1 |
DANIAU A L, DESPRAT S, ALEMAN J C, et al. Terrestrial plant microfossils in palaeoenvironmental studies, pollen, microcharcoal and phytolith: towards a comprehensive understanding of vegetation, fire and climate changes over the past one million years [J]. Revue de Micropaleontologie, 2019, 63: 1-35.
|
2 |
ZHAO Y, TZEDAKIS P C, LI Q, et al. Evolution of vegetation and climate variability on the Tibetan Plateau over the past 1.74 million years [J]. Science Advances, 2020, 6(19). DOI:10.1126/sciadv.aay6193 .
|
3 |
ZHANG N M, CAO X Y, XU Q H, et al. Vegetation change and human-environment interactions in the Qinghai Lake Basin, northeastern Tibetan Plateau, since the last Deglaciation [J]. Catena, 2022, 210. DOI:10.1016/j.catena.2021.105892 .
|
4 |
POSTIGO-MIJARRA J M, ALTOLAGUIRRE Y, MORENO- DOMÍNGUEZ R, et al. Climatic reconstruction at the early Miocene La Rinconada mine (Ribesalbes-Alcora Basin, eastern Spain) based on Coexistence Approach, CLAMP and LMA analysis [J]. Review of Palaeobotany and Palynology, 2022, 304. DOI:10.1016/j.revpalbo.2022.104714 .
|
5 |
WANG W M. Phytoliths reveal cycling Pleistocene climate changes at a Paleolithic site in the lower reaches of the Yangtze River, East China [J]. Review of Palaeobotany and Palynology, 2022, 306. DOI:10.1016/j.revpalbo.2022.104764 .
|
6 |
SHEN Y C, SWEENEY L, LIU M M, et al. Reconstructing burnt area during the Holocene: an Iberian case study [J]. Climate of the Past, 2022, 18(5): 1 189-1 201.
|
7 |
ANDERSON-CARPENTER L L, MCLACHLAN J S, JACKSON S T, et al. Ancient DNA from lake sediments: bridging the gap between paleoecology and genetics [J]. BMC Evolutionary Biology, 2011, 11(1). DOI:10.1186/1471-2148-11-30 .
|
8 |
PARDUCCI L, BENNETT K D, FICETOLA G F, et al. Ancient plant DNA in lake sediments [J]. The New Phytologist, 2017, 214(3): 924-942.
|
9 |
HIGUCHI R G, WRISCHNIK L A, OAKES E, et al. Mitochondrial DNA of the extinct quagga: relatedness and extent of postmortem change [J]. Journal of Molecular Evolution, 1987, 25(4): 283-287.
|
10 |
ENDICOTT P, HO S Y W, STRINGER C. Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and modern human origins [J]. Journal of Human Evolution, 2010, 59(1): 87-95.
|
11 |
LAZARIDIS I, PATTERSON N, MITTNIK A, et al. Ancient human genomes suggest three ancestral populations for present-day Europeans [J]. Nature, 2014, 513(7 518): 409-413.
|
12 |
FORSTER P, HARDING R, TORRONI A, et al. Origin and evolution of native American mtDNA variation: a reappraisal [J]. American Journal of Human Genetics, 1996, 59(4): 935-945.
|
13 |
PEDERSEN M W, RUTER A, SCHWEGER C, et al. Postglacial viability and colonization in North America’s ice-free corridor [J]. Nature, 2016, 537(7 618): 45-49.
|
14 |
SERRANO J G, ORDÓÑEZ A C, FREGEL R. Paleogenomics of the prehistory of Europe: human migrations, domestication and disease [J]. Annals of Human Biology, 2021, 48(3): 179-190.
|
15 |
LARSON G, ALBARELLA U, DOBNEY K, et al. Ancient DNA, pig domestication, and the spread of the Neolithic into Europe [J]. Proceedings of the National Academy of Sciences of the United States of America, 2007, 104(39): 15 276-15 281.
|
16 |
SMITH O, MOMBER G, BATES R, et al. Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago [J]. Science, 2015, 347: 998-1 001.
|
17 |
SHARMA P P, KALUZIAK S T, PÉREZ -PORRO A R, et al. Phylogenomic interrogation of arachnida reveals systemic conflicts in phylogenetic signal [J]. Molecular Biology and Evolution, 2014, 31(11): 2 963-2 984.
|
18 |
PETERSEN G, JOHANSEN B, SEBERG O. PCR and sequencing from a single pollen grain [J]. Plant Molecular Biology, 1996, 31(1): 189-191.
