LOGIN TO YOUR ACCOUNT

Username
Password
Remember Me
Or use your Academic/Social account:

CREATE AN ACCOUNT

Or use your Academic/Social account:

Congratulations!

You have just completed your registration at OpenAire.

Before you can login to the site, you will need to activate your account. An e-mail will be sent to you with the proper instructions.

Important!

Please note that this site is currently undergoing Beta testing.
Any new content you create is not guaranteed to be present to the final version of the site upon release.

Thank you for your patience,
OpenAire Dev Team.

Close This Message

CREATE AN ACCOUNT

Name:
Username:
Password:
Verify Password:
E-mail:
Verify E-mail:
*All Fields Are Required.
Please Verify You Are Human:
fbtwitterlinkedinvimeoflicker grey 14rssslideshare1
Waap, Silke
Languages: English
Types: Doctoral thesis
Subjects: QH301, QH426
This thesis provides a detailed study of the diet of various procellariiformes using new molecular approaches. Dietary studies remove fundamental blocks to our understanding of the structure of food webs, and provide insights into the demographic regulation of populations and the structuring of communities. The study species were the Band-rumped Storm-petrel (Hydrobates castro), Bulwer’s petrel (Bulweria bulwerii), Cory’s shearwater (Calonectris borealis) and White-faced Storm-petrel (Pelagodroma marina). The breeding colonies of the Madeiran-archipelago are Important Bird Areas (IBA) in the North-Atlantic, but little is known about the predator-prey relationships of its seabird populations. This probably relates to difficulties associated with obtaining robust prey estimates and the need to develop new methodologies to improving the resolution of species identification. Here, new molecular approaches were developed to recover prey from faeces and stomach contents using DNA-barcoding and high-throughput sequencing (HTS). The results obtained show clear improvements to the identification of the diets of procellariiformes, considerably outperforming morphological analysis, and retrieving prey identities from non-invasive faecal remains. Such approaches further showed that sympatric small seabirds of the sub-tropical NE-Atlantic significantly segregated their resources, while showing similar prey types with the species distributed in the Pacific, indicating that these petrels maintain foraging specialization across their distribution range. Foraging efficiency in seabirds has been widely hypothesized to change according to the moon cycle. Predators either optimise foraging during moonlit nights or reduce foraging effort because less accessible prey migrate downward the water column to avoid visual predators. I tested whether prey composition and diversity differ between moon-phases. However, I found no evidence for a significant influence of the moon on the diet of Bulwer’s petrel, contradicting previous ecological assumptions. The results highlight the potential of DNA methodologies to the understanding of marine food webs and predator-prey relationships and will certainly make important contributions to marine community ecology.
  • The results below are discovered through our pilot algorithms. Let us know how we are doing!

