Assessing the relationship of ancient and modern populations

Genetics

Volumn 208, Issue 1, 2018, Pages 383-398

  Schraiber, Joshua G ^a  

^a Temple University   (United States)

Author keywords

Ancient DNA; Diffusion theory; Population continuity; SNP data

Indexed keywords

ANCIENT DNA;

AGRICULTURE; ALLELE; ARTICLE; CONTROLLED STUDY; DNA CONTAMINATION; DNA SEQUENCE; EFFECTIVE POPULATION SIZE; ERROR; EUROPEAN; GENE FREQUENCY; GENOTYPE; HETEROZYGOSITY; HUMAN; MAXIMUM LIKELIHOOD METHOD; METHODOLOGY; POPULATION; POPULATION GROWTH; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; ALGORITHM; BIOLOGICAL MODEL; POPULATION GENETICS;

ALGORITHMS; ALLELES; DNA, ANCIENT; GENETICS, POPULATION; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 85040102395     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.117.300448     Document Type: Article

References (41)

1. Alexander, H. D., J. Novembre, and K. Lange, 2009 Fast modelbased estimation of ancestry in unrelated individuals. Genome Res. 19: 1655-1664.
2. Allentoft, M. E., M. Sikora, K. G. Sjögren, S. Rasmussen, M. Rasmussen et al., 2015 Population genomics of bronze age Eurasia. Nature 522: 167-172.
3. Baird, S. J. E., N. H. Barton, and A. M. Etheridge, 2003 The distribution of surviving blocks of an ancestral genome. Theor. Popul. Biol. 64: 451-471.
4. Chang, J. T., 1999 Recent common ancestors of all present-day individuals. Adv. Appl. Probab. 31: 1002-1026.
5. Dabney, J., M. Meyer, and S. Pääbo, 2013 Ancient DNA damage. Cold Spring Harb. Perspect. Biol. 5: a012567.
6. Donnelly P. K, and P. K, 1983 The probability that related individuals share some section of genome identical by descent. Theor. Popul. Biol. 23: 34-63.
7. Ewens, W. J., 2012 Mathematical Population Genetics 1: Theoretical Introduction, Vol. 27. Springer Science & Business Media, Berlin.
8. Falush, D., L. van Dorp, and D. Lawson, 2016 A tutorial on how (not) to over-interpret structure/admixture bar plots. bioRxiv doi: https://doi.org/10.1101/066431.
9. Fu, Q., C. Posth, M. Hajdinjak, M. Petr, S. Mallick et al., 2016 The genetic history of ice age Europe. Nature 534: 200-205.
10. Genomes Project Consortium, 2015 A global reference for human genetic variation. Nature 526: 68-74.
11. Green, R. E., J. Krause, A. W. Briggs, T. Maricic, U. Stenzel et al., 2010 A draft sequence of the Neandertal genome. Science 328: 710-722.
12. Griffiths, R. C., 2003 The frequency spectrum of a mutation, and its age, in a general diffusion model. Theor. Popul. Biol. 64: 241-251
13. Haak, W., I. Lazaridis, N. Patterson, N. Rohland, S. Mallick et al., 2015 Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522: 207-211.
14. Jewett, E. M., M. Steinrücken, and Y. S. Song, 2016 The effects of population size histories on estimates of selection coefficients from time-series genetic data. Mol. Biol. Evol. 33: 3002-3027.
15. Jónsson, H., A. Ginolhac, M. Schubert, P. L. Johnson, and L. Orlando, 2013 mapdamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29: 1682-1684.
16. Kamm, J. A., J. Terhorst, and Y. S. Song, 2017 Efficient computation of the joint sample frequency spectra for multiple populations. J. Comput. Graph. Stat. 26:182-194.
17. Karlin, S., and H. E. Taylor, 1981 A Second Course in Stochastic Processes. Elsevier, Amsterdam.
18. Kelleher, J., A. M. Etheridge, and G. McVean, 2016 Efficient coalescent simulation and genealogical analysis for large sample sizes. PLOS Comput. Biol. 12: e1004842.
