Genomic analyses reveal an absence of contemporary introgressive admixture between fin whales and blue whales, despite known hybrids


Autoři: Michael V. Westbury aff001;  Bent Petersen aff001;  Eline D. Lorenzen aff001
Působiště autorů: Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen K, Denmark aff001;  Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia aff002
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
doi: 10.1371/journal.pone.0222004

Souhrn

Fin whales (Balaenoptera physalus) and blue whales (B. musculus) are the two largest species on Earth and are widely distributed across the world’s oceans. Hybrids between these species appear to be relatively widespread and have been reported in both the North Atlantic and North Pacific; they are also relatively common, and have been proposed to occur once in every thousand fin whales. However, despite known hybridization, fin and blue whales are not sibling species. Rather, the closest living relative of fin whales are humpback whales (Megaptera novaeangliae). To improve the quality of fin whale data available for analysis, we assembled and annotated a fin whale nuclear genome using in-silico mate pair libraries and previously published short-read data. Using this assembly and genomic data from a humpback, blue, and bowhead whale, we investigated whether signatures of introgression between the fin and blue whale could be found. We find no signatures of contemporary admixture in the fin and blue whale genomes, although our analyses support ancestral gene flow between the species until 2.4–1.3 Ma. We propose the following explanations for our findings; i) fin/blue whale hybridization does not occur in the populations our samples originate from, ii) contemporary hybrids are a recent phenomenon and the genetic consequences have yet to become widespread across populations, or iii) fin/blue whale hybrids are under large negative selection, preventing them from backcrossing and contributing to the parental gene pools.

Klíčová slova:

Gene flow – Genome analysis – Genomic libraries – Humpback whales – Blue whales – Fin whales – Bowhead whales – Minke whales


Zdroje

1. Aguilar A, García-Vernet R. Fin Whale: Balaenoptera physalus. In: Würsig B, Thewissen JGM, Kovacs KM, editors. Encyclopedia of Marine Mammals (Third Edition). Academic Press; 2018. p. 368–71.

2. Árnason Ú, Lammers F, Kumar V, Nilsson MA, Janke A. Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow. Sci Adv. 2018 Apr;4(4):eaap9873.

3. Cocks AH. The fin whale fishery of 1886 on the Lapland coast. Zoologist. 1887;11:207–22.

4. Spilliaert R, Vikingsson G, Arnason U, Palsdottir A, Sigurjonsson J, Arnason A. Species hybridization between a female blue whale (Balaenoptera musculus) and a male fin whale (B. physalus): molecular and morphological documentation. J Hered. 1991;82(4):269–74. doi: 10.1093/oxfordjournals.jhered.a111085 1679066

5. Bérubé M, Aguilar A. A new hybrid between a blue whale, Balaenoptera musculus, and a fin whale, B. physalus: frequency and implications of hybridization. Mar Mamm Sci. 1998;14(1):82–98.

6. Arnason U, Spilliaert R, Pálsdóttir A, Arnason A. Molecular identification of hybrids between the two largest whale species, the blue whale (Balaenoptera musculus) and the fin whale (B. physalus). Hereditas. 1991;115(2):183–9. doi: 10.1111/j.1601-5223.1991.tb03554.x 1687408

7. Cipriano F, Palumbi SR. Genetic tracking of a protected whale. Nature. 1999 Jan 28;397:307.

8. Hatch LT, Dopman EB, Harrison RG. Phylogenetic relationships among the baleen whales based on maternally and paternally inherited characters. Mol Phylogenet Evol. 2006;41(1):12–27. doi: 10.1016/j.ympev.2006.05.023 16843014

9. Steeman ME, Hebsgaard MB, Fordyce RE, Ho SYW, Rabosky DL, Nielsen R, et al. Radiation of extant cetaceans driven by restructuring of the oceans. Syst Biol. 2009;58(6):573–85. doi: 10.1093/sysbio/syp060 20525610

10. Nowak RM, Walker EP. Walker’s Mammals of the World. Vol. 1. JHU Press; 1999.

11. Yim H-S, Cho YS, Guang X, Kang SG, Jeong J-Y, Cha S-S, et al. Minke whale genome and aquatic adaptation in cetaceans. Nat Genet. 2014;46(1):88–92. doi: 10.1038/ng.2835 24270359

12. Jiang H, Lei R, Ding S-W, Zhu S. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 2014;15:182. doi: 10.1186/1471-2105-15-182 24925680

13. Grau JH, Hackl T, Koepfli K-P, Hofreiter M. Improving draft genome contiguity with reference-derived in silico mate-pair libraries. Gigascience. 2018;7(5):giy029.

14. Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27(6):863–4. doi: 10.1093/bioinformatics/btr026 21278185

15. Bushnell B. BBTools software package. URL http://sourceforge%20net/projects/bbmap. 2014;

16. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012;1(1):18. doi: 10.1186/2047-217X-1-18 23587118

17. Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I. Sealer: a scalable gap-closing application for finishing draft genomes. BMC Bioinformatics. 2015;16:230. doi: 10.1186/s12859-015-0663-4 26209068

18. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072–5. doi: 10.1093/bioinformatics/btt086 23422339

19. Waterhouse RM, Seppey M, Simão FA, Manni M, Ioannidis P, Klioutchnikov G, et al. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol. 2017;35(3):543–8.

20. Smit AFA, Hubley R, Green P. RepeatMasker Open-4.0. 2013–2015.

21. Smit AFA, Hubley R. RepeatModeler Open-1.0. 2008–2015. http://www.repeatmasker.org

22. Holt C, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics. 2011;12:491. doi: 10.1186/1471-2105-12-491 22192575

23. Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007;23(9):1061–7. doi: 10.1093/bioinformatics/btm071 17332020

24. Parra G, Bradnam K, Ning Z, Keane T, Korf I. Assessing the gene space in draft genomes. Nucleic Acids Res. 2009;37(1):289–97. doi: 10.1093/nar/gkn916 19042974

25. Korf I. Gene finding in novel genomes. BMC Bioinformatics. 2004;5:59. doi: 10.1186/1471-2105-5-59 15144565

26. Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003;19:215–25.

27. Keane M, Semeiks J, Webb AE, Li YI, Quesada V, Craig T, et al. Insights into the evolution of longevity from the bowhead whale genome. Cell Rep. 2015;10(1):112–22. doi: 10.1016/j.celrep.2014.12.008 25565328

28. Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25(14):1754–60. doi: 10.1093/bioinformatics/btp324 19451168

29. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. doi: 10.1093/bioinformatics/btp352 19505943

30. Korneliussen TS, Albrechtsen A, Nielsen R. ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics. 2014;15:356. doi: 10.1186/s12859-014-0356-4 25420514

31. Quinlan AR. BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Curr Protoc Bioinformatics. 2014;47:11.12.1–34.

32. Cahill JA, Soares AER, Green RE, Shapiro B. Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data. Philos Trans R Soc Lond B Biol Sci. 2016;371(1699):20150138. doi: 10.1098/rstb.2015.0138 27325835

33. Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature. 2011;475(7357):493–6. doi: 10.1038/nature10231 21753753

34. Hudson RR. Generating samples under a Wright–Fisher neutral model of genetic variation. Bioinformatics. 2002;18(2):337–8. doi: 10.1093/bioinformatics/18.2.337 11847089

35. Poole MM, Darling J. Occurrences of humpback whales in French Polynesia. In: Proc Bienn 13th Biol Mar Mamm. 1999. p. 150.

36. Roman J, Palumbi SR. Whales before whaling in the North Atlantic. Science. 2003;301(5632):508–10. doi: 10.1126/science.1084524 12881568

37. Sears R, Perrin WF. Blue Whale: Balaenoptera musculus. In: Perrin WF, Würsig B, Thewissen JGM, editors. Encyclopedia of Marine Mammals (Second Edition). London: Academic Press; 2009. p. 120–4.


Článek vyšel v časopise

PLOS One


2019 Číslo 9

Nejčtenější v tomto čísle

Tomuto tématu se dále věnují…


Kurzy

Zvyšte si kvalifikaci online z pohodlí domova

Krvácení v důsledku portální hypertenze při jaterní cirhóze – od pohledu záchranné služby až po závěrečný hepato-gastroenterologický pohled
nový kurz
Autoři: PhDr. Petr Jaššo, MBA, MUDr. Hynek Fiala, Ph.D., prof. MUDr. Radan Brůha, CSc., MUDr. Tomáš Fejfar, Ph.D., MUDr. David Astapenko, Ph.D., prof. MUDr. Vladimír Černý, Ph.D.

Rozšíření možností lokální terapie atopické dermatitidy v ordinaci praktického lékaře či alergologa
Autoři: MUDr. Nina Benáková, Ph.D.

Léčba bolesti v ordinaci praktického lékaře
Autoři: MUDr. PhDr. Zdeňka Nováková, Ph.D.

Revmatoidní artritida: včas a k cíli
Autoři: MUDr. Heřman Mann

Jistoty a nástrahy antikoagulační léčby aneb kardiolog - neurolog - farmakolog - nefrolog - právník diskutují
Autoři: doc. MUDr. Štěpán Havránek, Ph.D., prof. MUDr. Roman Herzig, Ph.D., doc. MUDr. Karel Urbánek, Ph.D., prim. MUDr. Jan Vachek, MUDr. et Mgr. Jolana Těšínová, Ph.D.

Všechny kurzy
Kurzy Doporučená témata Časopisy
Přihlášení
Zapomenuté heslo

Nemáte účet?  Registrujte se

Zapomenuté heslo

Zadejte e-mailovou adresu se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.

Přihlášení

Nemáte účet?  Registrujte se