Profiling the dead: Generating microsatellite data from fossil bones of extinct megafauna-protocols, problems, and prospects

PLoS ONE

Volumn 6, Issue 1, 2011, Pages

  Allentoft, Morten E ^a,b   Oskam, Charlotte ^a   Houston, Jayne ^a   Hale, Marie L ^b   Gilbert, M Thomas P ^c   Rasmussen, Morten ^c   Spencer, Peter ^a   Jacomb, Christopher ^d   Willerslev, Eske ^c   Holdaway, Richard N ^b,e   Bunce, Michael ^a  

^a MURDOCH UNIVERSITY   (Australia)

^b UNIVERSITY OF CANTERBURY   (New Zealand)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

^d UNIVERSITY OF OTAGO   (New Zealand)

^e PALAECOL RESEARCH LTD   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MICROSATELLITE DNA; MITOCHONDRIAL DNA; PRIMER DNA;

ARTICLE; BONE; CONTROLLED STUDY; DINORNITHIFORMES; DNA DETERMINATION; DNA EXTRACTION; EGG SHELL; EXTINCT SPECIES; FOSSIL; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE LOCUS; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; HIGH THROUGHPUT SCREENING; MEGAFAUNA; MICROSATELLITE MARKER; MOA; NONHUMAN; POLYMERASE CHAIN REACTION; QUANTITATIVE STUDY; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; BIRD; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; SPECIES EXTINCTION;

AVES; DINORNIS; DINORNIS GIGANTEUS; DINORNIS ROBUSTUS; DINORNITHIFORMES;

ANIMALS; BONE AND BONES; DNA PRIMERS; DNA, MITOCHONDRIAL; EGG SHELL; EXTINCTION, BIOLOGICAL; FOSSILS; MICROSATELLITE REPEATS; PALAEOGNATHAE; RESEARCH DESIGN;

EID: 79551638609     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016670     Document Type: Article

References (59)

