Detection of grey seal Halichoerus grypus DNA in attack wounds on stranded harbour porpoises Phocoena phocoena

Bleijswijk, Judith van; Begeman, Lineke; Witte, Harry J.; IJsseldijk, Lonneke L.; Brasseur, S.M.J.M.; Gröne, Andrea; Leopold, M.F.

doi:10.3354/meps11004

Cited by 33 publications

(27 citation statements)

References 13 publications

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“…Parducci et al 2013;Pansu et al 2015b), mammals in five (e.g. Nichols & Spong 2014;van Bleijswijk et al 2014) and birds (in combination with other organisms) in just one study (Thomsen et al 2012b).…”

Section: Organisms Studiedmentioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

109

112

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Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

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Section: Organisms Studiedmentioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

109

112

View full text Add to dashboard Cite

show abstract

“…Interestingly, studies exploring killer whales populations that specialise in preying upon other great whales identified a switch to a sea otter and Steller sea lion diet (Mizroch & Rice 2006) as well as grey seals that switched from preying upon fish to harbour seals and porpoises (see van Bleijswijk et al 2014, van Neer et al 2015, might be explained by depletion of the original primary prey or individual prey preferences.…”

Section: Using Sea Otters As An Example) For Instance Femalementioning

confidence: 99%

Competition between marine mammals and fisheries in contemporary harvested marine ecosystems

Saavedra

Kuparinen²

2019

Mar. Ecol. Prog. Ser.

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Competitive interactions between marine mammals and fisheries represents one of the most complex challenges in marine resource management worldwide. The development of commercial fisheries and recovering marine mammal populations have contributed to decreasing of fish availability. Whilst ecosystem-based fisheries management (EBFM) can counteract this decrease, achieving the EBFM objectives faces certain major obstacles including insufficient or unreliable data, inapplicable assessment models as well as inadequate management decisions that do not account for fisheriesinduced morphological alterations (FIMA) and marine mammal management. Despite a body of evidence addressing various aspects of marine mammal-fisheries competition, little is known about the effects of marine mammal-fisheries biological interactions affecting the fish viability and food web stability. Here, we review the research done on marine mammal-fisheries competitive biological interactions (hereafter as 'biological competition') by focussing on: (1) the prerequisites for marine mammal-fisheries biological competition and the relevant methodologies to explore them and (2) recent studies revealing the implications of FIMA and trophic interactions for the biological competition. We also discuss on the implications of FIMA, eco-evolutionary feedback and preypredator dynamics for EBFM implementation in contemporary harvested ecosystems. Our main findings reveal a lack of data about marine mammals' prey choice and selectivity, the need for better representation of marine mammals in modelling approaches and lastly, the necessity for additional research linking FIMA, trophic interactions and the EBFM objectives. To conclude, interdisciplinary approaches may serve to link all of the efforts needed to effectively and holistically support the implementation of EBFM.

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“…De categorie 'slachtoffer door aanval grijze zeehond' is in 2013 toegevoegd naar aanleiding van het vinden van DNA van grijze zeehonden in bijtwonden van drie dood gevonden maar hele verse, gemutileerde bruinvissen (Van Bleijswijk et al, 2014). Histologisch onderzoek naar bijtwonden heeft aangetoond dat deze wonden zijn aangericht terwijl de bruinvis nog in leven was.…”

Section: Slachtoffer Door Aanval Grijze Zeehondunclassified

Postmortaal onderzoek van bruinvissen (Phocoena phocoena) uit Nederlandse wateren, 2016

IJsseldijk¹,

Kik²,

Solé³

et al. 2017

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Detection of grey seal Halichoerus grypus DNA in attack wounds on stranded harbour porpoises Phocoena phocoena

Cited by 33 publications

References 13 publications

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Competition between marine mammals and fisheries in contemporary harvested marine ecosystems

Postmortaal onderzoek van bruinvissen (Phocoena phocoena) uit Nederlandse wateren, 2016

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