Genetic Analysis of Arctic Polar Bear Populations using Historical Samples
- Authors: Kanapin A.A1, Samsonova A.A1, Abramov A.V2, Sablinenko M.V2, Platonov V.V2, Mustafin H.H3, Chekrygin S.A4, Hirata D.1
-
Affiliations:
- Peter the Great St. Petersburg Polytechnic University
- Institute of Zoology, Russian Academy of Sciences
- Moscow Institute of Physics and Technology
- St. Petersburg State University
- Issue: Vol 69, No 6 (2024)
- Pages: 1402-1406
- Section: Letters to the editor
- URL: https://kld-journal.fedlab.ru/0006-3029/article/view/676197
- DOI: https://doi.org/10.31857/S0006302924060251
- EDN: https://elibrary.ru/NIRPYU
- ID: 676197
Cite item
Abstract
About the authors
A. A Kanapin
Peter the Great St. Petersburg Polytechnic UniversitySt. Petersburg, Russia
A. A Samsonova
Peter the Great St. Petersburg Polytechnic UniversitySt. Petersburg, Russia
A. V Abramov
Institute of Zoology, Russian Academy of SciencesSt. Petersburg, Russia
M. V Sablinenko
Institute of Zoology, Russian Academy of SciencesSt. Petersburg, Russia
V. V Platonov
Institute of Zoology, Russian Academy of SciencesSt. Petersburg, Russia
H. H Mustafin
Moscow Institute of Physics and TechnologyDolgoprudny, Russia
S. A Chekrygin
St. Petersburg State UniversitySt. Petersburg, Russia
D. Hirata
Peter the Great St. Petersburg Polytechnic University
Email: dhirata59@gmail.com
St. Petersburg, Russia
References
- Supple M. A. and Shapiro B. Conservation of biodiversity in the genomics era. Genome Biol., 19, 131 (2018). doi: 10.1186/s13059-018-1520-3
- Theissinger K., Fernandes C., Formenti G., Bista I., Berg P. R., Bleidorn C., Bombarely A., Crottini A., Gallo G. R., Godoy J. A., Jentoft S., Malukiewicz J., Mouton A., Oomen R. A., Paez S., Palsb0ll P. J., Pampoulie Ch., Ruiz-López M. J., Secomandi S., Svardal H., Theofanopoulou C., de Vries J., Waldvogel A.-M., Zhang G., Jarvis E. D., Bálint M., Ciofi C., Waterhouse R. M., C Mazzoni. J., and Höglund J. How genomics can help biodiversity conservation. Trends Genet., 39, 545-559 (2023). doi: 10.1016/j.tig.2023.01.005
- Schmidt T. L., Thia J. A., and Hoffmann A. A. How can genomics help or hinder wildlife conservation? Annu Rev. Anim. Biosci., 12, 45-68 (2024). doi: 10.1146/annurev-animal-021022-051810
- Miller W., Schuster S. C., Welch A. J., Ratan A., Bedoya-Reina O. C., Zhao F., Kim H. L., Burhans R. C., Drautz D. I., Wittekindt N. E., Tomsho L. P., Ibarra-Laclette E., Herrera-Estrella L., Peacock E., Farley S., Sage G. K., Rode K., Obbard M., Montiel R., Bachmann L., Ingólfsson Ó., Aars J., Mailund Th., Wiig 0., Talbot S. L., and Lindqvist Ch. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc. Natl. Acad. Sci. USA, 109 (36), E2382-E2390 (2012). doi: 10.1073/pnas.1210506109
- Cahill J. A., Green R. E., Fulton T. L., Stiller M., Jay F., Ovsyanikov N., Salamzade R., St John J., Stirling I., Slatkin M., and Shapiro B. Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. PLoS Genet., 9, e1003345 (2013). doi: 10.1371/journal.pgen.1003345
- Liu S., Lorenzen E. D., Fumagalli M., Li B., Harris K., Xiong Z., Zhou L., Korneliussen T. S., Somel M., Babbitt C., Wray G., Li J., He W., Wang Zh., Fu W., Xiang X., Morgan C. C. Doherty A., O’Connell M. J., McInerney J. O., Born E. W., Dalén L., Dietz R., Orlando L., Sonne Ch., Zhang G., Nielsen R., Willerslev E., and Wang J. Population Genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell, 157, 785-794 (2014). doi: 10.1016/j.cell.2014.03.054
- Jensen E. L., Tschritter C., de Groot P. V. C., Hayward K. M., Branigan M., Dyck M., Clemente-Carvalho R. B. G., and Lougheed S. C. Canadian polar bear population structure using genome-wide markers. Ecol. Evol., 10, 3706-3714 (2020). doi: 10.1002/ece3.6159
