From ISOGG Wiki
In genetics, the mutation rate is a measure of the rate at which various types of mutations occur during some unit of time. Mutation rates are typically given for a specific class of mutation, for instance point mutations, small or large scale insertions or deletions. The rate of substitutions can be further subdivided into a mutation spectrum which describes the influence of genetic context on the mutation rate.
- Y-chromosome STR mutation rates. A downloadable spreadsheet provided by Tim Janzen showing comparative mutation rates for 113 Y-STR markers. The data has been compiled from a number of sources (John Chandler, Doug McDonald, Charles Kerchner, SMGF, Ysearch, YHRD, Marko Heinila, Chris Rottensteiner and from the peer-reviewed literature). [22 May 2017: This link returns: "File not found: Sorry, that file doesn’t live here any more. It might have been moved or made private. "]
- A table of mutation rates for 111 markers provided by Marko Heinila
- List of DYS markers and associated mutation rates from Wikipedia
- Mutation rates for the markers in the YHRD.org database
- Leo Little's chart of mutation rate effects The charts show the percentage of descendant haplotypes with at least 1 mutation after x years
- Top 50 mtDNA mutations from the Sorenson Molecular Genealogy Foundation (preserved in the Wayback Machine]
- Y-STR database A database of mutation rates of Y-STR markers using results from many studies compiled by the Hawgood DNA project
- Charles Kerchner's Y-STR Haplotype Observed Mutation Rates in Surname Projects Study and Log
- Mutation rates tutorial from DNA Heritage (Internet Archive version) N.B. DNA Heritage was acquired by Family Tree DNA in 2012.
- Sandy Paterson's TMRCA website (retrieved from Internet Archive, version dated 20 December 2012)
- Haplotype stability An essay by Ralph Taylor, Taylor Genes DNA Project, revised 27 October 2015.
- Robb J (2010). Deconstructing TMRCA and genetic distance. Essay published on John Barrett Robb's personal website on 13 October 2010.
- An overview and discussion of various DNA mutation rates and DNA haplotype mutation rates. Do the YSTR haplotypes in some Y chromosome male lines mutate faster than in other male lines? by Charles Kerchner, 7 January 2005, ast edited/updated 17 April 2008
- Message on the DNA Genealogy List from Tim Janzen: DYS markers categorized as fast, medium or slow rate of mutation
- Hutchison LAD et al. Direct determination of mutation characteristics of Y chromosome STR loci. A poster presented at the American Society of Human Genetics 2004 Annual Meeting, October 2004, Toronto, Ontario, Canada
- DNA dating: How molecular clocks are refining human evolution’s timeline by Bridget Alex and Priya Moorjani, The Conversation, 7 April 2017.
- Explainer: what is the molecular clock? by Al Tanner, The Conversation, 15 September 2015.
- Human Y chromosome mutation rates by Larry Moran, Sandwalk blog, 1 September 2009.
- Scally A (2106). Mutation rates and the evolution of germline structure. Preprint published online at BioRxiv on 16 May 2016.
- James X Sun, Agnar Helgason, Gisli Masson, Sigríður Sunna Ebenesersdóttir, Heng Li, Swapan Mallick, Sante Gnerre, Nick Patterson, Augustine Kong, David Reich & Kari Stefansson (2012). A direct characterization of human mutation based on microsatellites. Letter. Nature Genetics, 23 August 2012.
- Callaway, Ewen (2012). Fathers bequeath more mutations as they age. News article. Nature 488, 439 (23 August 2012).
- Ségurel L, Wyman MJ, Przeworski M (2014). Determinants of mutation rate variation in the human germline. Genomics and Human Genetics 15: 47-70.
Articles on mutation rates in the Y-chromosome
- Balanovsky O (2017). Toward a consensus on SNP and STR mutation rates on the human Y-chromosome. Human Genetics, published online 28 April 2017. Review article.
- Alessio Boattini A. Sarno S, Bini C et al (2016). Mutation rates and discriminating power for 13 rapidly-mutating Y-STRS between related and unrelated individuals. PLOS One. Published 1 November 2016.
- Willems T, Gymrek M, Poznik GD, Tyler-Smith S, The 1000 Genomes Project Y-Chromosome Working Group, Erlich Y. Population-scale sequencing data enable precise estimates of Y-STR mutation rates. American Journal of Human Genetics, published online 25 April 2016. Preprint available here.
