Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Anderson Carpenter, Lynn L ^a   McLachlan, Jason S ^a   Jackson, Stephen T ^b   Kuch, Melanie ^c   Lumibao, Candice Y ^a   Poinar, Hendrik N ^c  

^a UNIVERSITY OF NOTRE DAME   (United States)

^b UNIVERSITY OF WYOMING   (United States)

^c MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CENSUS; DNA; ENVIRONMENTAL CHANGE; EVOLUTIONARY BIOLOGY; FOSSIL RECORD; GENETIC ANALYSIS; GENETIC VARIATION; INHIBITION; LACUSTRINE DEPOSIT; MORPHOLOGY; PALEOECOLOGY; POLYMERASE CHAIN REACTION; QUATERNARY; TAXONOMY;

GREAT LAKES [NORTH AMERICA];

PLANT DNA;

ARTICLE; CLASSIFICATION; FOSSIL; GENETICS; MOLECULAR GENETICS; PHYLOGENY; PLANT; SEDIMENT; UNITED STATES;

DNA, PLANT; FOSSILS; GEOLOGIC SEDIMENTS; GREAT LAKES REGION; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANTS;

EID: 79251543637     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-30     Document Type: Article

References (62)

1. Paleoecology of range limits: beech in the upper peninsula of Michigan. KS Woods MB Davis, Ecology 1989 70 681 696 10.2307/1940219
2. The role of late Holocene climate variability in the expansion of yellow birch in the western Great Lakes region. ST Jackson RK Booth, Diversity and D (Pubitemid 34949572)
3. Validating the use of woodrat (Neotoma) middens for documenting natural invasions. ME Lyford ST Jackson ST Gray RJ Eddy, Journal of Biogeography 2004 31 333 342 10.1046/j.0305-0270.2003.00987.x (Pubitemid 38272254)
4. Role of multidecadal climate variability in a range extension of pinyon pine. ST Gray JL Betancourt ST Jackson RG Eddy, Ecology 2006 87 1124 1130 10.1890/0012-9658(2006)87[1124:ROMCVI]2.0.CO;2 16761590
5. Fire and other factors controlling Big Woods vegetation of Minnesota in the Mid-Nineteenth Century. E Grimm, Ecological Monographs 1984 54 291 311 10.2307/1942499
6. Mid-Holocene climate and the hemlock decline: the range limit of Tsuga canadensis in the western Great Lakes region, USA. R Calcote, The Holocene 2003 13 215 224 10.1191/0959683603hl608rp (Pubitemid 36247175)
7. Chloroplast DNA footprints of postglacial recolonization by oaks. RJ Petit E Pineau B Demesure R Bacilieri A Ducousso, Proceedings of the National Academy of Sciences 1997 94 9996 100001 10.1073/pnas.94.18.9996 (Pubitemid 27408179)
8. The genetic legacy of the Quaternary ice ages. GM Hewitt, Nature 2000 405 907 913 10.1038/35016000 10879524
9. Range shifts and adaptive responses to Quaternary climate change. MB Davis RG Shaw, Science 2001 292 673 679 10.1126/science.292.5517.673 11326089 (Pubitemid 32385531)
10. The spread of deciduous Quercus throughout Europe since the last glacial period. S Brewer R Cheddadi J-L de Beaulieu M Reille, Forest Ecology and Management 2002 156 27 48 10.1016/S0378-1127(01)00646-6 (Pubitemid 34196759)
11. Paleoecology meets genetics: deciphering past vegetational dynamics. FS Hu A Hampe RJ Petit, Frontiers in Ecology and the Environment 2009 7 371 379 10.1890/070160
12. Potential magnitude of future vegetation change in Eastern North America: comparisons with the past. JT Overpeck PJ Bartlein T Webb, Science 1991 254 692 695 10.1126/science.254.5032.692 17774796 (Pubitemid 21917387)
13. Projected distributions of novel and disappearing climates by 2100 AD. JW Williams ST Jackson JE Kutzbach, Proceedings of the National Academy of Sciences 2007 104 5738 5742 10.1073/pnas.0606292104 (Pubitemid 47175604)
