogroup was of 37.6% [
[8]
], prediction of haplogroup showed that mutation rate was higher in this lineage than the others in the analyzed individuals (Table S3). An unusual finding in this study is the haplogroup J, whose origin is located in Near East and then disseminated into North Africa, Europe, Central Asia, Pakistan and India; specifically J2 lineages spread into the Mediterranean area (www.isogg.org/tree/ISOGG_HapgrpJ13.html). Therefore this kind of analysis is important to get a best approximation to calculate divergent times between haplogroups in the populations [[7]
].These results are a complement of the previous data and will contribute to the genetic characterization of Ecuadorian population. However, it is necessary to increase the sample size to get more precise data of the Y chromosome's mutation rate.
Conflict of interest
None.
Role of funding
This research had financial support by Instituto de Investigaciones Biomédicas de la Universidad de las Américas and Cruz Vital – Cruz Roja Ecuatoriana from Quito, Ecuador.
Appendix A. Supplementary data
The following are Supplementary data to this article:
References
- The History and Geography of Human Genes.Princeton University Press, Princeton, New Jersey1994
- Genética Molecular Humana.Pearson Prentice-Hall, Madrid2004
- Mutations at Y-STR loci: implications for paternity testing and forensic analysis.Forensic Sci. Int. 2001; 118: 116-121https://doi.org/10.1016/S0379-0738(00)00480-1
- Estimating Y chromosome specific microsatellilte mutation frequencies using deep rooting pedigrees.Hum. Mol. Genet. 1997; 6: 799-803https://doi.org/10.1093/hmg/6.5.799
- Mutation rates at Y chromosome specific microsatellites.Hum. Mutat. 2005; 26: 520-528https://doi.org/10.1002/humu.20254
- Mutation rates at Y chromosome short tandem repeats in Texas population.Forensic Sci. Int. Genet. 2009; 3: 179-184https://doi.org/10.1016/j.fsigen.2009.01.007
- Y chromosomes of 40% Chinese descend from three neolithic super-grandfathers.PLoS One. 2014; 9: e105691https://doi.org/10.1371/journal.pone.0105691
- Characterization and Haplotype analysis of 11 Y-STR loci in Ecuadorian population.Forensic Sci. Int. 2013; 4: e310-e311https://doi.org/10.1016/j.fsigss.2013.10.158
- Twelve short tandem repeat loci Y chromosome haplotypes: genetic analysis on populations residing in North America.Forensic Sci. Int. 2005; 150: 1-15
- Mutation rates at 16 Y-chromosome STRs in the South China Han population.Int. J. Legal Med. 2013; 127: 369-372https://doi.org/10.1007/s00414-012-0786-3
- Mutation rate estimates for 110 Y-chromosome STRs combining population and father-son pair data.Eur. J. Hum. Genet. 2011; 19: 70-75https://doi.org/10.1038/ejhg.2010.154
- A comprehensive survey of human Y-chromosomal microsatellites.Am. J. Hum. Genet. 2004; 74: 1183-1197https://doi.org/10.1086/421531
- Y-chromosomal microsatellite mutation rates: differences in mutation rate between and within loci.Hum. Mutat. 2004; 23: 117-124https://doi.org/10.1002/humu.10294
- Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications.Am. J. Hum. Genet. 2010; 87: 341-353https://doi.org/10.1016/j.ajhg.2010.08.006
Article info
Publication history
Published online: September 20, 2015
Accepted:
September 18,
2015
Received:
August 30,
2015
Identification
Copyright
© 2015 Elsevier Ireland Ltd. Published by Elsevier Inc. All rights reserved.
