Environmental genomics of Late Pleistocene black bears and giant short-faced bears

Research output: Contribution to journalJournal articlepeer-review

Standard

Environmental genomics of Late Pleistocene black bears and giant short-faced bears. / Pedersen, Mikkel Winther; De Sanctis, Bianca; Saremi, Nedda F.; Sikora, Martin; Puckett, Emily E.; Gu, Zhenquan; Moon, Katherine L.; Kapp, Joshua D.; Vinner, Lasse; Vardanyan, Zaruhi; Ardelean, Ciprian F.; Arroyo-Cabrales, Joaquin; Cahill, James A.; Heintzman, Peter D.; Zazula, Grant; MacPhee, Ross D. E.; Shapiro, Beth; Durbin, Richard; Willerslev, Eske.

In: Current Biology, Vol. 31, No. 12, 2021, p. 2728-2736.e8.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Pedersen, MW, De Sanctis, B, Saremi, NF, Sikora, M, Puckett, EE, Gu, Z, Moon, KL, Kapp, JD, Vinner, L, Vardanyan, Z, Ardelean, CF, Arroyo-Cabrales, J, Cahill, JA, Heintzman, PD, Zazula, G, MacPhee, RDE, Shapiro, B, Durbin, R & Willerslev, E 2021, 'Environmental genomics of Late Pleistocene black bears and giant short-faced bears', Current Biology, vol. 31, no. 12, pp. 2728-2736.e8. https://doi.org/10.1016/j.cub.2021.04.027

APA

Pedersen, M. W., De Sanctis, B., Saremi, N. F., Sikora, M., Puckett, E. E., Gu, Z., Moon, K. L., Kapp, J. D., Vinner, L., Vardanyan, Z., Ardelean, C. F., Arroyo-Cabrales, J., Cahill, J. A., Heintzman, P. D., Zazula, G., MacPhee, R. D. E., Shapiro, B., Durbin, R., & Willerslev, E. (2021). Environmental genomics of Late Pleistocene black bears and giant short-faced bears. Current Biology, 31(12), 2728-2736.e8. https://doi.org/10.1016/j.cub.2021.04.027

Vancouver

Pedersen MW, De Sanctis B, Saremi NF, Sikora M, Puckett EE, Gu Z et al. Environmental genomics of Late Pleistocene black bears and giant short-faced bears. Current Biology. 2021;31(12):2728-2736.e8. https://doi.org/10.1016/j.cub.2021.04.027

Author

Pedersen, Mikkel Winther ; De Sanctis, Bianca ; Saremi, Nedda F. ; Sikora, Martin ; Puckett, Emily E. ; Gu, Zhenquan ; Moon, Katherine L. ; Kapp, Joshua D. ; Vinner, Lasse ; Vardanyan, Zaruhi ; Ardelean, Ciprian F. ; Arroyo-Cabrales, Joaquin ; Cahill, James A. ; Heintzman, Peter D. ; Zazula, Grant ; MacPhee, Ross D. E. ; Shapiro, Beth ; Durbin, Richard ; Willerslev, Eske. / Environmental genomics of Late Pleistocene black bears and giant short-faced bears. In: Current Biology. 2021 ; Vol. 31, No. 12. pp. 2728-2736.e8.