|
19 |
SUYAMA Y, KAWAMURO K, KINOSHITA I, et al. DNA sequence from a fossil pollen of Abies spp. from Pleistocene peat [J]. Genes & Genetic Systems, 1996, 71(3): 145-149.
|
20 |
TORTI A, LEVER M A, JORGENSEN B B. Origin, dynamics, and implications of extracellular DNA pools in marine sediments [J]. Marine Genomics, 2015, 24 Pt 3: 185-196.
|
21 |
CAPO E, GIGUET-COVEX C, ROUILLARD A, et al. Lake sedimentary DNA research on past terrestrial and aquatic biodiversity: overview and recommendations [J]. Quaternary, 2021, 4(1). DOI:10.3390/quat4010006 .
|
22 |
JIA W H, ANSLAN S, CHEN F H, et al. Sedimentary ancient DNA reveals past ecosystem and biodiversity changes on the Tibetan Plateau: overview and prospects [J]. Quaternary Science Reviews, 2022, 293. DOI:10.1016/j.quascirev.2022.107703 .
|
23 |
JOHNSON M D, FREELAND J R, PARDUCCI L, et al. Environmental DNA as an emerging tool in botanical research [J]. American Journal of Botany, 2023, 110(2). DOI:10.1002/ajb2.16120 .
|
24 |
PARDUCCI L, SUYAMA Y, LASCOUX M, et al. Ancient DNA from pollen: a genetic record of population history in Scots pine [J]. Molecular Ecology, 2005, 14(9): 2 873-2 882.
|
25 |
LI K, STOOF-LEICHSENRING K R, LIU S S, et al. Plant sedimentary DNA as a proxy for vegetation reconstruction in eastern and northern Asia [J]. Ecological Indicators, 2021, 132. DOI:10.1016/j.ecolind.2021.108303 .
|
26 |
WILLERSLEV E, CAPPELLINI E, BOOMSMA W, et al. Ancient biomolecules from deep ice cores reveal a forested southern Greenland [J]. Science, 2007, 317(5 834): 111-114.
|
27 |
WILLERSLEV E, HANSEN A J, BINLADEN J, et al. Diverse plant and animal genetic records from Holocene and Pleistocene sediments [J]. Science, 2003, 300(5 620): 791-795.
|
28 |
WILLERSLEV E, DAVISON J, MOORA M, et al. Fifty thousand years of Arctic vegetation and megafaunal diet [J]. Nature, 2014, 506(7 486): 47-51.
|
29 |
ZALE R, HUANG Y T, BIGLER C, et al. Growth of plants on the Late Weichselian ice-sheet during Greenland interstadial-1? [J]. Quaternary Science Reviews, 2018, 185: 222-229.
|
30 |
GIGUET-COVEX C, PANSU J, ARNAUD F, et al. Long livestock farming history and human landscape shaping revealed by lake sediment DNA [J]. Nature Communications, 2014, 5(1). DOI:10.1038/ncomms4211 .
|
31 |
PANSU J, GIGUET-COVEX C, FICETOLA G F, et al. Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA [J]. Molecular Ecology, 2015, 24(7): 1 485-1 498.
|
32 |
LIU S S, STOOF-LEICHSENRING K R, KRUSE S, et al. Holocene vegetation and plant diversity changes in the north-eastern siberian treeline region from pollen and sedimentary ancient DNA [J]. Frontiers in Ecology and Evolution, 2020, 8. DOI:10.3389/fevo.2020.560243 .
|
33 |
PARDUCCI L, VÄLIRANTA M, SALONEN J S, et al. Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA [J]. Philosophical Transactions of the Royal Society of London B Biological Sciences, 2015, 370(1 660). DOI:10.1098/rstb.2013.0382 .
|
34 |
RAWLENCE N J, LOWE D J, WOOD J R, et al. Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects [J]. Journal of Quaternary Science, 2014, 29(7): 610-626.
|
35 |
LINDAHL T. Instability and decay of the primary structure of DNA [J]. Nature, 1993, 362(6 422): 709-715.
|
36 |
MITCHELL D, WILLERSLEV E, HANSEN A. Damage and repair of ancient DNA [J]. Mutation Research, 2005, 571(1/2): 265-276.
|
37 |
DALÉN L, HEINTZMAN P D, KAPP J D, et al. Deep-time paleogenomics and the limits of DNA survival [J]. Science, 2023, 382(6 666): 48-53.