    • morphological characters and DNA barcoding........................................................... 47
    • 2.3.1 Study area and species................................................................................ 51
    • 2.3.2 Diet sampling and analysis ......................................................................... 51
    • 2.3.4 Statistical analysis ...................................................................................... 55
    • 2.4.1 Prey discrimination..................................................................................... 56
    • 2.4.2 Diet composition ........................................................................................ 60
    • 2.4.3 Diet of non-breeders ................................................................................... 64
    • 2.4.4 Sex and inter-annual variations in diet ....................................................... 64
    • 2.4.5 Seasonal variations in diet .......................................................................... 65
    • 2.5.1 The use of DNA barcoding in prey identification ...................................... 66
    • 2.5.2 Diet of non-breeders ................................................................................... 68
    • 2.5.3 The influence of sex on diet ....................................................................... 69
    • 2.5.4 Inter-annual and seasonal variations in diet ............................................... 70
    • 3.3 Material and Methods ....................................................................................... 90
    • 3.3.1 Ethical statement ........................................................................................ 90
    • 3.3.2 Sample collection ....................................................................................... 90
    • 3.3.4 DNA extraction, amplification and high-throughput sequencing .............. 91
    • 3.3.5 Reference dataset, alignment and tree ........................................................ 92
    • 3.3.6 NGS data analysis....................................................................................... 93
    • 3.4.2 Reference dataset........................................................................................ 95
    • 3.4.3 EPA placement of query reads ................................................................. 100
    • 3.4.4 Comparison with stomach contents.......................................................... 102
    • 4.3.3 Laboratory procedures and primers.......................................................... 124
    • 4.3.4 HTS data processing and prey assignments ............................................. 126
    • 4.3.5 Statistical analysis .................................................................................... 127
    • 4.4.1 Taxonomical coverage of primers set CrusF1/R1 .................................... 127
    • 4.4.2 HTS analysis and taxonomical assignments of queries............................ 128
    • 4.4.3 Comparisons of diets ................................................................................ 134
    • 4.4.4 Trophic segregation among petrels .......................................................... 136
    • 5.3.4 Identification and quantification of prey remains .................................... 155
    • 5.3.5 Statistical analysis .................................................................................... 156
    • Karpouzi VS, Watson R & Pauly D 2007. Modelling and mapping resource overlap between seabirds and fisheries on a global scale: a preliminary assessment. Marine Ecology Progress Series 343: 87-99
    • Klomp NI & Furness RW (1992). Patterns of chick feeding in Cory's Shearwaters and the associations with ambient light. Colonial Waterbirds 15: 95-102.
    • Kotler BP, Brown J, Mukherjee S, Berger-Tal O & Bouskila A (2010) Moonlight avoidance in gerbils reveals a sophisticated interplay among time allocation, vigilance and state-dependent foraging. Proceedings of the Royal Society B, 277: 1469-1474.
    • Kruskal JB & Wish M (1978) Multidimensional Scaling. Sage Publications, Beverly Hills.
    • Lyons KG & Schwartz MW (2001) Rare species loss alters ecosystem function - invasion resistance. Ecology Letters, 4: 358-365
    • McCann K, Hastings A & Huxel GR (1998) Weak trophic interactions and the balance of nature. Nature, 395: 794-798.
    • Miller MA, Pfeiffer W & Schwartz T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE). New Orleans, pp. 1-8.
    • Mougeot F & Bretagnolle V (2003) Predation risk and moonlight avoidance in nocturnal seabirds. Journal of Avian Biology, 31: 376-378.
    • Murata M (1988) On the flying behavior of neon flying squid Ommastrephes bartrami observed in the central and northwestern North Pacific. Nippon Suisan Gakkaishi, 54: 1167-1174
    • Neves VC, Nolf D & Clarke MR (2011) Diet of Bulwer's petrel in the Azores, NE Atlantic. Waterbirds, 34: 357-362
    • Ohman MD, Frost BW & Cohen EB (1983) Reverse diel vertical migration: an escape from invertebrate predators. Science 220:1404-1407.
    • Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH & Wagner H (2015) vegan: Community Ecology Package. R package version 2.2-1. http://CRAN.R-project.org/package=vegan
    • Palumbi SR (1996) Nucleic acids II: the polymerase chain reaction. In: Hillis DM, Mable BK, Moritz C (eds) Molecular Systematics. Sinauer, Sunderland, MA, pp 205-247.
    • Phalan B, Phillips RA, Silk JRD, Afanasyev V, Fukuda A, Fox J, Catry P, Higuchi H & Croxall JP (2007) Foraging behaviour of four albatross species by night and day. Marine Ecology Progress Series, 340: 271-286
    • Phillips RA (2006) Efficacy and effects of diet sampling of albatross chicks. Emu 106: 305-308