- Trombetta B, D'Atanasio E, Massaia A et al. Regional differences in the accumulation of SNPs on the male-specific portion of the human Y chromosome replicate autosomal patterns: implications for genetic dating. PLOS One Published online: 30 July 2015.
- Helgason A, Einarsson AW, Valdís B Guðmundsdóttir VB et al (2015). The Y-chromosome point mutation rate in humans (letter). Nature Genetics, published online 25 March 2015.
- Adamov D, Guryanov V, Karzhavin S, Tagankin V, Urasin V. Defining a new rate constant for Y-chromosome SNPs based on full sequencing data. Russian Journal of Genetic Genealogy 2015; 7(1).
- Ballantyne KN et al (2014). Toward male individualization with rapidly mutating y-chromosomal short tandem repeats. Human Mutation 2014; 35: 1021–1032.
- Chuan-Chao Wang C-C. Gilbert MT, Jin L, Li H (2014). Evaluating the Y chromosomal timescale in human demographic and lineage dating [review]. Investigative Genetics 2014; 5: 12.
- Wei W, Ayub Q, Xue Y, Tyler-Smith C (2013). A comparison of Y-chromosomal lineage dating using either resequencing or Y-SNP plus Y-STR genotyping. Forensic Science International Genetics 2013 Dec;7 (6): 568-72.
- Poznik GD, Henn BM, Yee MC et al (2013). Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science 2013 Aug 2; 341(6145):562-5.
- For a critique of this paper and the misconceptions behind it see the three-part series of articles by Melissa Wilson Ayres: Y and mtDNA are not Adam and Eve: Part 1; Y and mtDNA are not Adam and Eve: Part 2 - What it means to be the Most Recent Common Ancestor and Y and mtDNA are not Adam and Eve: Part 3 - Resolving a discrepancy.
- Wei W, Ayub Q, Chen Y, McCarthy S, Hou Y, Carbone I, Xue Y, Tyler-Smith C (2013). A calibrated human Y-chromosomal phylogeny based on resequencing. Genome Research 2013 Feb; 23(2):388-95.
- Concetta Burgarella and Miguel Navascués (2011). Mutation rate estimates for 110 Y-chromosome STRs combining population and father–son pair data. European Journal of Human Genetics 2011; 19, 70–75. Published online 8 September 2010.
- Xue, Y. and Tyler-Smith, C (2009). The hare and the tortoise: One small step for four SNPs, one giant leap for SNP-kind. Forensic Science International: Genetics 4(2):59-61.
- Yali Xue, Qiuju Wang, Quan Long et al (2009). Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree. Current Biology 2009 September 15; 19(17): 1453–1457.
- Anatole A. Klyosov (2009). DNA Genealogy, Mutation Rates, and Some Historical Evidence Written in Y-Chromosome, Part II: Walking the Map Journal of Genetic Genealogy Fall 2009, Volume 5, Number 2.
- Eckert KA, Hile SE (2009). Every microsatellite is different: Intrinsic DNA features dictate mutagenesis of common microsatellites present in the human genome. Molecular Carcinogenesis. 2009 Apr; 48(4): 379-88.
- Anatole Klyosov (2009). DNA Genealogy, Mutation Rates, and Some Historical Evidence Written in Y-Chromosome, Part I: Basic Principles and the Method Journal of Genetic Genealogy Fall 2009, Volume 5, Number 2.
- Whit Athey (2007). Mutation Rates – Who’s Got the Right Values? (editorial) Journal of Genetic Genealogy Volume 3, Number 2, Fall/autumn 2007.
- John Chandler (2006). Estimating per-locus mutation rates. Journal of Genetic Genealogy, Volume 2, Number 2, Fall/autumn 2006.
- Soares PA, Pereira F, Brion M (2005). Relative Y-STR mutation rates estimated from the variance inside SNP defined lineages International Congress Series 1288 (2006) 82–84. Progress in Forensic Genetics 11 — Proceedings of the 21st International ISFG Congress held in Ponta Delgada, The Azores, Portugal between 13 and 16 September 2005.
- Budowle B, Adamowicz M, Aranda XG et al (2005). Twelve short tandem repeat loci Y chromosome haplotypes: genetic analysis on populations residing in North America. Forensic Science International 2005 May 28; 150(1): 1-15.
