Project 4014
Project |
4014 |
Chief Investigator |
DEAGLE, Dr Bruce - Australian Antarctic Division |
Title |
Molecular analysis of diet and age of animal populations |
Project aims
Project gallery
Project Summary of the Season 2012/13
Five regions of humpback whale DNA that are equivalent to regions in humans and mice that change methylation state with age have been isolated. These will be investigated for age-related methylation changes in samples from a population of known-age whales. If we can confirm age-related methylation changes in these, we will proceed to estimate the age profile of other population
Project Summary of the Season 2013/14
A study of Adelie penguin diet was produced from this project that demonstrates that DNA-based analysis of food DNA in penguin scats can be used as a replacement for stomach flushing penguins to monitor their diet. It is desirable to avoid stomach flushing as a diet analysis method as it is harmful to the birds and denies food to their chicks. This study shows that our DNA-based method provides a means to obtain finer-scale data on feeding at different times than stomach flushing studies as many more samples can be collected. It also identified many more soft-bodied food species, such as jellyfish and salps. The project team found that Jellyfish are abundant in the diet of a range of seabirds species from which scats have been sampled in the Antarctic, sub-Antarctic and Tasmania, covering the entire latitudinal range of the Southern Ocean. Jellyfish were previously considered to be an unimportant food source for Southern Ocean predators, but this work demonstrates that to be untrue.
Project Summary of the Season 2014/15
The species that animals eat are clearly essential to their survival. Most animals feed on a range of other species, so measuring change in the species consumed in time or space is useful for identifying what is happening in the ecosystem in general if the study species is a large, generalist feeder. It also provides information on the ecology of that species in particular. In the past year in this project, we have been successful in extending our DNA-based diet analyses to albatross and to pygmy blue whales. Albatross feed on a wide range of prey, including many of the pelagic, higher-biomass fish, squid, jellyfish and crustaceans. They do this over very large areas of the ocean and for this reason some albatross such as the Black Browed Albatross are used as ecosystem indicator species. We have implemented the first DNA-based analyses of the diet of this species and have preliminary results on diet for most of its range. We have also worked on pygmy blue whale diet in an area near Sri Lanka where the species is often observed feeding and we have found that in this area the whales feed on prawns as well as krill, which is a novel observation. We have also worked on seal diet and several technical aspects of DNA-based diet work and published papers on this area to maintain the AAD genetics group's expertise in this area.
Project Summary of the Season 2015/16
Final Summary of Project Achievements
Category 1: Peer-reviewed literature
Deagle B.E., Thomas A.C., Shaffer A.K., Trites A.W., Jarman S.N. (2013) Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?, Molecular Ecology Resources 13(4). 620-633; [Ref: 15065]
Dunshea G., Barros N.B., Berens McCabe E.J., Gales N.J., Hindell M.A., Jarman S.N., Wells R.S. (2013) Stranded dolphin stomach contents represent the free-ranging population's diet, Biology Letters 9(3). 20121036; [Ref: 15067]
Jarman S.N., McInnes J.C., Faux C., Polanowski A.M., Marthick J., Deagle B.E., Southwell C., Emmerson L. (2013) Adélie Penguin Population Diet Monitoring by Analysis of Food DNA in Scats, PLoS ONE 8(12). e82227; [Ref: 15169]
Faux C., McInnes J.C., Jarman S.N. (2014) High-throughput real-time PCR and melt curve analysis for sexing Southern Ocean seabirds using fecal samples, Theriogenology 81(6). 870-874; [Ref: 15171]
Peters K.J., Ophelkeller K., Bott N.J., Deagle B.E., Jarman S.N., Goldsworthy S.D. (2014) Fine-scale diet of the Australian sea lion (Neophoca cinerea) using DNA-based analysis of faeces, Marine Ecology 1-21; [Ref: 15199]
Meyer B., Martini P., Biscontin A., De Pittà C., Romualdi C., Teschke M., Frickenhaus S., Harms L., Freier U., Jarman S., Kawaguchi S. (2015) Pyrosequencing and de novo assembly of Antarctic krill (Euphausia superba) transcriptome to study the adaptability of krill to climate-induced environmental changes, Molecular Ecology Resources 12pp; [Ref: 15522]
Deagle B.E., Jarman S.N., Coissac E., Pompanon F., Taberlet P. (2014) DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match, Biology Letters 10(9). 4pp; [Ref: 15573]
Thomas A.C., Jarman S.N., Haman K.H., Trites A.W., Deagle B.E. (2014) Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias, Molecular Ecology 23(15). 3706-3718; [Ref: 15574]
