1. College of Resource Environment and Tourism, Capital Normal University, Beijing 100048, China 2. Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems Research Group, Potsdam 14473, Germany 3. University of Potsdam, Institute of Environmental Science and Geography, Potsdam 14476, Germany 4. University of Potsdam, Institute of Biochemistry and Biology, Potsdam 14476, Germany 5. Group of Alpine Paleoecology and Human Adaptation (ALPHA), State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
Plant environmental DNA extracted from lacustrine sediments (sedimentary DNA, sedDNA) has been increasingly used to investigate past vegetation changes and human impacts at a high taxonomic resolution. However, the representation of vegetation communities surrounding the lake is still unclear. In this study, we compared plant sedDNA metabarcoding and pollen assemblages from 27 lake surface-sediment samples collected from alpine meadow on the central-eastern Tibetan Plateau to investigate the representation of sedDNA data. In general, the identified components of sedDNA are consistent with the counted pollen taxa and local plant communities. Relative to pollen identification, sedDNA data have higher taxonomic resolution, thus providing a potential approach for reconstructing past plant diversity. The sedDNA signal is strongly influenced by local plants while rarely affected by exogenous plants. Because of the overrepresentation of local plants and PCR bias, the abundance of sedDNA sequence types is very variable among sites, and should be treated with caution when investigating past vegetation cover and climate based on sedDNA data. Our finding suggests that sedDNA analysis can be a complementary approach for investigating the presence/absence of past plants and history of human land-use with higher taxonomic resolution.
C, Abel S, Horion T, Tagesson Keersmaecker W, De A W R, Seddon A M, Abdi R Fensholt (2021). The human-environment nexus and vegetation-rainfall sensitivity in tropical drylands.Nat Sustain, 4(1): 25–32 https://doi.org/10.1038/s41893-020-00597-z
2
I G, Alsos Y, Lammers N G, Yoccoz T, Jørgensen P, Sjögren L, Gielly M E Edwards (2018). Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation.PLoS One, 13(4): e0195403 https://doi.org/10.1371/journal.pone.0195403
3
I G, Alsos P, Sjögren M E, Edwards J Y, Landvik L, Gielly M, Forwick E, Coissac A G, Brown L V, Jakobsen M K, Føreid M W Pedersen (2016). Sedimentary ancient DNA from Lake Skartjørna, Svalbard: assessing the resilience of arctic flora to Holocene climate change.Holocene, 26(4): 627–642 https://doi.org/10.1177/0959683615612563
4
L L, Anderson-Carpenter J S, McLachlan S T, Jackson M, Kuch C Y, Lumibao H N Poinar (2011). Ancient DNA from lake sediments: bridging the gap between paleoecology and genetic.BMC Evol Biol, 11: 30 https://doi.org/10.1186/1471-2148-11-30
5
M A A, Baamrane W, Shehzad A, Ouhammou A, Abbad M, Naimi E, Coissac P, Taberlet M Znari (2012). Assessment of the food habits of the Moroccan dorcas gazelle in M′ Sabih Talaa, west central Morocco, using the trnL approach.PLoS One, 7: e35643 https://doi.org/10.1371/journal.pone.0035643
6
H H Birks (2003). The importance of plant macrofossils in the reconstruction of Lateglacial vegetation and climate: examples from Scotland, Western Norway, and Minnesota, USA.Quat Sci Rev, 22: 453–473 https://doi.org/10.1016/S0277-3791(02)00248-2
7
H J B, Birks J M Line (1992). The use of rarefaction analysis for estimating palynological richness from Quaternary pollen-analytical data.Holocene, 2(1): 1–10 https://doi.org/10.1177/095968369200200101