14. Late-Quaternary vegetation dynamics in North America: scaling from taxa to biomes. JW Williams BN Shuman T Webb PJ Bartlein PL Leduc, Ecological Monographs 2004 74 309 334 10.1890/02-4045 (Pubitemid 39182897)
15. Molecular indicators of tree migration capacity under rapid climate change. JS McLachlan JS Clark PS Manos, Ecology 2005 86 2088 2098 10.1890/04-1036 (Pubitemid 41117479)
16. Pollen dispersal models in Quaternary plant ecology: assumptions, parameters, and prescriptions. ST Jackson ME Lyford, Botanical Review 1999 65 39 75 10.1007/BF02856557 (Pubitemid 129512706)
17. Validation of pollen studies. ST Jackson RK Booth, Encyclopedia of Quaternary Science Elsevier Scientific Publishing Inc, Elias SA, 2007
18. Late Quaternary biogeography: linking biotic responses to environmental variability across time scales. ST Jackson, Frontiers of Biogeography Sinauer Associates, Lomolino M, Heaney L, 2004
19. Forest genetics in space and time. ST Jackson, New Phytologist 2006 171 1 3 10.1111/j.1469-8137.2006.01781.x 16771977 (Pubitemid 43847059)
20. Geographical variation of lodgepole pine in relation to population history. LC Cwynar GM MacDonald, American Naturalist 1987 129 463 469 10.1086/284651 (Pubitemid 19319213)
21. Chloroplast phylogeography of the common beech (Faguls Sylvatica L), in Europe. B Demesure B Comps RJ Petit, Evolution 1996 50 2515 2520 10.2307/2410719 (Pubitemid 27114684)
22. A new scenario for the Quaternary history of European beech populations: paleobotanical evidence and genetic consequences. D Magri GG Vendramin B Comps I Dupanloup T Geburek G Dušan M Latalowa T Litt L Paule JM Roure I Tantau WO Van Der Knapp RJ Petit JL De Beaulieu, New Phytologist 2006 171 199 221 10.1111/j.1469-8137.2006.01740.x 16771995 (Pubitemid 43847076)
23. Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. U Ramakrishnan EA Hadly, Molecular Ecology 2009 18 1310 1330 10.1111/j.1365-294X.2009.04092.x 19281471
24. Out of America: Ancient DNA evidence for a New World origin of Late Quaternary woolly mammoths. R Debruyne G Chu C King K Bos M Kuch C Schwartz P Szpak DR Gröcke P Matheus G Zazula D Guthrie D Froese B Buigues C de Marliave C Flemming D Poinar D Fisher J Southon AN Tikhonov RDE MacPhee HN Poinar, Current Biology 2008 18 1320 1326 10.1016/j.cub.2008.07.061 18771918
25. Genetic response to climate change: insights from ancient DNA and phylochronology. EA Hadly U Ramakrishnan YL Chan M van Tuinen K O'Keefe PA Spaeth CJ Conroy, PLoS Biology 2004 2 0001 0010 10.1371/journal.pbio.0020290 (Pubitemid 39532921)
26. Population genetics of ice age brown bears. JA Leonard RK Wayne A Cooper, Proceedings of the National Academy of Sciences 2000 97 1651 1654 10.1073/pnas.040453097 (Pubitemid 30118497)
27. Dynamics of Pleistocene population extinctions in Beringian brown bears. I Barnes P Matheus B Shapiro D Jensen A Cooper, Science 2002 295 2267 2270 10.1126/science.1067814 11910112 (Pubitemid 34258841)
28. Rise and fall of the Beringian steppe bison. B Shapiro AJ Drummond A Rambaut MC Wilson PE Matheus AV Sher OG Pybus M Thomas P Gilbert I Barnes J Binladen E Willerslev AJ Hansen GF Baryshnikov JA Burns S Davydov JC Driver DG Froese CR Harington G Keddie P Kosintsev ML Kunz LD Martin RO Stephenson J Storer R Tedford S Zimov A Cooper, Science 2004 306 1561 1565 10.1126/science.1101074 15567864 (Pubitemid 39564953)