Bibtex

@article{ab7b7c66a88e42518380a971e5beb6dc,
title = "Environmental genomics of Late Pleistocene black bears and giant short-faced bears",
abstract = "Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1–3 by allowing for parallel sequencing of DNA from all trophic levels.4–8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14–16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16–14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22–50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.",
keywords = "American black bear, ancient environmental genomics, environmental DNA, genomics, giant short-faced bear, paleoontology, phylogeny, population genetics",
author = "Pedersen, {Mikkel Winther} and {De Sanctis}, Bianca and Saremi, {Nedda F.} and Martin Sikora and Puckett, {Emily E.} and Zhenquan Gu and Moon, {Katherine L.} and Kapp, {Joshua D.} and Lasse Vinner and Zaruhi Vardanyan and Ardelean, {Ciprian F.} and Joaquin Arroyo-Cabrales and Cahill, {James A.} and Heintzman, {Peter D.} and Grant Zazula and MacPhee, {Ross D. E.} and Beth Shapiro and Richard Durbin and Eske Willerslev",
note = "Funding Information: We thank Richard E. Green for commenting on the manuscript. M.W.P. acknowledges support from the Carlsberg Foundation for a Carlsberg Internationalisation grant ( CF17-0275 ). B.D.S. acknowledges support from the Wellcome Trust program in Mathematical Genomics and Medicine ( WT220023 ). E.W. acknowledges support from the Lundbeck Foundation , the Wellcome Trust , the Carlsberg Foundation , Novo Foundation , and GRF EXC CRS Chair ( 44113220 ) - Cluster of Excellence “The Ocean Floor – Earth{\textquoteright}s Uncharted Interface.” E.W. would also like to thank Illumina for their collaboration and St. John{\textquoteright}s College, Cambridge, for providing an excellent environment for scientific thought. R.D. acknowledges support from the Wellcome Trust (grant agreement WT207492 ). The Arctodus genome sequencing was supported by NSF ICER-1850949 and NSF DEB-1754451 , and by a grant from the Gordon and Betty Moore Foundation ( GBMF 58362 ). We thank the Tr{\textquoteright}ondek Hwech{\textquoteright}in and placer gold mining community for their continued support and partnership with paleontological research in the Klondike goldfields. Funding Information: We thank Richard E. Green for commenting on the manuscript. M.W.P. acknowledges support from the Carlsberg Foundation for a Carlsberg Internationalisation grant (CF17-0275). B.D.S. acknowledges support from the Wellcome Trust program in Mathematical Genomics and Medicine (WT220023). E.W. acknowledges support from the Lundbeck Foundation, the Wellcome Trust, the Carlsberg Foundation, Novo Foundation, and GRF EXC CRS Chair (44113220) - Cluster of Excellence ?The Ocean Floor ? Earth's Uncharted Interface.? E.W. would also like to thank Illumina for their collaboration and St. John's College, Cambridge, for providing an excellent environment for scientific thought. R.D. acknowledges support from the Wellcome Trust (grant agreement WT207492). The Arctodus genome sequencing was supported by NSF ICER-1850949 and NSF DEB-1754451, and by a grant from the Gordon and Betty Moore Foundation (GBMF 58362). We thank the Tr'ondek Hwech'in and placer gold mining community for their continued support and partnership with paleontological research in the Klondike goldfields. E.W. conceived the project. E.W. R.D. B.S. M.W.P. B.D.S. and M.S. designed the research. G.Z. R.D.E.M. and C.F.A. provided samples and information about paleontological/archaeological context. M.W.P. Z.G. L.V. and Z.V. carried out ancient eDNA laboratory work. P.D.H. K.L.M. and J.D.K. carried out the fossil DNA laboratory work, with input from B.S. N.F.S. undertook the computational analysis of the fossil data with input from P.D.H. B.S. and J.A.C. B.D.S. carried out the computational analyses of the black bear genomes and environmental genomes with input from M.S. R.D. and M.W.P. E.E.P. provided data and interpretation for the black bear results. M.W.P. B.D.S. B.S. R.D. and E.W. wrote the paper and STAR Methods, with input from E.E.P. P.D.H. R.D.E.M. and all co-authors. All authors declare no competing interests. Publisher Copyright: {\textcopyright} 2021 The Author(s)",
year = "2021",
doi = "10.1016/j.cub.2021.04.027",
language = "English",
volume = "31",
pages = "2728--2736.e8",
journal = "Current Biology",
issn = "0960-9822",
publisher = "Cell Press",
number = "12",

}

RIS

TY - JOUR

T1 - Environmental genomics of Late Pleistocene black bears and giant short-faced bears

AU - Pedersen, Mikkel Winther

AU - De Sanctis, Bianca

AU - Saremi, Nedda F.

AU - Sikora, Martin

AU - Puckett, Emily E.

AU - Gu, Zhenquan

AU - Moon, Katherine L.

AU - Kapp, Joshua D.

AU - Vinner, Lasse

AU - Vardanyan, Zaruhi

AU - Ardelean, Ciprian F.

AU - Arroyo-Cabrales, Joaquin

AU - Cahill, James A.