1. Abdelkrim J, Robertson BC, Stanton JAL, Gemmell NJ (2009) Fast, costeffective development of species-specific microsatellite markers by genomic sequencing. Biotechniques 46: 185-192.
2. Allentoft ME, Schuster S, Holdaway RN, Hale ML, McLay E, et al. (2009) Identification of microsatellites from an extinct moa species using highthroughput (454) sequence data. Biotechniques 46: 195-200.
3. Santana QC, Coetzee MPA, Steenkamp ET, Mlonyeni OX, Hammond GNA, et al. (2009) Microsatellite discovery by deep sequencing of enriched genomic libraries. Biotechniques 46: 217-223.
4. Bunce M, Worthy TH, Phillips MJ, Holdaway RN, Willerslev E, et al. (2009) The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. Proc Natl Acad Sci USA 106: 20646-20651.
5. Holdaway RN, Jacomb C (2000) Rapid extinction of the moas (Aves: Dinorinthiformes): Model, test, and implications. Science 287: 2250-2254.
6. Worthy TH, Holdaway RN (1996) Quaternary fossil faunas, overlapping taphonomies, and palaeofaunal reconstruction in north Canterbury, South Island, New Zealand. J R Soc NZ 26: 275-361.
7. Worthy TH, Holdaway RN (2002) The lost world of the Moa. Christchurch: Canterbury University Press.718 p.
8. Wood JR, Worthy TH, Rawlence NJ, Jones SM, Read SE (2008) A deposition mechanism for Holocene miring bone deposits, South Island, New Zealand. J Taphonomy 6: 1-20.
9. Oskam CL, Haile J, McLay E, Rigby P, Allentoft ME, et al. (2010) Fossil avian eggshell preserves ancient DNA. Proc R Soc B 277: 1991-2000.
10. Allentoft ME, Bunce M, Scofield RP, Hale ML, Holdaway RN (2010) Highly skewed sex ratios and biased fossil deposition of moa: ancient DNA provides new insight on New Zealand's extinct megafauna. Quaternary Sci Rev 29: 753-762.
11. Rawlence NJ, Wood JR, Armstrong KN, Cooper A (2009) DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa. Proc R Soc B 276: 3395-3402.
12. Wood JR, Rawlence NJ, Rogers GM, Austin JJ, Worthy TH, et al. (2008) Coprolite deposits reveal the diet and ecology of the extinct New Zealand megaherbivore moa (Aves, Dinornithiformes). Quaternary Sci Rev 27: 2593-2602.
13. Bunce M, Worthy TH, Ford T, Hoppitt W, Willerslev E, et al. (2003) Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 425: 172-175.
14. Huynen L, Millar CD, Scofield RP, Lambert DM (2003) Nuclear DNA sequences detect species limits in ancient moa. Nature 425: 175-178.
15. Wattier R, Engel CR, Saumitou-Laprade P, Valero M (1998) Short allele dominance as a source of heterozygote deficiency at microsatellite loci: experimental evidence at the dinucleotide locus Gv1CT in Gracilaria gracilis (Rhodophyta). Mol Ecol 7: 1569-1573.
16. Navidi W, Arnheim N, Waterman MS (1992) A multiple-tubes approach for accurate genotyping of very small DNA samples by using PCR - statistical considerations. Am J of Hum Genet 50: 347-359.
17. Miller CR, Joyce P, Waits LP (2002) Assessing allelic dropout and genotype reliability using maximum likelihood. Genetics 160: 357-366.
18. Taberlet P, Griffin S, Goossens B, Questiau S, Manceau V, et al. (1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucl Acids Res 24: 3189-3194.
19. Roeder AD, Elsmore P, Greenhalgh M, McDonald A (2009) Maximizing DNA profiling success from sub-optimal quantities of DNA: A staged approach. Forensic Sci Int Genet 3: 128-137.
20. Parsons KM (2001) Reliable microsatellite genotyping of dolphin DNA from faeces. Mol Ecol Notes 1: 341-344.
21. Frantz AC, Pope LC, Carpenter PJ, Roper TJ, Wilson GJ, et al. (2003) Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Mol Ecol 12: 1649-1661.
22. Morin PA, Chambers KE, Boesch C, Vigilant L (2001) Quantitative polymerase chain reaction analysis ofDNA fromnoninvasive samples for accuratemicrosatellite genotyping of wild chimpanzees (Pan troglodytes verus). Mol Ecol 10: 1835-1844.
23. Goossens B, Waits LP, Taberlet P (1998) Plucked hair samples as a source of DNA: reliability of dinucleotide microsatellite genotyping. Mol Ecol 7: 1237-1241.
24. Sefc KM, Payne RB, Sorenson MD (2003) Microsatellite amplification from museum feather samples: Effects of fragment size and template concentration on genotyping errors. Auk 120: 982-989.
25. Arandjelovic M, Guschanski K, Schubert G, Harris TR, Thalmann O, et al. (2009) Two-step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples. Mol Ecol Res 9: 28-36.
26. Balogh MK, Burger J, Bender M, Schneider PM, Alt KW (2003) STR genotyping and mtDNA sequencing of latent fingerprint on paper. Forensic Sci Int 137: 188-195.
27. Yang DY, Eng B, Waye JS, Dudar JC, Saunders SR (1998) Technical note: Improved DNA extraction from ancient bones using silica-based spin columns. Am J Phy Anthropology 105: 539-543.
28. Maricic T, Paabo S (2009) Optimization of 454 sequencing library preparation from small amounts of DNA permits sequence determination of both DNA strands. Biotechniques 46: 51-57.
