Fifty thousand years of Arctic vegetation and megafaunal diet

Subjects

Abstract

Although it is generally agreed that the Arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr bp (before present). For much of the period investigated, Arctic vegetation consisted of dry steppe-tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25–15 kyr bp), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr bp, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such, our findings question the predominance of a Late Quaternary graminoid-dominated Arctic mammoth steppe.

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Figure 1: Sample localities.
Figure 2: Taxonomic diversity of Arctic plant assemblages during the last 50 kyr.
Figure 3: Proportional abundance of two families—Teratocephalidae and Cephalobidae—among the total soil nematode community at contemporary tundra and steppe sites in Yukon, Canada.
Figure 4: Plant growth form composition over time and across sample types, estimated by high-throughput sequencing of DNA from 242 permafrost samples.

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Acknowledgements

We thank A. Lister, R. D. Guthrie, M. Hofreiter and L. Parducci for thoughts and discussions on our findings and K. Andersen for help identifying possible contamination. We thank T. B. Brand, P. S. Olsen, V. Mirré, L. J. Gillespie, J. M. Saarela, J. Doubt, M. Lomonosova, D. Shaulo, J. E. Eriksen, S. Ickert-Bond, T. Ager, D. Bielman, M. Hajibabaei, A. Telka and S. Zimov for help and providing samples. We thank the Danish National Sequencing Centre. This work was supported by the European Union 6th framework project ECOCHANGE (GOCE-2006-036866, coordinated by P.T.), the Danish National Research Foundation (Centre of Excellence to E.W.), the European Regional Development Fund (Centre of Excellence FIBIR and IUT 20-28 to J.D., M.M. and M.Z.), the Research Council of Norway (191627/V40 to C.B.), the Australian Research Council (DP0558446 to R.G.R.), a Marie Curie International Outgoing Fellowship (PIOF-GA-2009-253376 to E.D.L.) and a Carlsberg Foundation Fellowship (to M.V.).

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The paper represents the joint efforts of several research groups, headed by various people within each group. Rather than publishing a number of independent papers, we have chosen to combine our data in this paper in the belief that this creates a more comprehensive story. The authorship reflects this joint effort. The ECOCHANGE team designed and initiated the project. E.W., M.E.E., J.M., E.D.L., M.V., G.G., J.H., J.C., I.G.A., P.M., D.F., G.Z., A.T., J.A., A.S., G.S., R.G.R., R.D.E.M., M.T.P.G., A.C. and K.H.K. collected the samples. G.G., R.E., A.K.B., J.H.S., C.B., L.G., E.C. and P.T. constructed the plant DNA taxonomic reference libraries and provided taxonomic assignments of the sediment data with input from I.G.A., E.B., S.B., L.S.E., M.E.E. and D.M. E.D.L., M.V., J.H., L.S.E., S.B., C.C., P.W., L.G., G.G. and J.H.S. conducted the genetics laboratory work. T.G. did the dating. F.P., D.R. and V.N. produced and analysed the data concerning the reliability of the trnL approach for estimating herbivore diet. J.D., M.M., M.Z., E.C., M.V., M.R., J.C., S.B., P.B.P., R.C., H.B., R.R., T.M. and P.T. did the analyses. E.D.L. and J.D. produced the figures. E.W. wrote most of the text with input from all authors, in particular J.D., M.M., M.Z., E.D.L., M.E.E., M.V., P.B.P., D.M., K.A.B., N.Y., L.O., C.B., P.T. and R.D.E.M.

Corresponding author

Correspondence to Eske Willerslev.

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Competing interests

The authors note that L.G. and P.T. are co-inventors of patents related to the gh primers and the use of the P6 loop of the chloroplast trnL (UAA) intron for plant identification using degraded template DNA. These patents only restrict commercial applications and have no impact on the use of this locus by academic researchers.

Additional information

All the raw and filtered data concerning plants, nematodes, megafauna and sheep diet are available either from Extended Data and Supplementary Data, or from the Dryad Digital Repository: http://doi.org/10.5061/dryad.ph8s5.

Extended data figures and tables

Extended Data Figure 1 Permafrost sample locality details.

a, Radiocarbon dating chronology for the main section at the Main River site, Russia, from which nearly all Main River samples are derived. b, View of the 2009 Duvanny Yar exposure, northeast Siberia. c, yedoma sandy silt in upper c. 12 m of the exposure at Duvanny Yar exposure, northeast Siberia. A large syngenetic ice wedge (top centre) within the yedoma is truncated by a thaw unconformity at a depth of c. 1.9 m below the ground surface, marking the maximum postglacial thaw depth after deposition of the yedoma had ended. People shown for scale, with DNA sediment sample holes to the right of the person on right. d, Calibrated radiocarbon date distributions plotted against depth above river level at Duvanny Yar exposure, northeast Siberia. Although there are some finite dates below 20 m, the general curve shape suggests the radiocarbon dating limit occurs at about this level. e, f, The two Svalbard sites at Colesdalen (e) and Endalen (f).