Redd K.S., Ling S.D., Frusher S.D., Jarman S.N., Johnson C.R. (2014) Using molecular prey detection to quantify rock lobster predation on barrens-forming sea urchins, Molecular Ecology 23(15). 3849-3869; [Ref: 15575]
Polanowski A.M., Robbins J., Chandler J., Jarman S.N. (2014) Epigenetic estimation of age in humpback whales, Molecular Ecology Resources 14(5). 976-987; [Ref: 15576]
Thomas A.C., Deagle B.E., Eveson J.P., Harsch C.H., Trites A.W. (2016) Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material, Molecular Energy Resources 16(3). 714-726; [Ref: 15796]
De Paoli-Iseppi R., Polanowski A.M., McMahon C., Deagle B.E., Dickinson J.L., Hindell M.A., Jarman S. N. (2017) DNA methylation levels in candidate genes associated with chronological age in mammals are not conserved in a long-lived seabird, PLOS ONE 12 1-20; [Ref: 16044]
McInnes J.C., Jarman S. N., Lea M-A. , Raymond B., Deagle B.E., Phillips R.A., Catry P., Stanworth A., Weimerskirch H., Kusch A., Gras M., Cherel Y., Maschette D., Alderman R. (2017) DNA metabarcoding as a marine conservation and management tool: a circumpolar examination of fishery discards in the diet of threatened albatross, Frontiers in Marine Science 4. 22pp; [Ref: 16045]
De Paoli-Iseppi R., Deagle B.E., McMahon C.R., Hindell M.A., Dickinson J.L., Jarman S. N. (2017) Measuring animal age with DNA methylation: from humans to wild animals, Frontiers in Genetics 8. 8pp; [Ref: 16046]
McInnes J.C., Alderman R., Lea M.A., Deagle B.E., Phillips R.A., Stanworth A., Thompson D.R., Catry P., Weimerskirch H., Suazo C.G., Gras M., Jarman S.N., Raymond B. (2017) High occurrence of jellyfish predation by black-browed and Campbell albatross identified by DNA metabarcoding, Molecular Ecology 4831-4845; [Ref: 16079]
McInnes J.C., Alderman R., Deagle B.E., Lea M-A. , Raymond B., Jarman S.N. (2017) Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates, Methods in Ecology and Evolution 192-202; [Ref: 16080]
Jarman S.N., Polanowski A.M., Faux C.E., Robbins J., De Paoli-Iseppi R., Bravington M., Deagle B.E. (2015) Molecular biomarkers for chronological age in animal ecology, Molecular Ecology 4826-4847; [Ref: 16081]
McInnes J.C., Raymond B., Phillips R.A., Jarman S.N., Lea M-A. , Alderman R. (2016) A review of methods used to analyse albatross diets -Assessing priorities across their range, ICES Journal of Marine Science 2125–2137; [Ref: 16082]
McInnes J.C., Emmerson L., Southwell C., Faux C., Jarman S.N. (2015) Simultaneous DNA-based diet analysis of breeding, non-breeding and chick Adélie penguins, Royal Society Open Science .; [Ref: 16083]
de Vos A., Faux C.E., Marthick J., Dickinson J., Jarman S.N. (2018) New Determination of Prey and Parasite Species for Northern Indian Ocean Blue Whales, Frontiers in Marine Science .; [Ref: 16084]
De Paoli-Iseppi R., Deagle B.E., Polanowski A.M., McMahon C.R., Dickinson J.L., Hindell M.A., Jarman S.N. (2019) Age estimation in a long-lived seabird (Ardenna tenuirostris) using DNA methylation-based biomarkers, Molecular Ecology Resources 19(2). 411-425; [Ref: 16215]
Cavallo C.R., Chiaradia A., Deagle B.E., McInnes J.C., Gomez S.S., Hays G.C., Reina R.D. (2018) Molecular analysis of predator scats reveals role of salps in temperate inshore food webs, Frontiers in Marine Science .; [Ref: 16283]
Frugone M.J., Lowther A., Noll D., Ramos B., Pistorius P., Dantas G.P.M., Petry M.V., Bonadonna F., Steinfurth A., Polanowski A.M., Raya Rey A., Lois N.A., Putz K., Trathan P., Wienecke B., Poulin E., Vianna J.A. (2018) Contrasting phylogeographic pattern among Eudyptes penguins around the Southern Ocean, Scientific Reports 8 .; [Ref: 16284]
Frugone M.J., Lopez M.E., Cole T., Lowther A., Pistorius P., Dantas G., Petry M.V., Bonadonna F., Putz K., Trathan P., Polanowski A., Wienecke B., Segovia N., Bi K., Wang C., Jonathan M., Vianna J.A., Poulin E., Bowie R. (2019) More than the eye can see: genomic insights into the drivers of genetic differentiation in Royal/Macaroni penguins across the Southern Ocean, Molecular Phylogenetics and Evolution 139 .; [Ref: 16293]
Category 2: International meeting papers
Deagle B., McInnes J., Emmerson L., Dunn M., Adlard S., Waluda C. (2018) Adélie penguin diet: a pilot study directly comparing data from stomach flushing with faecal DNA analysis. (24 June 2018), CCAMLR Document WG-EMM-18/29 .; [Ref: 16282]
Bravington M., Jarman S., Skaug H.J. (2014) Antarctic Blue Whale surveys: augmenting via genetics for close-kin and ordinal age, International Whaling Commission Scientific Committee meeting (SC65b), Bled, Slovenia, May 2014 SC/65b/SH17; [Ref: 15345]
Category 3: Thesis, higher degree
McInnes J.C. (2017) The development and application of DNA metabarcoding to non-invasively assess albatross diets, PhD Thesis University of Tasmania 1-197; [Ref: 16043]
Dunshea G. (2012) Ecological Diagnostics for Marine Mammals: Appraisal of molecular-based methods for dietary and age estimation, PhD Thesis, University of Tasmania, Australia 164 pp; [Ref: 14967]