8
H J B, Birks H H Birks (2016). How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras?.New Phytol, 209(2): 499–506 https://doi.org/10.1111/nph.13657
9
F, Boyer C, Mercier A, Bonin Bras Y, Le P, Taberlet E Coissac (2016). OBITools: a unix-inspired software package for DNA metabarcoding.Mol Ecol Resour, 16: 176–182 https://doi.org/10.1111/1755-0998.12428
10
X Cao, F Tian, K Li, J Ni (2020). Atlas of pollen and spores for common plants from the east Tibetan Plateau. National Tibetan Plateau Data Center10.11888/Paleoenv.tpdc.270735
11
X, Cao F, Tian K, Li J, Ni X, Yu L, Liu N Wang (2021). Lake surface sediment pollen dataset for the alpine meadow vegetation type from the eastern Tibetan Plateau and its potential in past climate reconstructions.Earth Syst Sci Data, 13: 3525–3537 https://doi.org/10.5194/essd-13-3525-2021
12
F, Chen L, Ding S, Piao T, Zhou B, Xu T, Yao X Li (2021). The Tibetan Plateau as the engine for Asian environmental change: the Tibetan Plateau Earth system research into a new era.Sci Bull (Beijing), 66: 1263–1266 https://doi.org/10.1016/j.scib.2021.04.017
13
K Fægri, J Iversen (1975). Textbook of pollen analysis. Copenhagen: Munksgaard
14
J, Han M, Cai Z, Shao F, Liu Q, Zhang S, Zhang J, Yu X, Li Z, Zhang D Zhu (2021). Vegetation and climate change since the late glacial period on the southern Tibetan Plateau.Palaeogeogr Palaeoclimatol Palaeoecol, 572: 110403 https://doi.org/10.1016/j.palaeo.2021.110403
15
J, He K, Yang W, Tang H, Lu J, Qin Y, Chen X Li (2020). The first high-resolution meteorological forcing dataset for land process studies over China.Sci Data, 7(1): 25 https://doi.org/10.1038/s41597-020-0369-y
16
U, Herzschuh H J B, Birks J, Ni Y, Zhao H, Liu X, Liu G Grosse (2010). Holocene land-cover changes on the Tibetan Plateau.Holocene, 20(1): 91–104 https://doi.org/10.1177/0959683609348882
17
U, Herzschuh H, Kürschner S Mischke (2006). Temperature variability and vertical vegetation belt shifts during the last ~50000 yr in the Qilian Mountains (NE margin of the Tibetan Plateau, China).Quat Res, 66(1): 133–146 https://doi.org/10.1016/j.yqres.2006.03.001
18
M O, Hill H G Jr Gauch (1980). Detrended correspondence analysis: an improved ordination technique.Vegetatio, 42(1–3): 47–58 https://doi.org/10.1007/BF00048870
19
S, Huang K R, Stoof-Leichsenring S, Liu J, Courtin A A, Andreev L A, Pestryakova U Herzschuh (2021). Plant sedimentary ancient DNA from Far East Russia covering the last 28000 years reveals different assembly rules in cold and warm climates.Front Ecol Evol, 9: 763747 https://doi.org/10.3389/fevo.2021.763747
20
Institute of Geographic Sciences and Natural Resources Research CAS (1990). Atlas of Qinghai-Tibet Plateau. Beijing: Science Press
21
S T Jackson (1990). Pollen source area and representation in small lakes of the northeast United States.Rev Palaeobot Palynol, 63(1–2): 53–76 https://doi.org/10.1016/0034-6667(90)90006-5
W H Jia (2020). Modern-process studies of plant DNA in lake sediments, Qinghai-Tibetan Plateau and arid northwestern China. Dissertation for Master’s Degree. Beijing: Capital Normal University
24
W, Jia S, Anslan F, Chen X, Cao H, Dong K, Dulias Z, Gu L, Heinecke H, Jiang S, Kruse W, Kang K, Li S, Liu X, Liu Y, Liu J, Ni A, Schwalb K R, Stoof-Leichsenring W, Shen F, Tian J, Wang Y, Wang Y, Wang H, Xu X, Yang D, Zhang U Herzschuh (2022a). Sedimentary ancient DNA reveals past ecosystem and biodiversity changes on the Tibetan Plateau: overview and prospects.Quat Sci Rev, 293: 107703 https://doi.org/10.1016/j.quascirev.2022.107703
