Strong male bias drives germline mutation in chimpanzees
TLDR
Overall, the mutation rate per year in chimps is similar to that in humans, but the male mutation bias with age is stronger, and mutation rates and patterns differ between closely related species.Abstract:
Germline mutation determines rates of molecular evolution, genetic diversity, and fitness load. In humans, the average point mutation rate is 1.2 × 10−8 per base pair per generation, with every additional year of father’s age contributing two mutations across the genome and males contributing three to four times as many mutations as females. To assess whether such patterns are shared with our closest living relatives, we sequenced the genomes of a nine-member pedigree of Western chimpanzees, Pan troglodytes verus. Our results indicate a mutation rate of 1.2 × 10−8 per base pair per generation, but a male contribution seven to eight times that of females and a paternal age effect of three mutations per year of father’s age. Thus, mutation rates and patterns differ between closely related species.read more
Citations
More filters
Journal ArticleDOI
Genetic drift, selection and the evolution of the mutation rate
Michael Lynch,Matthew S. Ackerman,Jean-François Gout,Hongan Long,Way Sung,W. Kelley Thomas,Patricia L. Foster +6 more
TL;DR: This work concludes that the drift-barrier hypothesis is consistent with comparative measures of mutation rates, provides a simple explanation for the existence of error-prone polymerases and yields a formal counter-argument to the view that selection fine-tunes gene-specific mutation rates.
Journal ArticleDOI
Timing, rates and spectra of human germline mutation
Raheleh Rahbari,Arthur Wuster,Sarah J. Lindsay,Robert J Hardwick,Ludmil B. Alexandrov,Saeed Al Turki,Anna F. Dominiczak,Andrew D. Morris,David J. Porteous,Blair H. Smith,Michael R. Stratton,Matthew E. Hurles +11 more
TL;DR: The data suggest that the mutation rate per cell division is higher during both early embryogenesis and differentiation of primordial germ cells but is reduced substantially during post-pubertal spermatogenesis, which has important consequences for the recurrence risks of disorders caused by de novo mutations.
Journal ArticleDOI
A high-coverage Neandertal genome from Vindija Cave in Croatia
Kay Prüfer,Cesare de Filippo,Steffi Grote,Fabrizio Mafessoni,Petra Korlević,Mateja Hajdinjak,Benjamin Vernot,Laurits Skov,PingHsun Hsieh,Stéphane Peyrégne,David Reher,Charlotte Hopfe,Sarah Nagel,Tomislav Maricic,Qiaomei Fu,Christoph Theunert,Christoph Theunert,Rebekah L. Rogers,Pontus Skoglund,Manjusha Chintalapati,Michael Dannemann,Bradley J. Nelson,Felix M. Key,Pavao Rudan,Željko Kućan,Ivan Gušić,Liubov V. Golovanova,Vladimir B. Doronichev,Nick Patterson,David Reich,David Reich,David Reich,Evan E. Eichler,Montgomery Slatkin,Mikkel H. Schierup,Aida M. Andrés,Janet Kelso,Matthias Meyer,Svante Pääbo +38 more
TL;DR: The genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, is sequenced to ~30-fold genomic coverage, allowing 10 to 20% more Ne andertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
Journal ArticleDOI
Determinants of genetic diversity
Hans Ellegren,Nicolas Galtier +1 more
TL;DR: Comparative population genomics is on its way to providing a solution to 'Lewontin's paradox' — the discrepancy between the many orders of magnitude of variation in population size and the much narrower distribution of diversity levels.
Journal ArticleDOI
Determinants of Mutation Rate Variation in the Human Germline
TL;DR: It is now feasible to count de novo mutations in transmissions from parents to offspring, and this direct approach yields a mutation rate that is twofold lower than previous estimates, calling into question the authors' understanding of the chronology of human evolution and raising the possibility that mutation rates have evolved relatively rapidly.
References
More filters
Journal ArticleDOI
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna,Matthew Hanna,Eric Banks,Andrey Sivachenko,Kristian Cibulskis,Andrew Kernytsky,Kiran V. Garimella,David Altshuler,Stacey Gabriel,Mark J. Daly,Mark A. DePristo +10 more
TL;DR: The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
Journal ArticleDOI
The estimation of map distances from recombination values.
