Statistical guidelines for detecting past population shifts using ancient DNA

Molecular Biology and Evolution

Volumn 29, Issue 9, 2012, Pages 2241-2251

  Mourier, Tobias ^a   Ho, Simon Y W ^b   Gilbert, M Thomas P ^a   Willerslev, Eske ^a   Orlando, Ludovic ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF SYDNEY   (Australia)

Author keywords

ancient DNA; Population bottlenecks; serial coalescent

Indexed keywords

DNA;

ARTICLE; CONCEPTUAL FRAMEWORK; DEMOGRAPHY; HEALTH CARE PLANNING; POPULATION DYNAMICS; POPULATION GENETICS; PRACTICE GUIDELINE; QUANTITATIVE ANALYSIS; SAMPLING; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS;

ANIMALS; COMPUTER SIMULATION; DNA, MITOCHONDRIAL; GENETICS, POPULATION; GUIDELINES AS TOPIC; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION DYNAMICS;

EID: 84865503238     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss094     Document Type: Article

References (59)

1. Adams AM, Hudson RR. 2004. Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms. Genetics 168: 1699-1712. (Pubitemid 40007380)
2. Albrechtsen A, Nielsen FC, Nielsen R. 2010. Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol. 27:2534-2547.
3. Alter SE, Palumbi SR. 2009. Comparing evolutionary patterns and variability in the mitochondrial control region and cytochrome B in three species of baleen whales. J Mol Evol. 68:97-111.
4. Anderson CN, Ramakrishnan U, Chan YL, Hadly EA. 2005. Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bioinformatics 21:1733-1734. (Pubitemid 40542747)
5. Barnett R, Shapiro B, Barnes I, et al. (17 co-authors). 2009. Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Mol Ecol. 18:1668-1677.
6. Beaumont MA. 2004. Recent developments in genetic data analysis: what can they tell us about human demographic history? Heredity 92:365-379. (Pubitemid 38673702)
7. Briggs AW, Good JM, Green RE, et al. (18 co-authors). 2009. Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 325:318-321.
8. Burbano HA, Hodges E, Green RE, et al. (20 co-authors). 2010. Targeted investigation of the Neandertal genome by array-based sequence capture. Science 328:723-725.
9. Campos PF, Kristensen T, Orlando L, et al. (13 co-authors). 2010. Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene. Mol Ecol. 19:4863-4875.
10. Campos PF, Willerslev E, Sher A, et al. (20 co-authors). 2010. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proc Natl Acad Sci USA. 107:5675-5680.
11. Cann RL, Stoneking M, Wilson AC. 1987. Mitochondrial DNA and human evolution. Nature 325:31-36. (Pubitemid 17059465)
12. Chikhi L. 2008. Genetic markers: how accurate can genetic data be? Heredity 101:471-472.
13. Chikhi L, Sousa VC, Luisi P, Goossens B, Beaumont MA. 2010. The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics 186:983-995.
14. Clark PU, Dyke AS, Shakun JD, Carlson AE, Clark J, Wohlfarth B, Mitrovica JX, Hostetler SW, McCabe AM. 2009. The Last Glacial Maximum. Science 325:710-714.
15. Cornuet JM, Santos F, Beaumont MA, Robert CP, Marin JM, Balding DJ, Guillemaud T, Estoup A. 2008. Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics 24:2713-2719. (Pubitemid 352722613)
16. Debruyne R, Chu G, King CE, et al. (21 co-authors). 2008. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr Biol. 18:1320-1326.
17. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 22:1185-1192. (Pubitemid 40577756)
18. Endicott P, Ho SY. 2008. A Bayesian evaluation of human mitochondrial substitution rates. Am J Hum Genet. 82:895-902.
19. Excoffier L, Yang Z. 1999. Substitution rate variation among sites in mitochondrial hypervariable region I of humans and chimpanzees. Mol Biol Evol. 16:1357-1368. (Pubitemid 29473230)
20. Fu YX. 1996. New statistical tests of neutrality for DNA samples from a population. Genetics 143:557-570.
21. Fu YX, Li WH. 1993. Statistical tests of neutrality of mutations. Genetics 133:693-709.
22. Geraldes A, Basset P, Gibson B, Smith KL, Harr B, Yu HT, Bulatova N, Ziv Y, Nachman MW. 2008. Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes. Mol Ecol. 17:5349-5363.
23. Gilbert MT, Drautz DI, Lesk AM, et al. (33 co-authors). 2008. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proc Natl Acad Sci USA. 105:8327-8332. (Pubitemid 351904755)
24. Green RE, Krause J, Briggs AW, et al. (56 co-authors). 2010. A draft sequence of the Neandertal genome. Science 328:710-722.
25. Heled J, Drummond AJ. 2008. Bayesian inference of population size history from multiple loci. BMC Evol Biol. 8:289.
26. Ho SY, Gilbert MT. 2010. Ancient mitogenomics. Mitochondrion 10:1-11.
27. Ho SY, Shapiro B. 2011. Skyline-plot methods for estimating demographic history from nucleotide sequences. Mol Ecol Resour. 11:423-434.
28. Howell N, Smejkal CB, Mackey DA, Chinnery PF, Turnbull DM, Herrnstadt C. 2003. The pedigree rate of sequence divergence in the human mitochondrial genome: there is a difference between phylogenetic and pedigree rates. Am J Hum Genet. 72:659-670. (Pubitemid 36255964)
