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High genomic diversity in the endangered East Greenland Svalbard Barents Sea stock of bowhead whales (Balaena mysticetus)

  • Kovacs, K. M. et al. The endangered Spitsbergen bowhead whales’ secrets revealed after hundreds of years in hiding. Biol. Lett. https://doi.org/10.1098/rsbl.2020.0148 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cooke, J. & Reeves, R. Balaena mysticetus (East Greenland-Svalbard-Barents Sea subpopulation). The IUCN Red List of Threatened Species 2018, e.T2472A50348144 (2018). https://doi.org/10.2305/IUCN.UK.2018-1.RLTS.T2472A50348144.en

  • Allen, R. C. & Keay, I. Bowhead whales in the eastern Arctic, 1611–1911: Population reconstruction with historical whaling records. Environ. Hist. 12, 89–113 (2006).

    Article 

    Google Scholar 

  • Reeves, R. R. Spitsbergen bowhead stock: A short review. Mar. Fish. Rev. 42, 65–69 (1980).

    Google Scholar 

  • Shelden, K. E. W. & Rugh, D. J. The Bowhead Whale, Balaena mysticetus: Its Historic and Current Status. Mar. Fish. Rev. 57, 1–20 (1995).

    Google Scholar 

  • Gilg, O. & Born, E. W. Recent sightings of the bowhead whale (Balaena mysticetus) in Northeast Greenland and the Greenland Sea. Polar Biol. 28, 796–801. https://doi.org/10.1007/s00300-005-0001-9 (2005).

    Article 

    Google Scholar 

  • Boertmann, D., Kyhn, L. A., Witting, L. & Heide-Jørgensen, M. P. A hidden getaway for bowhead whales in the Greenland Sea. Polar Biol. 38, 1315–1319. https://doi.org/10.1007/s00300-015-1695-y (2015).

    Article 

    Google Scholar 

  • Wiig, Ø., Bachmann, L., Janik, V., Kovac, K. & Lydersen, C. Spitsbergen bowhead whales revisited. Mar. Mamm. Sci. 23, 688–693. https://doi.org/10.1111/j.1748-7692.2007.02373.x (2007).

    Article 

    Google Scholar 

  • Wiig, Ø., Bachmann, L., Øien, N., Kovacs, K. & Lydersen, C. Observations of bowhead whales (Balaena mysticetus) in the Svalbard area 1940–2009. Polar Biol. 33, 979–984. https://doi.org/10.1007/s00300-010-0776-1 (2010).

    Article 

    Google Scholar 

  • Lydersen, C. et al. Lost highway not forgotten: Satellite tracking of a bowhead whale (Balaena mysticetus) from the critically endangered Spitsbergen stock. Arctic 65, 76–86. https://doi.org/10.14430/arctic4167 (2012).

    Article 

    Google Scholar 

  • Vacquié-Garcia, J. et al. Late summer distribution and abundance of ice-associated whales in the Norwegian High Arctic. Endang. Spec. Res. 32, 59–70. https://doi.org/10.3354/esr00791 (2017).

    Article 

    Google Scholar 

  • Givens, G. H. & Heide-Jørgensen, M. P. Abundance. In The Bowhead Whale: Balaena Mysticetus: Biology and Human Interactions (eds George, J. C. & Thewissen, J. G. M.) 77–86 (Academic Press, 2020).

    Google Scholar 

  • Rooney, A. P., Honeycutt, R. L. & Derr, J. N. Historical population size change of bowhead whales inferred from DNA sequence polymorphism data. Evolution 55, 1678–1685. https://doi.org/10.1111/j.0014-3820.2001.tb00687.x (2001).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Borge, T., Bachmann, L., Bjørnstad, G. & Wiig, Ø. Genetic variation in Holocene bowhead whales from Svalbard. Mol. Ecol. 16, 2223–2235. https://doi.org/10.1111/j.1365-294X.2007.03287.x (2007).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • LeDuc, R. G. et al. Genetic analyses (mtDNA and microsatellites) of Okhotsk and Bering/Chukchi/Beaufort Seas populations of bowhead whales. J. Cetacean Res. Manag. 7, 107–111 (2005).

    Google Scholar 

  • Meschersky, I. G., Chichkina, A. N., Shpak, O. V. & Rozhnov, V. V. Molecular genetic analysis of the Shantar Summer Group of bowhead whales (Balaena mysticetus L.) in the Okhotsk Sea. Russ. J. Genet. 50, 395–405. https://doi.org/10.1134/S1022795414040097 (2014).

    CAS 
    Article 

    Google Scholar 

  • Bachmann, L. et al. Mitogenomics and the genetic differentiation of contemporary Balaena mysticetus (Cetacea) from Svalbard. Zool. J. Linn. Soc. 191, 1192–1203. https://doi.org/10.1093/zoolinnean/zlaa082 (2021).