AU - Heintzman, Peter D.

AU - Zazula, Grant

AU - MacPhee, Ross D. E.

AU - Shapiro, Beth

AU - Durbin, Richard

AU - Willerslev, Eske

N1 - Funding Information: We thank Richard E. Green for commenting on the manuscript. M.W.P. acknowledges support from the Carlsberg Foundation for a Carlsberg Internationalisation grant ( CF17-0275 ). B.D.S. acknowledges support from the Wellcome Trust program in Mathematical Genomics and Medicine ( WT220023 ). E.W. acknowledges support from the Lundbeck Foundation , the Wellcome Trust , the Carlsberg Foundation , Novo Foundation , and GRF EXC CRS Chair ( 44113220 ) - Cluster of Excellence “The Ocean Floor – Earth’s Uncharted Interface.” E.W. would also like to thank Illumina for their collaboration and St. John’s College, Cambridge, for providing an excellent environment for scientific thought. R.D. acknowledges support from the Wellcome Trust (grant agreement WT207492 ). The Arctodus genome sequencing was supported by NSF ICER-1850949 and NSF DEB-1754451 , and by a grant from the Gordon and Betty Moore Foundation ( GBMF 58362 ). We thank the Tr’ondek Hwech’in and placer gold mining community for their continued support and partnership with paleontological research in the Klondike goldfields. Funding Information: We thank Richard E. Green for commenting on the manuscript. M.W.P. acknowledges support from the Carlsberg Foundation for a Carlsberg Internationalisation grant (CF17-0275). B.D.S. acknowledges support from the Wellcome Trust program in Mathematical Genomics and Medicine (WT220023). E.W. acknowledges support from the Lundbeck Foundation, the Wellcome Trust, the Carlsberg Foundation, Novo Foundation, and GRF EXC CRS Chair (44113220) - Cluster of Excellence ?The Ocean Floor ? Earth's Uncharted Interface.? E.W. would also like to thank Illumina for their collaboration and St. John's College, Cambridge, for providing an excellent environment for scientific thought. R.D. acknowledges support from the Wellcome Trust (grant agreement WT207492). The Arctodus genome sequencing was supported by NSF ICER-1850949 and NSF DEB-1754451, and by a grant from the Gordon and Betty Moore Foundation (GBMF 58362). We thank the Tr'ondek Hwech'in and placer gold mining community for their continued support and partnership with paleontological research in the Klondike goldfields. E.W. conceived the project. E.W. R.D. B.S. M.W.P. B.D.S. and M.S. designed the research. G.Z. R.D.E.M. and C.F.A. provided samples and information about paleontological/archaeological context. M.W.P. Z.G. L.V. and Z.V. carried out ancient eDNA laboratory work. P.D.H. K.L.M. and J.D.K. carried out the fossil DNA laboratory work, with input from B.S. N.F.S. undertook the computational analysis of the fossil data with input from P.D.H. B.S. and J.A.C. B.D.S. carried out the computational analyses of the black bear genomes and environmental genomes with input from M.S. R.D. and M.W.P. E.E.P. provided data and interpretation for the black bear results. M.W.P. B.D.S. B.S. R.D. and E.W. wrote the paper and STAR Methods, with input from E.E.P. P.D.H. R.D.E.M. and all co-authors. All authors declare no competing interests. Publisher Copyright: © 2021 The Author(s)

PY - 2021

Y1 - 2021

N2 - Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1–3 by allowing for parallel sequencing of DNA from all trophic levels.4–8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14–16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16–14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22–50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.

AB - Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1–3 by allowing for parallel sequencing of DNA from all trophic levels.4–8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14–16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16–14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22–50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.

KW - American black bear

KW - ancient environmental genomics

KW - environmental DNA

KW - genomics

KW - giant short-faced bear

KW - paleoontology

KW - phylogeny

KW - population genetics

U2 - 10.1016/j.cub.2021.04.027

DO - 10.1016/j.cub.2021.04.027

M3 - Journal article

C2 - 33878301

AN - SCOPUS:85106967916

VL - 31

SP - 2728-2736.e8

JO - Current Biology

JF - Current Biology

SN - 0960-9822

IS - 12

ER -

ID: 273063133