25
W, Jia X, Liu K R, Stoof-Leichsenring S, Liu K, Li U Herzschuh (2022b). Preservation of sedimentary plant DNA in related to lake water chemistry.Environ DNA, 4(2): 425–439 https://doi.org/10.1002/edn3.259
26
W Jia, K Stoof-Leichsenring, S Liu, K Li, S Huang, X Liu, J Ni, X Cao, L Pestryakova, S Mischke, U Herzschuh (2021). Metabarcoding of modern sedimentary DNA from the Tibetan Plateau and Siberia as a training dataset for vegetation reconstructions. EGU General Assembly, EGU21–14835
27
T, Jørgensen J, Haile P, Möller A, Andreev S, Boessenkool M, Rasmussen F, Kienast E, Coissac P, Taberlet C, Brochmann N H, Bigelow K, Andersen L, Orlando M T P, Gilbert E Willerslev (2012). A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability.Mol Ecol, 21: 1989–2003 https://doi.org/10.1111/j.1365-294X.2011.05287.x
28
C, Kanz P, Aldebert N, Althorpe W, Baker A, Baldwin K, Bates P, Browne A V D, Broek M, Castro G, Cochrane K, Duggan R, Eberhardt N, Faruque J, Gamble F G, Diez N, Harte T, Kulikova Q, Lin V, Lombard R, Lopez R, Mancuso M, McHale F, Nardone V, Silventoinen S, Sobhany P, Stoehr M A, Tuli K, Tzouvara R, Vaughan D, Wu W M, Zhu R Apweileret (2005). The EMBL Nucleotide Sequence Database.Nucleic Acids Res, 33: D29–D33
29
L Liu, N Wang, Y Zhang, X Yu, X Cao (2023). Performance of pollen-based vegetation cover reconstruction using lake and soil samples on the Tibetan Plateau. Veget Hist Archaeobot, 10.1007/s00334-022-00891-0
30
S, Liu S, Kruse D, Scherler R H, Ree H H, Zimmermann K R, Stoof-Leichsenring L S, Epp S, Mischke U Herzschuh (2021). Sedimentary ancient DNA reveals a threat of warming-induced alpine habitat loss to Tibetan Plateau plant diversity.Nat Commun, 12(1): 2995 https://doi.org/10.1038/s41467-021-22986-4
31
Q, Ma L, Zhu X, Lü J, Wang J, Ju T, Kasper G, Daut T Haberzettl (2019). Late glacial and Holocene vegetation and climate variations at Lake Tangra Yumco, central Tibetan Plateau.Global Planet Change, 174: 16–25 https://doi.org/10.1016/j.gloplacha.2019.01.004
32
J, Madeja A, Wacnik A, Zyga E, Stankiewicz E, Wypasek W, Guminski K Harmata (2009). Bacterial ancient DNA as an indicator of human presence in the past: its correlation with palynological and archaeological data.J Quaternary Sci, 24(4): 317–321 https://doi.org/10.1002/jqs.1237
33
L J Maher (1981). Statistics for microfossil concentration measurements employing samples spiked with marker grains.Rev Palaeobot Palynol, 32: 153–191 https://doi.org/10.1016/0034-6667(81)90002-6
34
G, Miehe S, Miehe J, Böhner K, Kaiser I, Hensen D, Madsen J, Liu L Opgenoorth (2014). How old is the human footprint in the world’s largest alpine ecosystem?.A review of multiproxy records from the Tibetan Plateau from the ecologists’ viewpoint. Quat Sci Rev, 86: 190–209 https://doi.org/10.1016/j.quascirev.2013.12.004
35
G, Miehe P M, Schleuss E, Seeber W, Babel T, Biermann M, Braendle F, Chen H, Coners T, Foken T, Gerken H F, Graf G, Guggenberger S, Hafner M, Holzapfel J, Ingrisch Y, Kuzyakov Z, Lai L, Lehnert C, Leuschner X, Li J, Liu S, Liu Y, Ma S, Miehe V, Mosbrugger H J, Noltie J, Schmidt S, Spielvogel S, Unteregelsbacher Y, Wang S, Willinghöfer X, Xu Y, Yang S, Zhang L, Opgenoorth K Wesche (2019). The Kobresia pygmaea ecosystem of the Tibetan highlands – origin, functioning and degradation of the world’s largest pastoral alpine ecosystem: Kobresia pastures of Tibet.Sci Total Environ, 648: 754–771 https://doi.org/10.1016/j.scitotenv.2018.08.164
36