29. DNA from pollen: principles and potential. KD Bennett L Parducci, The Holocene 2006 16 1031 1034 10.1177/0959683606069383 (Pubitemid 47110024)
30. Ancient plant DNA in archaeobotany. A Schlumbaum M Tensen V Jaenicke-Despres, Vegetation History and Archaeobotany 2008 17 233 244 10.1007/s00334-007-0125-7 (Pubitemid 351190242)
31. Ancient plant DNA: review and prospects. F Gugerli L Parducci RJ Petit, New Phytologist 2005 166 409 418 10.1111/j.1469-8137.2005.01360.x 15819905 (Pubitemid 40561035)
32. Ancient DNA: Do it right or not at all. A Cooper HN Poinar, Science 2000 289 1139 10.1126/science.289.5482.1139b 10970224 (Pubitemid 30650710)
33. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. M Hofreiter V Jaenicke D Serre A Haeseler S Pääbo, Nucleic Acids Research 2001 29 4793 4799 10.1093/nar/29.23. 4793 11726688 (Pubitemid 33133550)
34. A multidisciplinary study of archaeological grape seeds. E Cappellini MT Gilbert F Geuna G Fiorentino A Hall J Thomas-Oates P Ashton D Ashford P Arthur P Campos J Kool E Willerslev M Collins, Naturwissenschaften 2010 97 205 217 10.1007/s00114-009-0629-3 20033124
35. Ancient olive DNA in pits: preservation, amplification and sequence analysis. R Elbaum C Melamed-Bessudo E Boaretto E Galili S Lev-Yadun AA Levy S Weiner, Journal of Archaeological Science 2006 33 77 88 10.1016/j.jas.2005.06. 011 (Pubitemid 43124647)
36. Morphological and genetic studies of waterlogged Prunus species from the Roman viscus Tagetium, Switzerland. B Pollmann S Jacomet A Schlumbaum, Jounal of Archaeological Science 2005 32 1471 1480 10.1016/j.jas.2005.04.002 (Pubitemid 40984461)
37. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. HN Poinar C Schwartz Ji Shapiro B Qi RDE MacPhee B Buigues A Tikhonov DH Huson LP Tomsho A Auch M Rampp W Miller SC Schuster, Science 2006 311 392 394 10.1126/science.1123360 16368896 (Pubitemid 43132666)
38. Genetic analyses from ancient DNA. S Pääbo H Poinar D Serre V Jaenicke-Després J Hebler N Rohland M Kuch J Krause L Vigilant M Hofreiter, Annual Review of Genetics 2004 38 645 679 15568989 (Pubitemid 40013740)
39. Ancient DNA. E Willerslev A Cooper, Proceedings of the Royal Society B-Biological Sciences 2005 272 3 16 10.1098/rspb.2004.2813
40. The core-freezer - A new sampler for lake sediments. J Shapiro, Ecology 1958 39 748 10.2307/1931618
41. Coring of soft lake sediments. HE Wright, Boreas 1980 9 107 114 10.1111/j.1502-3885.1980.tb01032.x
42. A spare-rod piston sample for lake sediments. HE Wright, Journal of Sedimentary Petrology 1967 37 975 976
43. Diverse plant and animal DNA from Holocene and Pleistocene sedimentary records. E Willerslev AJ Hansen J Binladen TB Brand MTP Gilbert BA Shapiro M Bunce C Wiuf DA Gilichinsky A Cooper, Science 2003 300 791 795 10.1126/science.1084114 12702808 (Pubitemid 36532113)
44. Columbines: a geographically widespread species flock. SA Hodges ML Arnold, Proceedings of the National Academy of Sciences 1994 91 5129 5132 10.1073/pnas.91.11.5129 (Pubitemid 24177806)
45. A quantitative approach to detect and overcome PCR inhibition in ancient DNA extracts. CE King R Debruyne M Kuch C Schwartz HN Poinar, Biotechniques 2009 47 941 949 10.2144/000113244 20041847