Extended Data Figure 2 MOTU characterization and data consistency.

ac, Graphs showing the consistency of the DNA-based approach using permafrost samples across the different time periods: average marker size per sample (a); number of reads per sample (b); number of taxa per sample (c). d, WebLogos showing the match between the gh primers and their target sequences in the main plant families involved in the estimation of the proportions of forbs and graminoids70.

Extended Data Figure 3 Temporal classification of samples, assemblage variation in time and data robustness.

ad, K-means clustering of permafrost plant assemblages. a, Cluster identity of samples derived from pre-LGM, LGM and post-LGM periods for values of K between 2 and 10. Each bar represents a separate sample; different colours reflect different cluster identities. b, The Calinski–Harabasz criterion for different levels of K. Higher values indicate stronger support for a level of partitioning. c, d, Heat maps showing the proportional occurrence of samples from pre-LGM, LGM and post-LGM periods in different clusters, for K = 2 (c) and K = 3 (d). Colours vary from red (low values) to white (high values). eg, Assemblage variation in time and space. e, Nonmetric multidimensional scaling (NMDS) ordination revealed significant variation (PERMANOVA, P < 0.01) in fossil/ancient plant assemblage composition during the three palaeoclimatic periods. f, The effect of spatial distance on similarity when assemblages from different palaeoclimatic periods were compared. The vertical axis represents similarity in floristic composition measured as 1-Bray–Curtis similarity, the horizontal axis depicts ln of distance between sampled communities in kilometres. The greater the spatial distance between pairs of assemblages, the more dissimilar they were. However, the rate of the decay differed depending on which two climatic periods were compared (full model P < 0.001). The weakest distance decay in similarity was observed in the case of comparisons between pre-LGM and post-LGM assemblages. Even if pre-LGM and post-LGM samples came from the same geographic area, their floristic compositions were dissimilar. g, Results of randomization tests. Mean proportional composition of different growth form types in LGM and post-LGM samples. The bars around sample means indicate 95% quantiles derived from 999 bootstrap replicates (where bootstrap N was set to the number of samples in the post-LGM data set; see methods for details). h, Counts of MOTUs exhibiting different growth forms binned over 5-kyr time intervals. The analysis included 218 of the 242 sediment samples, as described in Fig. 4. Numbers immediately below the columns indicate sample sizes. Median (central dot), quartile (box), maximum and minimum (whiskers) counts are shown.

Extended Data Table 1 Site information of the 21 permafrost localities (shown in Fig. 1)
Extended Data Table 2 Statistics regarding length of the P6 loop amplified with the gh primers41 for the most important plant families of the two growth forms (graminoids and forbs)
Extended Data Table 3 Locality information of the seven contemporary tundra and steppe sites in Yukon, Canada, which were analysed for nematode faunal composition (shown in Fig. 3)
Extended Data Table 4 Proportion of 17 permafrost sediments with sequences of the two indicator nematode families Cephalobidae and Teratocephalidae
Extended Data Table 5 Herbivorous mammal taxa derived from Main River permafrost samples for which plant data were available
Extended Data Table 6 Sample information of the eight megafauna gut and coprolite samples from woolly mammoth (Mammuthus primigenius), bison (Bison sp.), woolly rhinoceros (Coelodonta antiquitatis) and horse (Equus lambei) (shown in Fig. 1)

Supplementary information

Supplementary Data 1

Sample information of the 242 Holarctic permafrost samples, classified by region and age group. (XLSX 30 kb)

Supplementary Data 2

Counts of sequence reads corresponding to 154 trnL chloroplast plant MOTUs derived from 242 Holarctic permafrost samples. (XLSX 136 kb)

Supplementary Data 3

Influence of LGM definition on analysis of plant community differences using Permanova and mean within period similarity. (XLSX 14 kb)

Supplementary Data 4

List of plant MOTUs, and their occurrence in the three palaeoclimatic periods, to which the sediment plastid trnL gh region reads were assigned. (XLSX 18 kb)

Supplementary Data 5

List of plant MOTUs, and their occurrence in the three palaeoclimatic periods, of the three families Asteraceae, Cyperaceae and Poaceae) to which the sediment ITS region reads were assigned. (XLSX 15 kb)

Supplementary Data 6

MOTU Identification and counts of sequences of DNA-based diet analysis of wholly mammoth, wholly rhinoceros, horse, and bison using coprolite/gut content. (XLSX 14 kb)

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Willerslev, E., Davison, J., Moora, M. et al. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 506, 47–51 (2014). https://doi.org/10.1038/nature12921

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