29. Meyer M, Briggs AW, Maricic T, Hober B, Hoffner BH, et al. (2008) From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucl Acids Res 36.
30. Faircloth BC (2008) MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Mol Ecol Res 8: 92-94.
31. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, et al. (2007) Primer3Plus, an enhanced web interface to Primer3. Nucl Acids Res 35: W71-W74.
32. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6: 288-295.
33. Rousset F (2008) GENEPOP' 007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Res 8: 103-106.
34. van Oosterhout C, Weetman D, Hutchinson WF (2006) Estimation and adjustment of microsatellite null alleles in nonequilibrium populations. Mol Ecol Notes 6: 255-256.
35. Taberlet P, Luikart G (1999) Non-invasive genetic sampling and individual identification. Biol J Linn Soc 68: 41-55.
36. Waits LP, Luikart G, Taberlet P (2001) Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol Ecol 10: 249-256.
37. Brennan PLR, Hyseni C (2008) Development of microsatellite markers for parentage analysis in the great tinamou (Tinamus major). Mol Ecol Res 8: 933-935.
38. Kimwele CN, Graves JA, Burke T, Hanotte O (1998) Development of microsatellite markers for parentage typing of chicks in the ostrich Struthio camelus. Mol Ecol 7: 249-251.
39. Tang B, Huang YH, Lin L, Hu XX, Feng JD, et al. (2003) Isolation and characterization of 70 novel microsatellite markers from ostrich (Struthio camelus) genome. Genome 46: 833-840.
40. Taylor EL, Vercoe P, Cockrem J, Groth D, Wetherall JD, et al. (1999) Isolation and characterization of microsatellite loci in the emu, Dromaius novaehollandiae, and cross-species amplification within Ratitae. Mol Ecol 8: 1963-1964.
41. Ward WK, McPartlan HC, Matthews ME, Robinson NA (1998) Ostrich microsatellite polymorphisms at the VIAS-OS4, VIAS-OS8, VIAS-OS14, VIAS-OS22, and VIAS-OS29 loci. Anim Genet 29: 331.
42. Huang Y, Liu Q, Tang B, Lin L, Liu W, et al. (2008) A preliminary microsatellite genetic map of the ostrich (Struthio camelus). Cytogenet Genome Res 121: 130-136.
43. Dawson DA, Horsburgh GJ, Kupper C, Stewart IRK, Ball AD, et al. (2010) New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utility - as demonstrated for birds. Mol Ecol Res 10: 475-494.
44. Pertoldi C, Hansen MM, Loeschcke V, Madsen AB, Jacobsen L, et al. (2001) Genetic consequences of population decline in the European otter (Lutra lutra): an assessment of microsatellite DNA variation in Danish otters from 1883 to 1993. Proc R Soc B 268: 1775-1781.
45. Bourke B, Frantz A, Lavers C, Davison A, Dawson D, et al. (2010) Genetic signatures of population change in the British golden eagle (Aquila chrysaetos). Conserv Genet;DOI 10.1007/s10592-010-0076-x.
46. Petren K, Grant PR, Grant BR, Clack AA, Lescano NV (2010) Multilocus genotypes from Charles Darwin's finches: biodiversity lost since the voyage of the Beagle. Phil Trans R Soc B 365: 1009-1018.
47. Whitehouse AM, Harley EH (2001) Post-bottleneck genetic diversity of elephant populations in South Africa, revealed using microsatellite analysis. Mol Ecol 10: 2139-2149.
48. Duckett P, Stow A (2010) Rapid isolation and characterisation of microsatellite loci from a widespread Australian gecko, the Tree Dtella, Gehyra variegata. Conserv Genet Res;DOI 10.1007/s12686-010-9248-8.
49. Clay C, Gleeson D, Howitt R, Lawrence H, Abdelkrim J, et al. (2010) Characterisation of microsatellite markers for the primitive New Zealand frog, Leiopelma hochstetteri. Conserv Genet Res: DOI 10.1007/s12686-010-9211-8.
50. Castoe TA, Poole AW, Gu WJ, de Koning APJ, Daza JM, et al. (2009) Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Mol Ecol Res 10: 341-347.
51. Primmer CR, Raudsepp T, Chowdhary BP, Moller AR, Ellegren H (1997) Low frequency of microsatellites in the avian genome. Genome Res 7: 471-482.
52. Gagneux P, Boesch C, Woodruff DS (1997) Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair. Mol Ecol 6: 861-868.
53. Morin PA, Leduc RG, Archer FI, Martien KK, Huebinger R, et al. (2009) Significant deviations from Hardy-Weinberg equilibrium caused by low levels of microsatellite genotyping errors. Mol Ecol Res 9: 498-504.
54. Bonin A, Bellemain E, Eidesen PB, Pompanon F, Brochmann C, et al. (2004) How to track and assess genotyping errors in population genetics studies. Mol Ecol 13: 3261-3273.
55. Hoffman JI, Amos W(2005)Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion. Mol Ecol 14: 599-612.
56. Miller JM, Hallager S, Monfort SL, Newby J, Bishop K, et al. (2010) Phylogeographic analysis of nuclear and mtDNA supports subspecies designations in the ostrich (Struthio camelus). Conserv Genet;DOI 10.1007/s10592-10010-10149-x.
57. Willerslev E, Cooper A (2005) Ancient DNA. Proc R Soc B 272: 3-16.
58. Anderson CNK, 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.
59. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol B 7.