    • Poos MS & Jackson DA (2012) Addressing the removal of rare species in multivariate bioassessments: The impact of methodological choices. Ecological Indicators, 18: 82-90
    • Price MN, Dehal PS & Arkin AP (2010) FastTree 2: Approximately MaximumLikelihood Trees for Large Alignments. PLoS ONE, 5(3): e9490
    • Queiroga H, Almeida MJ, Alpuim T, Flores AAV, Francisco S, Gonzalez-Gordillo JI, Miranda AI, Silva I & Paula J (2006) Wind and tide control of megalopal supply to estuarine crab populations on the Portuguese west coast, 307: 21-36
    • R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.Rproject.org/
    • Ralph CP, Nagata SE & Ralph CJ (1985) Analysis of droppings to describe diets of small birds. Journal of Field Ornithology, 56: 165-174
    • Ratnasingham S & Hebert PDN (2007) BOLD: the barcode of life data system (www.barcodinglife.org). Molecular Ecology Notes 7: 355-364.
    • Regular PM, Hedd A & Montevecchi WA (2011) Fishing in the dark: a pursuit-diving seabird modifies foraging behavior in response to nocturnal light levels. PLoS ONE 6: e26763
    • Riou S & Hamer KC (2008) Predation risk and reproductive effort: impacts of moonlight on food provisioning and chick growth in Manx shearwaters. Animal Behaviour 76: 1743-1748
    • Rubolini D, Maggini I, Ambrosini R, Imperio S, Paiva VH, Gaibani G, Saino N & Cecere, JG (2014) The Effect of Moonlight on Scopoli's Shearwater Calonectris diomedea Colony Attendance Patterns and Nocturnal Foraging: A Test of the Foraging Efficiency Hypothesis. Ethology, 121: 284-299
    • Schneider DC (2007) Seabirds and fronts: a brief overview. Polar Research 8:17-21
    • Skov MW, Hartnoll RG, Ruwa RK, Shunula JP, Vannini M & Cannicci S (2004) Marching to a different drummer: crabs synchronize reproduction to a 14 th lunar tidal cycle. Ecology, 86:1164-1171
    • Spear LB, Ainley DG & Walker WA (2007) Foraging dynamics of seabirds in the Eastern Tropical Pacific Ocean. Studies  in  Avian  Biology 35:1−99
    • Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22: 2688- 2690
    • Tollit DJ, Schulze AD, Trites AW, Olesiuk PF, Crockford SJ, Gelatt TS, Ream RR, & Miller KM (2009) Development and application of DNA techniques for validating and improving pinniped diet estimates. Ecological Applications 19: 889-905.
    • Vogler AP & Monaghan MT (2007) Recent advances in DNA taxonomy. Journal of Zoological Systematics and Evolutionary Research, 45: 1-10.
    • Watanabe H, Moku M, Kawaguchi K, Ishimaru K & Ohno A (1999) Diel vertical migration of myctophid fishes (family Myctophidae) in the transitional waters of the western North Pacific. Fisheries Oceanography 8:115-127
    • Wilson RP (1984) An improved stomach pump for penguins and other seabirds. Journal of Field Ornithology, 55: 109-112
    • Yamamoto T, Takahashi A, Yoda K, Katsumata N & Watanabe S (2008) The lunar cycle affects at-sea behaviour in a pelagic seabird, the streaked shearwater, Calonectris leucomelas. Animal Behaviour 76: 1647-1652.
    • Zaret TM & Suffern JS (1976) Vertical migration in zooplankton as a predator avoidance mechanism. Limnology and Oceanography, 21: 804-813.
    • Zhang C, Abello P & Ernest N (1999) Endogenous tidal and semilunar moulting rhythms in early juvenile shore crabs Carcinus maenas: implications for adaptation to a high intertidal habitat. Marine Ecology Progress Series, 191:257- 266
    • Zonfrillo B (1986) Diet of Bulwer's petrel Bulweria bulwerii in the Madeiran archipelago. Ibis,128: 570-572
    • Ballance LT & Pitman RL (1999) Foraging ecology of tropical seabirds. In: Adams, NJ & Slotow RH (eds) Proc. 22 International Ornithology Congress, Durban: 2057- 2071. Johannesburg
    • Bohmann K, Jomadjem A, Noer C, Rasmussen M, Zeale M, Clare EL, Willerslev E & Gilber MTP (2011) Molecular dietary analysis of two African free-tailed bats (Molossidae) using high throughput sequencing. PLoS ONE. 6: e21441
    • Awkerman J, Fukuda A, Higuchi H & Anderson D (2005) Foraging activity and submesoscale habitat use of waved albatrosses Phoebastria irrorata during chickbrooding period. Marine Ecology Progress Series 291: 289-300
    • Ballance LT, Pitman RL & Reilly SB (1997) Seabird community structure along a productivity gradient: importance of com- petition and energetic constraint. Ecology 78: 1502-1518
    • Barnett A, Redd KS, Frusher SD, Stevens JD & Semmens JM (2010) Non-lethal method to obtain stomach samples from a large marine predator and the use of DNA analysis to improve dietary information. Journal of Experimental Marine Biology and Ecology 393: 188-192
    • Benoit-Bird KJ, Au WWL & Wisdoma DW (2009a) Nocturnal light and lunar cycle effects on diel migration of micronekton. Limnology and Oceanography 54: 1789- 1800
    • Benoit-Bird KJ, Dahood AD & Würsig B (2009b) Using active acoustics to compare lunar effects on predator-prey behavior in two marine mammal species. Marine Ecology Progress Series 395: 119-135
    • Berger SA, Krompass D & Stamatakis A (2011) Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood. Systematic Biology 60: 291-302
    • Bowser AK, Diamond AW & Addison JA (2013) From Puffins to Plankton: A DNABased Analysis of a Seabird Food Chain in the Northern Gulf of Maine. PLoS ONE, 8(12), e83152.
    • Clare EL, Symondson WOC, Broders H, Fabianek F, Fraser E, Mackenzie A, Boughen A, Hamilton R, Willis C, Martinex F, Menzies A, Norquay K, Brigham M, Poissant J, Rintoul J, Barclay R & Reimer J (2013a) The diet of Myotis lucifugus across Canada: assessing habitat quality and dietary variability. Molecular Ecology 23: 3618-3632
  • Inferred research data

    The results below are discovered through our pilot algorithms. Let us know how we are doing!

    Title Trust
    61
    61%
  • No similar publications.

Share - Bookmark

Funded by projects

  • FCT | SFRH/BD/73656/2010
  • FCT | PTDC/MAR/121071/2010

Cite this article