- Luke A. D. Hutchison, Natalie M. Myres, Jacob E. Ekins et al, Sorenson Molecular Genealogy Foundation (2004). Direct determination of mutation characteristics of Y chromosome STR loci Presented at the American Society of Human Genetics 2004 Annual Meeting, October 2004, Toronto, Ontario, Canada.
- Ellegren H (2004). Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics 5: 435-445. A useful review article providing an overview of mutations occur.
- Zhivotovsky LA, Peter A. Underhill PA, Cinnioğlu C et al (2004). The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time. American Journal of Human Genetics 2004 January; 74(1): 50–61.
- Dupuy B. Myhre, Stenersen M, Egeland T, Olaisen B (2003). Y-chromosomal microsatellite mutation rates: Differences in mutation rate between and within loci. Human Mutation 2003 23 (2): 117-124.
- Ulrike Holtkemper, Burkhard Rolf, Carsten Hohoff et al (2001). Mutation rates at two human Y-chromosomal microsatellite loci using small pool PCR techniques. Human Molecular Genetics 2001; 10 (6): 629-633.
- Concetta Burgarella and Miguel Navascués (2011). Mutation rate estimates for 110 Y-chromosome STRs combining population and father–son pair data. European Journal of Human Genetics 2011; 19: 70–75.
- Kaye N. Ballantyne, Miriam Goedbloed, Rixun Fang et al (2010). Mutability of Y-Chromosomal Microsatellites: Rates, Characteristics, Molecular Bases, and Forensic Implications. American Journal of Human Genetics Volume 87, Issue 3, 10 September 2010: 341-353.
- Ge J, Budowle B, Aranda XG, Planz JV, Eisenberg AJ, Chakraborty R (2009). Mutation rates at Y chromosome short tandem repeats in Texas populations. Forensic Science International: Genetics. 2009 Jun;3(3):179-84.
- Decker AE, Kline MC, Redman JW, Reid TM, Butler JM (2008). Analysis of mutations in father–son pairs with 17 Y-STR loci. 'Forensic Science International: Genetics 2 2008: e31–e35
- Gusmão L, Sánchez-Diz P, Calafell F et al (2005). Mutation rates at Y chromosome specific microsatellites. Human Mutation 2005 Dec; 26(6): 520-528.
- Manfred Kayser, Lutz Roewer, Minttu Hedman et al (2000). Characteristics and Frequency of Germline Mutations at Microsatellite Loci from the Human Y Chromosome, as Revealed by Direct Observation in Father/Son Pair. American Journal of Human Genetics 2000; 66: 1580–1588.
Articles on mutation rates in mtDNA
- Rieux A, Eriksson A, Li M et (2014). Improved calibration of the human mitochondrial clock using ancient genomes. Molecular Biology and Evolution 31 (10): 2780–2792.
- Fu Q, Mittnik A, Johnson PLF et al (2013). A revised timescale for human evolution based on mitochondrial genomes. Current Biology 2013; 23 (7): 553–559.
- Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards MB (2009). Correcting for purifying selection: an improved human mitochondrial molecular clock. American Journal of Human Genetics 2009 Jun; 84(6): 740-59. Epub 2009 Jun 4.
- SigurDardo´ttir S, Helgason A, Jeffrey R. Gulcher JR, Stefansson K, Donnelly P (2000). The Mutation Rate in the Human mtDNA Control Region American Journal of Human Genetics 2000; 66: 1599–1609.
- Palamara PF, Franciolo LC, Wilton PR et al (2015). Leveraging distant relatedness to quantify human mutation and gene-conversion rates. American Journal of Human Genetics (article in press).
- Francioli LC, Polak PP, Koren A et al (2015). Genome-wide patterns and properties of de novo mutations in humans. Nature Genetics. Published online 18 May 2015.
- Besenbacher Sm Liu S, Izarzugaza JMG (2014). Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. Nature Communications. Published online 19 January 2015.
- Campbell CD, Eichler EE (2013). Properties and rates of germline mutations in humans. Trends in Genetics 2013; 29 (10): 575–584.
- Augustine Kong, Michael L. Frigge, Gisli Masson, et al (2012). Rate of de novo mutations and the importance of father's age to disease risk. Nature 488, 471–475 (23 August 2012).