B, Niemeyer L S, Epp K R, Stoof-Leichsenring L A, Pestryakova U Herzschuh (2017). A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline.Mol Ecol Resour, 17(6): e46–e62 https://doi.org/10.1111/1755-0998.12689
37
D Nychka, R Furrer, J Paige, S Sain (2019). Fields: Tools for spatial data, version 9.6.1
38
J Oksanen, F G Blanchet, M Friendly, R Kindt, P Legendre, D McGlinn, P R Minchin, R B O’Hara, G L Simpson, P Solymos, M H H Stevens, E Szoecs, H Wagner (2019). vegan: Community Ecology Package, version 2.5–4
39
L, Parducci I G, Alsos P, Unneberg M W, Pedersen L, Han Y, Lammers J S, Salonen M M, Väliranta T, Slotte B Wohlfarth (2019). Shotgun environmental DNA, pollen, and macrofossil analysis of lateglacial lake sediments from southern Sweden.Front Ecol Evol, 7: 189 https://doi.org/10.3389/fevo.2019.00189
40
L, Parducci T, Jorgensen M M, Tollefsrud E, Elverland T, Alm S L, Fontana K D, Bennett J, Haile I, Matetovici Y, Suyama M E, Edwards K, Andersen M, Rasmussen S, Boessenkool E, Coissac C, Brochmann P, Taberlet M, Houmark-Nielsen N K, Larsen L, Orlando M T P, Gilbert K H, Kjaer I G, Alsos E Willerslev (2012). Glacial survival of boreal trees in northern Scandinavia.Science, 335: 1083–1086 https://doi.org/10.1126/science.1216043
41
S, Piao G, Yin J, Tan L, Cheng M, Huang Y, Li R, Liu J, Mao R B, Myneni S, Peng B, Poulter X, Shi Z, Xiao N, Zeng Z, Zeng Y Wang (2015). Detection and attribution of vegetation greening trend in China over the last 30 years.Glob Change Biol, 21(4): 1601–1609 https://doi.org/10.1111/gcb.12795
42
S Piao, X Zhang, T Wang, E Liang, S Wang, J Zhu, B Niu (2019). Responses and feedback of the Tibetan Plateau’s alpine ecosystem to climate change. Chin Sci Bull, 64(27): 2842–2855 (in Chinese) 10.1360/TB-2019-0074
43
I C Prentice (1980). Multidimensional scaling as a research tool in Quaternary palynology: a review of theory and methods.Rev Palaeobot Palynol, 31: 71–104 https://doi.org/10.1016/0034-6667(80)90023-8
44
R Core Team (2019). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna
45
J, Shen X, Liu M, Ryo S, Wang X Yang (2005). A high-resolution climatic change since the Late Glacial Age inferred from multi-proxy of sediments in Qinghai Lake.Sci China Earth Sci, 48(6): 742–751 https://doi.org/10.1360/03yd0148
46
E M, Soininen G, Gauthier F, Bilodeau D, Berteaux L, Gielly P, Taberlet G, Gussarova E, Bellemain K, Hassel H K, Stenøien L, Epp A, Schrøder-Nielsen C, Brochmann N G Yoccoz (2015). Highly overlapping winter diet in two sympatric lemming species revealed by DNA metabarcoding.PLoS One, 10(1): e0115335 https://doi.org/10.1371/journal.pone.0115335
47
J H, Sønstebø L, Gielly A K, Brysting R, Elven M, Edwards J, Haile E, Willerslev E, Coissac D, Rioux J, Sannier P, Taberlet C Brochmann (2010). Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate.Mol Ecol Resour, 10(6): 1009–1018 https://doi.org/10.1111/j.1755-0998.2010.02855.x
48
K R, Stoof-Leichsenring S, Liu W, Jia K, Li L A, Pestryakova S, Mischke X, Cao X, Liu J, Ni S, Neuhaus U Herzschuh (2020). Plant diversity in sedimentary DNA obtained from high-latitude (Siberia) and high-elevation lakes (China).Biodivers Data J, 8: e57089 https://doi.org/10.3897/BDJ.8.e57089
49
P, Taberlet E, Coissac F, Pompanon L, Gielly C, Miquel A, Valentini T, Vermat G, Corthier C, Brochmann E Willerslev (2007). Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding.Nucleic Acids Res, 35(3): e14 https://doi.org/10.1093/nar/gkl938
50
L Y Tang, L Y Mao, J W Shu, C H Li, C M Shen, Z Z Zhou (2017). Atlas of Quaternary Pollen and Spores in China. Beijing: Science Press