|
38 |
WILLERSLEV E, COOPER A. Ancient DNA [J]. Proceedings of the Royal Society, 2005, 272(1 558): 3-16.
|
39 |
PANIERI G, LUGLI S, MANZI V, et al. Ribosomal RNA gene fragments from fossilized cyanobacteria identified in primary gypsum from the late Miocene, Italy [J]. Geobiology, 2010, 8. DOI:10.1111/j.1472-4669.2009.00230.x .
|
40 |
JIA W H, LIU X Q, STOOF-LEICHSENRING K R, et al. Preservation of sedimentary plant DNA is related to lake water chemistry [J]. Environmental DNA, 2022, 4(2): 425-439.
|
41 |
CAPPELLINI E, PROHASKA A, RACIMO F, et al. Ancient biomolecules and evolutionary inference [J]. Annual Review of Biochemistry, 2018, 87: 1 029-1 060.
|
42 |
da FONSECA R R, SMITH B D, WALES N, et al. The origin and evolution of maize in the southwestern United States [J]. Nature Plants, 2015, 1(1). DOI:10.1038/nplants.2014.3 .
|
43 |
MASCHER M, SCHUENEMANN V J, DAVIDOVICH U, et al. Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley [J]. Nature Genetics, 2016, 48(9): 1 089-1 093.
|
44 |
ZOLITSCHKA B, FRANCUS P, OJALA A E K, et al. Varves in lake sediments—a review [J]. Quaternary Science Reviews, 2015, 117: 1-41.
|
45 |
PEDERSEN M W, GINOLHAC A, ORLANDO L, et al. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa [J]. Quaternary Science Reviews, 2013, 75: 161-168.
|
46 |
BIRKS H J, BIRKS H H. How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras? [J]. New Phytologist, 2016, 209(2): 499-506.
|
47 |
ZAVALA E I, JACOBS Z, VERNOT B, et al. Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave [J]. Nature, 2021, 595(7 867): 399-403.
|
48 |
DÍAZ F P, LATORRE C, CARRASCO-PUGA G, et al. Multiscale climate change impacts on plant diversity in the Atacama Desert [J]. Global Change Biology, 2019, 25(5): 1 733-1 745.
|
49 |
ROBE P, NALIN R, CAPELLANO C, et al. Extraction of DNA from soil [J]. European Journal of Soil Biology, 2003, 39(4): 183-190.
|
50 |
THOMSEN P F, KIELGAST J, IVERSEN L L, et al. Detection of a diverse marine fish fauna using environmental DNA from seawater samples [J]. PLoS ONE, 2012, 7(8). DOI:10.1371/journal.pone.0041732 .
|
51 |
ROHLAND N, GLOCKE I, AXIMU-PETRI A, et al. Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing [J]. Nature Protocols, 2018, 13(11): 2 447-2 461.
|
52 |
TABERLET P, COISSAC E, POMPANON F, et al. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding [J]. Nucleic Acids Research, 2007, 35(3). DOI:10.1093/nar/gkl938 .
|
53 |
MURCHIE T J, KUCH M, DUGGAN A T, et al. Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set [J]. Quaternary Research, 2021, 99: 305-328.
|
54 |
THOMSEN P F, WILLERSLEV E. Environmental DNA—an emerging tool in conservation for monitoring past and present biodiversity [J]. Biological Conservation, 2015, 183: 4-18.
|
55 |
CHEN Lian, WU Lin, LIU Yan, et al. Application of environmental DNA metabarcoding in ecology [J]. Acta Ecologica Sinica, 2016, 36(15): 4 573-4 582.
|
|
陈炼, 吴琳, 刘燕, 等. 环境DNA metabarcoding及其在生态学研究中的应用 [J]. 生态学报, 2016, 36(15): 4 573-4 582.
|
56 |
RIAZ T, SHEHZAD W, VIARI A, et al. ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis [J]. Nucleic Acids Research, 2011, 39(21). DOI:10.1093/nar/gkr732 .
|
57 |
REVÉRET A, RIJAL D P, HEINTZMAN P D, et al. Environmental DNA of aquatic macrophytes: the potential for reconstructing past and present vegetation and environments [J]. Freshwater Biology, 2023, 68(11): 1 929-1 950.
|
58 |
YU D W, JI Y Q, EMERSON B C, et al. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring [J]. Methods in Ecology and Evolution, 2012, 3(4): 613-623.