29. Jackson JA, Baker CS, Vant M, Steel DJ, Medrano-Gonzalez L, Palumbi SR. 2009. Big and slow: phylogenetic estimates of molecular evolution in baleen whales (suborder mysticeti). Mol Biol Evol. 26:2427-2440.
30. Johnson JA, Dunn PO, Bouzat JL. 2007. Effects of recent population bottlenecks on reconstructing the demographic history of prairie-chickens. Mol Ecol. 16:2203-2222. (Pubitemid 46897151)
31. Jakobsson M. 2009. COMPASS: a program for generating serial samples under an infinite sites model. Bioinformatics 25:2845-2847.
32. Knapp M, Rohland N, Weinstock J, Baryshnikov G, Sher A, Nagel D, Rabeder G, Pinhasi R, Schmidt HA, Hofreiter M. 2009. First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns. Mol Ecol. 18:1225-1238.
33. Koh HS, Lee WJ, Kocher TD. 2000. The genetic relationships of two subspecies of striped field mice, Apodemus agrarius coreae and Apodemus agrarius chejuensis. Heredity 85:30-36. (Pubitemid 30647941)
34. Kuhner MK. 2006. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 22:768-770.
35. Li H, Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475:493-496.
36. Lorenzen ED, Nogues-Bravo D, Orlando L, et al. (55 co-authors). 2011. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479:359-364.
37. Luikart G, Allendorf FW, Cornuet JM, Sherwin WB. 1998. Distortion of allele frequency distributions provides a test for recent population bottlenecks. J Hered. 89:238-247. (Pubitemid 28292519)
38. Morin PA, Archer FI, Foote AD, et al. (16 co-authors). 2010. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res. 20:908-916.
39. Myers S, Fefferman C, Patterson N. 2008. Can one learn history from the allelic spectrum? Theor Popul Biol. 73:342-348.
40. Nabholz B, Glemin S, Galtier N. 2008. Strong variations of mitochondrial mutation rate across mammals-the longevity hypothesis. Mol Biol Evol. 25:120-130.
41. Nystrom V, Dalen L, Vartanyan S, Liden K, Ryman N, Angerbjorn A. 2010. Temporal genetic change in the last remaining population of woolly mammoth. Proc Biol Sci. 277:2331-2337.
42. Orlando L, Bonjean D, Bocherens H, Thenot A, Argant A, Otte M, Hanni C. 2002. Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time. Mol Biol Evol. 19:1920-1933. (Pubitemid 35388115)
43. Orlando L, Ginolhac A, Raghavan M, et al. (17 co-authors). 2011. True single-molecule DNA sequencing of a pleistocene horse bone. Genome Res. 21:1705-1719.
44. Poinar HN, Schwarz C, Qi J, et al. (13 co-authors). 2006. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311:392-394. (Pubitemid 43132666)
45. Prost S, Smirnov N, Fedorov VB, Sommer RS, Stiller M, Nagel D, Knapp M, Hofreiter M. 2010. Influence of climate warming on arctic mammals? New insights from ancient DNA studies of the collared lemming Dicrostonyx torquatus. PLoS One 5:e10447.
46. Pybus OG, Rambaut A. 2002. GENIE: estimating demographic history from molecular phylogenies. Bioinformatics 18:1404-1405. (Pubitemid 35244201)
47. Pybus OG, Rambaut A, Harvey PH. 2000. An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155:1429-1437. (Pubitemid 30463449)
48. Ramakrishnan U, Hadly EA, Mountain JL. 2005. Detecting past population bottlenecks using temporal genetic data. Mol Ecol. 14:2915-2922.
49. Ramos-Onsins SE, Rozas J. 2002. Statistical properties of new neutrality tests against population growth. Mol Biol Evol. 19:2092-2100. (Pubitemid 35440445)
50. Rasmussen M, Guo X, Wang Y, et al. (58 co-authors). 2011. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334:94-98.
51. Rasmussen M, Li Y, Lindgreen S, et al. (52 co-authors). 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463:757-762.
52. Romero IG, Manica A, Goudet J, Handley LL, Balloux F. 2009. How accurate is the current picture of human genetic variation? Heredity 102:120-126.
53. Rooney AP, Honeycutt RL, Derr JN. 2001. Historical population size change of bowhead whales inferred from DNA sequence polymorphism data. Evolution 55:1678-1685. (Pubitemid 32908229)
54. Shapiro B, Drummond AJ, Rambaut A, et al. (27 co-authors). 2004. Rise and fall of the Beringian steppe bison. Science 306:1561-1565. (Pubitemid 39564953)
55. Stiller M, Knapp M, Stenzel U, Hofreiter M, Meyer M. 2009. Direct multiplex sequencing (DMPS)-a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Res. 19:1843-1848.
56. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595. (Pubitemid 19274682)
57. Valdiosera CE, Garcia-Garitagoitia JL, Garcia N, et al. (11 co-authors). 2008. Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos). Proc Natl Acad Sci USA. 105:5123-5128. (Pubitemid 351738520)
58. Wakeley J. 1999. Nonequilibrium migration in human history. Genetics 153:1863-1871.
59. Wilson IJ, Weale ME, Balding DJ. 2003. Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities. J R Stat Soc Ser A Stat Soc. 166:155-201.