19. Korneliussen, T. S., A. Albrechtsen, and R. Nielsen, 2014 ANGSD: analysis of next generation sequencing data. BMC Bioinformatics 15: 356.
20. Kousathanas, A., C. Leuenberger, V. Link, C. Sell, J. Burger et al., 2017 Inferring heterozygosity from ancient and low coverage genomes. Genetics 205: 317-332.
21. Lazaridis, I., N. Patterson, A. Mittnik, G. Renaud, S. Mallick et al., 2014 Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513: 409-413.
22. Lazaridis, I., D. Nadel, G. Rollefson, D C. Merrett, N. Rohland et al., 2016 Genomic insights into the origin of farming in the ancient near east. Nature 536: 419-424.
23. Lipson, M., and D. Reich, 2017 A working model of the deep relationships of diverse modern human genetic lineages outside of Africa. Mol. Biol. Evol. 34: 889-902.
24. Lipson, M., P.-R. Loh, N. Patterson, P. Moorjani, Y.-C. Ko et al., 2014 Reconstructing Austronesian population history in island Southeast Asia. Nat. Commun. 5: 4689.
25. Mathieson, I., I. Lazaridis, N. Rohland, S. Mallick, N. Patterson et al., 2015 Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528: 499-503.
26. Meyer, M., M. Kircher, M. T. Gansauge, H. Li, F. Racimo et al., 2012 A high-coverage genome sequence from an archaic Denisovan individual. Science 338: 222-226.
27. Nielsen, R., and J. Signorovitch, 2003 Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. Theor. Popul. Biol. 63: 245-255.
28. Nielsen, R., T. Korneliussen, A. Albrechtsen, Y. Li, and J. Wang, 2012 SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data. PLoS One 7: e37558.
29. Patterson, N., P. Moorjani, Y. Luo, S. Mallick, N. Rohland et al., 2012 Ancient admixture in human history. Genetics 192: 1065-1093.
30. Peter, B. M., 2016 Admixture, population structure, and F-statistics. Genetics 202: 1485-1501.
31. Pickrell, J. K., and J. K. Pritchard, 2012 Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8: e1002967.
32. Pinhasi, R., D. Fernandes, K. Sirak, M. Novak, S. Connell et al., 2015 Optimal ancient DNA yields from the inner ear part of the human petrous bone. PLoS One 10: e0129102.
33. Pritchard, J. K., M. Stephens, and P. Donnelly, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
34. Racimo, F., G. Renaud, and M. Slatkin, 2016 Joint estimation of contamination, error and demography for nuclear DNA from ancient humans. PLoS Genet. 12: e1005972.
35. Rasmussen, M., S. L. Anzick, M. R. Waters, P. Skoglund, M. DeGiorgio et al., 2014 The genome of a late Pleistocene human from a clovis burial site in western Montana. Nature 506: 225-229.
36. Rohde, D. L., S. Olson, and J. T. Chang. 2004 Modelling the recent common ancestry of all living humans. Nature 431: 562-566.
37. Sawyer, S., J. Krause, K. Guschanski, V. Savolainen, and S. Pääbo, 2012 Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS One 7: e34131.
38. Schraiber, J. G., S. N. Evans, and M. Slatkin. 2016 Bayesian inference of natural selection from allele frequency time series. Genetics 203: 493-511.
39. Sjödin, P., P. Skoglund, and M. Jakobsson, 2014 Assessing the maximum contribution from ancient populations. Mol. Biol. Evol. 31: 1248-1260.
40. Skoglund, P., H. Malmström, M. Raghavan, J. Storå, P. Hall et al., 2012 Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336: 466-469.
41. Skoglund, P., H. Malmström, A. Omrak, M. Raghavan, C. Valdiosera et al., 2014 Genomic diversity and admixture differs for stone-age Scandinavian foragers and farmers. Science 344: 747-750.