Braak C J F, ter P F M Verdonschot (1995). Canonical correspondence analysis and related multivariate methods in aquatic ecology.Aquat Sci, 57(3): 255–289 https://doi.org/10.1007/BF00877430
53
F, Tian X, Cao R, Zhang Q, Xu W, Ding X, Liu B, Pan J Chen (2020). Spatial homogenization of soil-surface pollen assemblages improves the reliability of pollen-climate calibration-set.Sci China Earth Sci, 63(11): 1758–1766 https://doi.org/10.1007/s11430-019-9643-0
54
B Wang (2006). The Asian Monsoon. Berlin, Heidelberg: Springer
55
F X Wang, N F Qian, Y L Zhang, H Q Yang (1995). Pollen Flora of China. Beijing: Science Press
56
N, Wang L, Liu Y, Zhang X Cao (2022). A modern pollen data set for the forest–meadow–steppe ecotone from the Tibetan Plateau and its potential use in past vegetation reconstruction.Boreas, 51(4): 847–858 https://doi.org/10.1111/bor.12589
57
Y, Wang U Herzschuh (2011). Reassessment of Holocene vegetation change on the upper Tibetan Plateau using the pollen–based REVEALS model.Rev Palaeobot Palynol, 168(1): 31–40 https://doi.org/10.1016/j.revpalbo.2011.09.004
58
Y, Wang M W, Pedersen I G, Alsos Sanctis B, De F, Racimo A, Prohaska E, Coissac H L, Owens M K F, Merkel A, Fernandez-Guerra A, Rouillard Y, Lammers A, Alberti F, Denoeud D, Money A H, Ruter H, McColl N K, Larsen A A, Cherezova M E, Edwards G B, Fedorov J, Haile L, Orlando L, Vinner T S, Korneliussen D W, Beilman A A, Bjørk J, Cao C, Dockter J, Esdale G, Gusarova K K, Kjeldsen J, Mangerud J T, Rasic B, Skadhauge J I, Svendsen A, Tikhonov P, Wincker Y, Xing Y, Zhang D G, Froese C, Rahbek D N, Bravo P B, Holden N R, Edwards R, Durbin D J, Meltzer K H, Kjær P, Möller E Willerslev (2021). Late Quaternary dynamics of Arctic biota from ancient environmental genomics.Nature, 600(7887): 86–92 https://doi.org/10.1038/s41586-021-04016-x
59
E, Willerslev J, Davison M, Moora M, Zobel E, Coissac M E, Edwards E D, Lorenzen M, Vestergård G, Gussarova J, Haile J, Craine L, Gielly S, Boessenkool L S, Epp P B, Pearman R, Cheddadi D, Murray K A, Bråthen N, Yoccoz H, Binney C, Cruaud P, Wincker T, Goslar I G, Alsos E, Bellemain A K, Brysting R, Elven J H, Sønstebø J, Murton A, Sher M, Rasmussen R, Rønn T, Mourier A, Cooper J, Austin P, Möller D, Froese G, Zazula F, Pompanon D, Rioux V, Niderkorn A, Tikhonov G, Savvinov R G, Roberts R D E, MacPhee M T P, Gilbert K H, Kjær L, Orlando C, Brochmann P Taberlet (2014). Fifty thousand years of Arctic vegetation and megafaunal diet.Nature, 506(7486): 47–51 https://doi.org/10.1038/nature12921
60
Z Y Wu (1995). The Vegetation of China. Beijing: Science Press (in Chinese)
61
N G, Yoccoz K A, Bråthen L, Gielly J, Haile M E, Edwards T, Goslar Stedingk H, Von A K, Brysting E, Coissac F, Pompanon J H, Sønstebø C, Miquel A, Valentini Bello F, De J, Chave W, Thuiller P, Wincker C, Cruaud F, Gavory M, Rasmussen M T, Gilbert L, Orlando C, Brochmann E, Willerslev P Taberlet (2012). DNA from soil mirrors plant taxonomic and growth form diversity.Mol Ecol, 21(15): 3647–3655 https://doi.org/10.1111/j.1365-294X.2012.05545.x
62
X, Zhou J, Yu R N, Spengler H, Shen K, Zhao J, Ge Y, Bao J, Liu Q, Yang G, Chen P, Jia X Li (2020). 5200-year-old cereal grains from the eastern Altai Mountains redate the trans-Eurasian crop exchange.Nat Plants, 6: 78–87 https://doi.org/10.1038/s41477-019-0581-y
63
L, Zhu X, Lü J, Wang P, Peng T, Kasper G, Daut T, Haberzettl P, Frenzel Q, Li R, Yang A, Schwalb R Mäusbacher (2015). Climate change on the Tibetan Plateau in response to shifting atmospheric circulation since the LGM.Sci Rep, 5: 13318 https://doi.org/10.1038/srep13318