    Article 

    Google Scholar 

  • Grond, J., Płecha, M., Hahn, C., Wiig, Ø. & Bachmann, L. Mitochondrial genomes of ancient bowhead whales (Balaena mysticetus) from Svalbard. Mitochondrial DNA Part B 4, 4152–4154. https://doi.org/10.1080/23802359.2019.1693284 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nyhus, E. S. et al. Mitogenomes of contemporary Spitsbergen stock bowhead whales (Balaena mysticetus). Mitochondrial DNA Part B 1, 898–900. https://doi.org/10.1080/23802359.2016.1258345 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Andrews, S. FastQC: A Quality Control Tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).

  • Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. https://doi.org/10.1093/bioinformatics/btu170 (2014).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Keane, M. et al. Insights into the evolution of longevity from the bowhead whale genome. Cell Rep. 10, 112–122. https://doi.org/10.1016/j.celrep.2014.12.008) (2015).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993. https://doi.org/10.1093/bioinformatics/btr509 (2011).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158. https://doi.org/10.1093/bioinformatics/btr330 (2011).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ortiz, E. M. vcf2phylip v2.0: Convert a VCF matrix into several matrix formats for phylogenetic analysis. zenodo.org, https://zenodo.org/record/2540861#.YDUOKy1Q0f0 (2019).

  • Huson, D. H. & Bryant, D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23, 254–267. https://doi.org/10.1093/molbev/msj030 (2006).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Purcell, S. et al. PLINK: A tool set for whole-genome and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–576. https://doi.org/10.1086/519795 (2007).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/ (2020).

  • Knaus, B. J. & Grunwald, N. J. VcfR: An R package to manipulate and visualize VCF format data. bioRxiv, 041277 (2016). https://doi.org/10.1101/041277

  • Jombart, T. & Ahmed, I. adegenet 1.3–1: New tools for the analysis of genome-wide SNP data. Bioinformatics 27, 3070–3071. https://doi.org/10.1093/bioinformatics/btr521 (2011).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hanghøj, K., Moltke, I., Alstrup Andersen, P., Manica, A. & Korneliussen, T. S. Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding. GigaScience 8, giz034. https://doi.org/10.1093/gigascience/giz034 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: Analysis of next generation sequencing data. BMC Bioinform. 15, 356. https://doi.org/10.1186/s12859-014-0356-4 (2014).

    Article 

    Google Scholar 

  • Renaud, G., Hanghøj, K., Korneliussen, T. S., Willerslev, E. & Orlando, L. Joint estimates of heterozygosity and runs of homozygosity for modern and ancient samples. Genetics 212, 587–614. https://doi.org/10.1534/genetics.119.302057 (2019).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Grabherr, M. G. et al. Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics 26, 1145–1151. https://doi.org/10.1093/bioinformatics/btq102 (2010).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079. https://doi.org/10.1093/bioinformatics/btp352 (2009).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Westbury, M. V. et al. Extended and continuous decline in effective population size results in low genomic diversity in the world’s rarest hyena species, the brown hyena. Mol. Biol. Evol. 35, 1225–1237. https://doi.org/10.1093/molbev/msy037 (2018).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. & Durbin, R. Inference of human population history from whole genome sequence of a single individual. Nature 475, 493–496. https://doi.org/10.1038/nature10231 (2011).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Westbury, M. V., Petersen, B., Garde, E., Heide-Jørgensen, M. P. & Lorenzen, E. D. Narwhal genome reveals long-term low genetic diversity despite current large abundance size. iScience 15, 592–599. https://doi.org/10.1016/j.isci.2019.03.023 (2019).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Taylor, B. et al. Synthesis of lines of evidence for population structure for bowhead whales in the Bering-Chukchi-Beaufort region. Paper SC/59/BRG35 presented to the IWC Scientific Committee, Anchorage, Alaska (2007).

  • Phillips, C. D. et al. Molecular insights into the historic demography of bowhead whales: Understanding the evolutionary basis of contemporary management practices. Ecol. Evol. 3, 18–37. https://doi.org/10.1002/ece3.374 (2012).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Liu, X. & Fu, Y. X. Stairway Plot 2: Demographic history inference with folded SNP frequency spectra. Genome Biol. 21, 280. https://doi.org/10.1186/s13059-020-02196-9 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Westbury, M. V. et al. Speciation in the face of gene flow within the toothed whale superfamily Delphinoidea. bioRxiv, https://doi.org/10.1101/2020.10.23.352286 (2020).

  • Westbury, M. V. et al. Ecological specialisation and evolutionary reticulation in extant Hyaenidae. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msab055 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • IWC. Report of the Scientific Committee Virtual Meeting, 11–26 May 2020. J. Cetacean Res. Manag. (Supplement) 22, 1–122 (2021).

  • Jonsgård, Å. A right whale (Balaena sp.), in all probability a Greenland right whale (Balaena mysticetus) observed in the Barents Sea. Norsk Hvalfangst-Tidende 53, 311–313 (1964).

    Google Scholar 

  • De Jong, C. The hunt of the Greenland whale: A short history and statistical sources. Rep. Int. Whaling Comm. Spec. Issue 5, 83–106 (1983).