|
59 |
QUINCE C, WALKER A W, SIMPSON J T, et al. Shotgun metagenomics, from sampling to analysis[J]. Nature Biotechnology, 2017, 35: 833-844.
|
60 |
WEYRICH L S, DUCHENE S, SOUBRIER J, et al. Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus[J]. Nature, 2017, 544: 357-361.
|
61 |
TABERLET P, COISSAC E, POMPANON F, et al. Towards next-generation biodiversity assessment using DNA metabarcoding [J]. Molecular Ecology, 2012, 21(8): 2 045-2 050.
|
62 |
BENSON D A, CAVANAUGH M, CLARK K, et al. GenBank [J]. Nucleic Acids Research, 2017, 45(Database issue). DOI:10.1093/nar/gkw1070 .
|
63 |
LEINONEN R, AKHTAR R, BIRNEY E, et al. The European nucleotide archive [J]. Nucleic Acids Research, 2011, 39(): D28-D31.
|
64 |
SØNSTEBØ J H, GIELLY L, BRYSTING A K, et al. Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate [J]. Molecular Ecology Resources, 2010, 10(6): 1 009-1 018.
|
65 |
WANG Y C, PEDERSEN M W, ALSOS I G, et al. Late Quaternary dynamics of Arctic biota from ancient environmental genomics [J]. Nature, 2021, 600: 86-92.
|
66 |
ALSOS I G, LAMMERS Y, YOCCOZ N G, et al. Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation [J]. PLoS ONE, 2018, 13(4). DOI:10.1371/journal.pone.0195403 .
|
67 |
ARMBRECHT L H, COOLEN M J L, LEJZEROWICZ F, et al. Ancient DNA from marine sediments: precautions and considerations for seafloor coring, sample handling and data generation [J]. Earth-Science Reviews, 2019, 196. DOI:10.1016/j.earscirev.2019.102887 .
|
68 |
ALSOS I G, SJÖGREN P, EDWARDS M E, et al. Sedimentary ancient DNA from Lake Skartjørna, Svalbard: assessing the resilience of arctic flora to Holocene climate change [J]. Holocene, 2016, 26(4): 627-642.
|
69 |
CLARKE C L, ALSOS I G, EDWARDS M E, et al. A 24,000-year ancient DNA and pollen record from the Polar Urals reveals temporal dynamics of arctic and boreal plant communities [J]. Quaternary Science Reviews, 2020, 247. DOI:10.1016/j.quascirev.2020.106564 .
|
70 |
SAWYER S, KRAUSE J, GUSCHANSKI K, et al. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA[J]. PLoS ONE, 2012, 7(3). DOI:10.1371/journal.pone.0034131 .
|
71 |
JÓNSSON H, GINOLHAC A, SCHUBERT M, et al. MapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters[J]. Bioinformatics, 2013, 29(13): 1 682-1 684.
|
72 |
VAROTTO C, PINDO M, BERTONI E, et al. A pilot study of eDNA metabarcoding to estimate plant biodiversity by an alpine glacier core (Adamello glacier, North Italy) [J]. Scientific Reports, 2021, 11. DOI:10.1038/s41598-020-79738-5 .
|
73 |
KJÆR K H, WINTHER PEDERSEN M, de SANCTIS B, et al. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA [J]. Nature, 2022, 612(7 939): 283-291.
|
74 |
PARDUCCI L, JØRGENSEN T, TOLLEFSRUD M M, et al. Glacial survival of boreal trees in northern Scandinavia[J]. Science, 2012, 335(6072): 1 083-1 086.
|
75 |
PARDUCCI L, MATETOVICI I, FONTANA S L, et al. Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia[J]. Molecular Ecology, 2013, 22(13): 3 511-3 524.
|
76 |
EPP L S, GUSSAROVA G, BOESSENKOOL S, et al. Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes[J]. Quaternary Science Reviews, 2015, 117: 152-163.
|
77 |
BREMOND L, FAVIER C, FICETOLA G F, et al. Five thousand years of tropical lake sediment DNA records from Benin [J]. Quaternary Science Reviews, 2017, 170: 203-211.
|
78 |
NIEMEYER B, EPP L S, STOOF-LEICHSENRING K R, et al. A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline [J]. Molecular Ecology Resources, 2017, 17(6): e46-e62.