- Laidre K. L., Supple M. A., Born E. W., Regehr E. V., Wiig Ø., Ugarte F., Aars J., Dietz R., Sonne C., Hegelund P., Isaksen C., Akse G. B., Cohen B. H., Stern. L., Moon T., Vollmers Ch., Corbett-Detig R., Paetkau D., and Shapiro B. Glacial ice supports a distinct and undocumented polar bear subpopulation persisting in late 21st-century sea-ice conditions. Science, 376, 13331338 (2022). doi: 10.1126/science.abk2793
- Lan T., Leppälä K., Tomlin C., Talbot S. L., Sage G. K., Farley S. D., Shideler R. T., Bachmann L., Wiig Ø., AlbertV. A., Salojärvi J., Mailund Th., Drautz-Moses D. I., Schuster S. C., Herrera-Estrella L., and Lindqvist Ch. Insights into bear evolution from a Pleistocene polar bear genome. Proc. Natl. Acad. Sci. USA, 119, e2200016119 (2022). doi: 10.1073/pnas.2200016119
- Wang M.-S., Murray G. G. R., Mann D., Groves P., Vershinina A. O., Supple M. A., Kapp J. D., Corbett-Detig R., Crump S. E., Stirling I., Laidre K. L., Kunz M., Dalén L., Green R. E., and Shapiro B. A polar bear paleogenome reveals extensive ancient gene flow from polar bears into brown bears. Nature Ecol. Evol., 6, 936-944 (2022). doi: 10.1038/s41559-022-01753-8
- Peacock E., Sonsthagen S. A., Obbard M. E., Boltunov A., Regehr E. V., Ovsyanikov N., Aars J., Atkinson S. N., Sage G. K., Hope A. G., E. Zeyl, L. Bachmann, D. Ehrich, K. T. Scribner, S. C. Amstrup, S. Belikov, E. W. Born, A. E. Derocher, I. Stirling, M. K. Taylor, Ø. Wiig, D. Paetkau, and Talbot S. L. Implications of the circumpolar genetic structure of polar bears for their conservation in a rapidly warming Arctic. PLoS One, 10, e112021 (2015). doi: 10.1371/journal.pone.0112021
- Malenfant R. M., Davis C. S., Cullingham C. I., and Coltman D. W. Circumpolar genetic structure and recent gene flow of polar bears: a reanalysis. PLoS One, 11, e0148967 (2016). doi: 10.1371/journal.pone.0148967
- Sorokin P. A., Zvychaynaya E. Y., Ivanov E. A., Mizin I. A., Mordvintsev I. N., Platonov N. G., Isachenko A. I., Lazareva R. E., and Rozhnov V. V. Population genetic structure in polar bears (Ursus maritimus) from the Russian Arctic Seas. Russ. J. Genet., 59, 1320-1332 (2023). doi: 10.1134/S1022795423120128
- Johnson K. R. and Owens I. F. P. A global approach for natural history museum collections. Science, 379, 11921194 (2023). doi: 10.1126/science.adf6434
- Orlando L., Allaby R., Skoglund P., Der Sarkissian C., Stockhammer P. W., Ávila-Arcos M. C., Fu Q., Krause J., Willerslev E., Stone A. C., and Warinner Ch. Ancient DNA analysis. Nature Rev. Methods Primers, 1, 14 (2021). doi: 10.1038/s43586-020-00011-0
- Díez-Del-Molino D., Sánchez-Barreiro F., Barnes I., Gilbert M. T. P., and Dalén L. Quantifying temporal genomic erosion in endangered species. Trends Ecol. Evol., 33, 176-185 (2018). doi: 10.1016/j.tree.2017.12.002
- Card D. C., Shapiro B., Giribet G., Moritz C., and Edwards S. V. Museum genomics. Annu. Rev. Genet., 55, 633-659 (2021). doi: 10.1146/annurev-genet-071719-020506
- Raxworthy C. J. and Smith B. T. Mining museums for historical DNA: advances and challenges in museomics. Trends Ecol. Evol., 36, 1049-1060 (2021). doi: 10.1016/j.tree.2021.07.009
- Benham P. M. and Bowie R. C. K. Natural history collections as a resource for conservation genomics: Understanding the past to preserve the future. J. Hered., 114, 367-384 (2023). doi: 10.1093/jhered/esac066
- Dabney J., Knapp M., Glocke I., Gansauge M.-T., Weihmann A., Nickel B., Valdiosera C., García N., Pääbo S., Arsuaga J.-L., and Meyer M. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. USA, 110, 15758-15763 (2013). doi: 10.1073/pnas.1314445110
- Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv, 1303.3997 [q-bio.GN] (2013). Available from: http://arxiv.org/abs/1303.3997.
- Korneliussen T. S., Albrechtsen A., and Nielsen R. ANGSD: Analysis of next generation sequencing data. BMC Bioinformatics, 15, 356 (2014). doi: 10.1186/s12859-014-0356-4
Supplementary files