    Google Scholar 

  • Weslawski, J. M., Hacquebord, L., Stempniewicz, L. & Malinga, M. Greenland whales and walruses in the Svalbard food web before and after exploitation. Oceanologia 2, 37–56 (2000).

    Google Scholar 

  • George, J. C. et al. Age and growth estimates of bowhead whales (Balaena mysticetus) via aspartic acid racemization. Can. J. Zool. 77, 571–580. https://doi.org/10.1139/z99-015 (1999).

    Article 

    Google Scholar 

  • de Jager, D. et al. High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes. Sci. Rep. 11, 4540. https://doi.org/10.1038/s41598-021-83823-8 (2021).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Belikov, S. E., Gorbunov, Y. A. & Shil’nikov, V. I. Distribution of pinnipedia and cetacea in Soviet arctic seas and the Bering Sea in winter. Sov. J. Marine Biology 15, 251–257 (1989).

    Google Scholar 

  • Gavrilo, M. V. Status of the bowhead whale Balaena mysticetus in the waters of Franz Josef Land Archipelago. Paper SC/66a/BRG20 Presented to the IWC Scientific Committee, May 2015, San Diego, USA (2015).

  • Heide-Jorgensen, M. P., Hansen, R. G. & Shpak, O. V. Distribution, migrations, and ecology of the Atlantic and the Okhotsk Sea Populations. In The Bowhead Whale: Balaena Mysticetus: Biology and Human Interactions (eds George, J. C. & Thewissen, J. G. M.) 57–75 (Academic Press, 2020).

    Google Scholar 

  • Petrov, S. A. et al. The results of marine mammal countins during the four expeditions in the Arctic in 2014 and 2015. Collection of scientific papers 9th International Conference ‘Marine mammals of the Holarctic’, Astrakhan, Russia, 2016. 91–102 (2018).

  • Gavrilo, M. V. & Tretiakov V. Y. Observation of bowhead whales (Balaena mysticetus) in the East-Siberian Sea during 2007 season with record-low ice cover – Marine mammals of the Holarctic. In: Collection of Scientific Papers. Odessa, 191–194 (2008).

  • Citta, J. J., Quakenbush, L. & George, J. C. Distribution and behavior of Bering-Chukchi-Beaufort bowhead whales as inferred by telemetry. In The Bowhead Whale: Balaena Mysticetus: Biology and Human Interactions (eds George, J. C. & Thewissen, J. G. M.) 31–56 (Academic Press, 2021). https://doi.org/10.1016/B978-0-12-818969-6.00004-2.

    Chapter 

    Google Scholar 

  • Arnason, Ú., Lammers, F., Kumar, V., Nilsson, M. A. & Janke, A. Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow. Sci. Adv. 4, eaap9873. https://doi.org/10.1126/sciadv.aap9873 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bazin, E., Glémin, S. & Galtier, N. Population size does not influence mitochondrial genetic diversity in animals. Science 312, 570–572. https://doi.org/10.1126/science.1122033 (2006).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Corbett-Detig, R., Hartl, D. L. & Sackton, T. B. Natural selection constrains neutral diversity across a wide range of species. PLoS Biol. 13, e1002112. https://doi.org/10.1371/journal.pbio.1002112 (2015).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Vachon, F., Whitehead, H. & Frasier, T. R. What factors shape genetic diversity in cetaceans?. Ecol. Evol. 8, 1554–1572. https://doi.org/10.1002/ece3.3727 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kumar, S. & Subramanian, S. Mutation rates in mammalian genomes. Proc. Natl. Acad. Sci. U.S.A. 99, 803–808. https://doi.org/10.1073/pnas.022629899 (2002).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bininda-Emonds, O. R. P. Fast genes and slow clades: Comparative rates of molecular evolution in mammals. Evol. Bioinf. 3, 59–85. https://doi.org/10.1177/117693430700300008 (2007).

    CAS 
    Article 

    Google Scholar 

  • Jackson, J. A. et al. Big and slow: Phylogenetic estimates of molecular evolution in baleen whales (Suborder Mysticeti). Mol. Biol. Evol. 26, 2427–2440. https://doi.org/10.1093/molbev/msp169 (2009).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Foote, A. D. et al. Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts. Nat. Commun. 4, 1667. https://doi.org/10.1038/ncomms2714 (2013).

    CAS 
    Article 

    Google Scholar 

  • Wiig, Ø., Bachmann, L. & Hufthammer, A. K. Late Pleistocene and Holocene occurrence of bowhead whales (Balaena mysticetus) along the coasts of Norway. Polar Biol. 42, 645–656. https://doi.org/10.1007/s00300-019-02460-0 (2018).

    Article 

    Google Scholar 

  • Alter, S. E. et al. Gene flow on ice: The role of sea ice and whaling in shaping Holarctic genetic diversity and population differentiation in bowhead whales (Balaena mysticetus). Ecol. Evol. 2, 2895–2911. https://doi.org/10.1093/zoolinnean/zlaa082 (2012).

    Article 

    Google Scholar 


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