|
79 |
CLARKE C L, EDWARDS M E, BROWN A G, et al. Holocene floristic diversity and richness in northeast Norway revealed by sedimentary ancient DNA(sedaDNA) and pollen [J]. Boreas, 2018, 48(2): 299-316.
|
80 |
GARCÉS-PASTOR S, COISSAC E, LAVERGNE S, et al. High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change [J]. Nature Communications, 2022, 13(1). DOI:10.1038/s41467-022-34010-4 .
|
81 |
BOESSENKOOL S, MCGLYNN G, EPP L S, et al. Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity[J]. Conservation Biology, 2014, 28(2): 446-455.
|
82 |
DOMMAIN R, ANDAMA M, McDONOUGH M M, et al. The challenges of reconstructing tropical biodiversity with sedimentary ancient DNA: a 2200-year-long metagenomic record from bwindi impenetrable forest, Uganda[J]. Frontiers in Ecology and Evolution, 2020, 8. DOI:10.3389/fevo.2020.00218 .
|
83 |
HAILE J, HOLDAWAY R, OLIVER K, et al. Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?[J]. Molecular Biology and Evolution, 2007, 24(4): 982-989.
|
84 |
PARDUCCI L, ALSOS I G, UNNEBERG P, et al. Shotgun environmental DNA, pollen, and macrofossil analysis of lateglacial lake sediments from southern Sweden[J]. Frontiers in Ecology and Evolution, 2019, 7. DOI:10.3389/fevo.2019.00189 .
|
85 |
MA Rui, CHEN Jianhui, LIU Jianbao, et al. Progress in the application of lake sediment DNA in climate and environmental change and ecosystem response [J]. Journal of Lake Sciences, 2021, 33(3): 653-666.
|
|
马睿, 陈建徽, 刘建宝, 等. 湖泊沉积物DNA在气候环境变化和生态系统响应研究中的应用[J]. 湖泊科学, 2021, 33(3): 653-666.
|
86 |
PEDERSEN M W, OVERBALLE-PETERSEN S, ERMINI L, et al. Ancient and modern environmental DNA [J]. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences, 2015, 370(1 660). DOI:10.1098/rstb.2013.0383 .
|
87 |
VOLDSTAD L H, ALSOS I G, FARNSWORTH W R, et al. A complete Holocene lake sediment ancient DNA record reveals long-standing high Arctic plant diversity hotspot in northern Svalbard [J]. Quaternary Science Reviews, 2020, 234. DOI:10.1016/j.quascirev.2020.106207 .
|
88 |
LIU S S, KRUSE S, SCHERLER D, et al. Sedimentary ancient DNA reveals a threat of warming-induced alpine habitat loss to Tibetan Plateau plant diversity [J]. Nature Communications, 2021, 12(1). DOI:10.1038/s41467-021-22986-4 .
|
89 |
WANG Rong, ZHANG Ke, LIU Jianbao, et al. The importance of lake ecosystem evolution for anthropocene research [J]. Journal of Lake Sciences, 2024,36(2):333-338.
|
|
王荣,张科,刘建宝,等.湖泊流域生态系统演化对人类世研究的重要意义[J].湖泊科学,2024,36(2):333-338.
|
90 |
LENDVAY B, BÁLINT M, PÁL I, et al. Plant macrofossils from lake sediment as the material to assess ancient genetic diversity: did deforestation influence Norway spruce (Picea abies) in the South Carpathians?[J]. Quaternary International, 2018, 477: 106-116.
|
91 |
BIRKS H H. Plant macrofossil introduction [M]. Amsterdam:Elsevier,2007.
|
92 |
SJÖGREN P, EDWARDS M E, GIELLY L, et al. Lake sedimentary DNA accurately records 20th century introductions of exotic conifers in Scotland[J]. New Phytologist, 2017, 213(2): 929-941.
|
93 |
JØRGENSEN T, HAILE J, MÖLLER P, et al. A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability[J]. Molecular Ecology, 2012, 21(8): 1 989-2 003.
|
94 |
PORTER T M, GOLDING G B, KING C, et al. Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility [J]. Molecular Ecology Resources, 2013, 13(5): 798-810.
|
95 |
FICETOLA G F, TABERLET P, COISSAC E. How to limit false positives in environmental DNA and metabarcoding? [J]. Molecular Ecology Resources, 2016, 16(3): 604-607.
|
96 |
BIRKS H H, BIRKS H J B. Future uses of pollen analysis must include plant macrofossils [J]. Journal of Biogeography, 2000, 27(1): 31-35.
|