TL;DR: The genetic map is a tool to quantify the distance between genes on a chromosome, based on the observed frequency of crossovers during cell division, which is used to estimate the total distance between chromosomes.
Journal ArticleDOI
Merlin--rapid analysis of dense genetic maps using sparse gene flow trees.
TL;DR: The multipoint engine for rapid likelihood inference (Merlin) is a computer program that uses sparse inheritance trees for pedigree analysis; it performs rapid haplotyping, genotype error detection and affected pair linkage analyses and can handle more markers than other pedigree analysis packages.
Journal ArticleDOI
Initial sequence of the chimpanzee genome and comparison with the human genome
Tarjei S. Mikkelsen,LaDeana W. Hillier,Evan E. Eichler,Michael C. Zody,David B. Jaffe,Shiaw-Pyng Yang,Wolfgang Enard,Ines Hellmann,Kerstin Lindblad-Toh,Tasha K. Altheide,Nicoletta Archidiacono,Peer Bork,Jonathan Butler,Jean L. Chang,Ze Cheng,Asif T. Chinwalla,Pieter J. de Jong,Kimberley D. Delehaunty,Catrina Fronick,Lucinda L. Fulton,Yoav Gilad,Gustavo Glusman,Sante Gnerre,Tina Graves,Toshiyuki Hayakawa,Karen E. Hayden,Xiaoqiu Huang,Hongkai Ji,W. James Kent,Mary Claire King,Edward J. Kulbokasl,Ming K. Lee,Ge Liu,Carlos López-Otín,Kateryna D. Makova,Orna Man,Elaine R. Mardis,Evan Mauceli,Tracie L. Miner,William E. Nash,Joanne O. Nelson,Svante Pääbo,Nick Patterson,Craig Pohl,Katherine S. Pollard,Kay Prüfer,Xose S. Puente,David Reich,Mariano Rocchi,Kate R. Rosenbloom,Maryellen Ruvolo,Daniel J. Richter,Stephen F. Schaffner,Arian F.A. Smit,Scott M. Smith,Mikita Suyama,James E. Taylor,David Torrents,Eray Tüzün,Ajit Varki,Gloria Velasco,Mario Ventura,John W. Wallis,Michael C. Wendl,Richard K. Wilson,Eric S. Lander,Robert H. Waterston +66 more
TL;DR: It is found that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.
Journal ArticleDOI
A high-resolution recombination map of the human genome
Augustine Kong,Daniel F. Gudbjartsson,Jesus Sainz,Gudrun M. Jonsdottir,Sigurjon A. Gudjonsson,Bjorgvin Richardsson,Sigrun Sigurdardottir,John Barnard,Bjorn Hallbeck,Gisli Masson,Adam Shlien,Stefan T Palsson,Michael L. Frigge,Thorgeir E. Thorgeirsson,Jeffrey R. Gulcher,Kari Stefansson +15 more
TL;DR: Recombination rates are significantly correlated with both cytogenetic structures and sequence and paternal chromosomes show many differences in locations of recombination maxima, suggesting that there is some underlying component determined by both genetic and environmental factors that affects maternal recombination rates.
Related Papers (5)
Rate of de novo mutations and the importance of father’s age to disease risk
Augustine Kong,Michael L. Frigge,Gisli Masson,Søren Besenbacher,Søren Besenbacher,Patrick Sulem,Gisli Magnusson,Sigurjon A. Gudjonsson,Asgeir Sigurdsson,Aslaug Jonasdottir,Adalbjorg Jonasdottir,Wendy S.W. Wong,Gunnar Th. Sigurdsson,G. Bragi Walters,Stacy Steinberg,Hannes Helgason,Gudmar Thorleifsson,Daniel F. Gudbjartsson,Agnar Helgason,Agnar Helgason,Olafur T. Magnusson,Unnur Thorsteinsdottir,Unnur Thorsteinsdottir,Kari Stefansson,Kari Stefansson +24 more
Revising the human mutation rate: implications for understanding human evolution
Aylwyn Scally,Richard Durbin +1 more