46. TCS: a computer program to estimate gene genealogies. M Clement D Posada KA Crandall, Molecular Ecology 2000 9 1657 1659 10.1046/j.1365-294x.2000.01020.x 11050560
47. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. AR Templeton KA Crandall CF Sing, Genetics 1992 132 619 633 1385266
48. Ancient DNA. M Hofreiter D Serre HN Poinar M Kuch S Pääbo, Nature Reviews Genetics 2001 2 353 359 10.1038/35072071 11331901 (Pubitemid 33673073)
49. Ancient DNA reveals late survival of mammoth and horse in interior Alaska. J Haile DG Froese RD Macphee RG Roberts LJ Arnold AV Reyes M Rasmussen R Nielsen BW Brook S Robinson M Demuro MT Gilbert K Munch JJ Austin A Cooper I Barnes P Möller E Willerslev, Proceedings of the National Academy of Sciences 2009 106 22352 22357 10.1073/pnas.0912510106
50. Analysis of short DNA fragments from Holocene peatmoss samples. Y Suyama U Gunnarsson L Parducci, The Holocene 2008 18 1003 1006 10.1177/0959683608093540
51. Ancient DNA from pollen: a genetic record of population history in Scots pine. L Parducci Y Suyama M Lascoux KD Bennett, Molecular Ecology 2005 14 2873 2882 10.1111/j.1365-294X.2005.02644.x 16029485 (Pubitemid 41576968)
52. Ecological restoration in the light of ecological history. ST Jackson RJ Hobbs, Science 2009 325 567 569 10.1126/science.1172977 19644108
53. A framework for assisted migration in an era of climate change. JS McLachlan JJ Hellmann MW Schwartz, Conservation Biology 2007 21 297 302 10.1111/j.1523-1739.2007.00676.x 17391179 (Pubitemid 46474754)
54. A diatom-inferred water depth reconstruction for an Upper Peninsula, Michigan lake. RB Brugam K McKeever L Kolasa, Journal of Paleolimnology 1998 20 267 276 10.1023/A:1007948616511 (Pubitemid 28503783)
55. Paleoecology and high-resolution paleohydrology of a kettle peatland in upper Michigan. RK Booth ST Jackson CED Gray, Quaternary Research 2004 61 1 13 10.1016/j.yqres.2003.07.013 (Pubitemid 38300734)
56. Holocene vegetation development of hemlock-hardwood forests in the Upper Peninsula of Michigan. K Reeves, M.S. thesis University of Wyoming, Department of Botany 2006
57. Bayesian inference of errors in ancient DNA caused by postmortem degradation. LM Mateiu BH Rannala, Molecular Biology and Evolution 2008 25 1503 1511 10.1093/molbev/msn095 18420593 (Pubitemid 351882025)
58. Macrofossil and pollen representation of coniferous trees in modern sediments from Washington. PW Dunwiddie, Ecology 67 58 68 10.2307/1938503
59. Rates of sediment accumulation in pollen cores from small lakes and mires of eastern North America. RS Webb TI Webb, Quaternary Research 1988 30 284 297 10.1016/0033-5894(88)90004-X (Pubitemid 19303071)
60. Ancient DNA chronology within sediment deposits: Are paleobiological reconstructions possible and is DNA leaching a factor? J Haile R Holdaway K Oliver M Bunce MTP Gilbert R Nielsen K Munch SYW Ho B Shapiro E Willerslev, Molecular Biology and Evolution 2007 24 982 989 10.1093/molbev/msm016 17255121 (Pubitemid 46536709)
61. Application of organic geochemistry to paleolimnological reconstructions: a summary of examples from the Laurentian Great Lakes. PA Meyers, Organic Geochemistry 2003 34 261 289 10.1016/S0146-6380(02)00168-7 (Pubitemid 36229819)
62. JP Smol, Pollution of lakes and rivers: a paleoenvironmental perspective Oxford: Blackwell Publishing 2008