Final Report Summary - KWAF10 (Killer Whales) The description of genome-wide nucleotide variation across numerous individuals within a single species provides a powerful tool with which to uncover the species’ population history, past and present migrations, range expansions or contractions, and even adaptation to changing environments or niches. However, despite the power of such data, its use has until recently been limited to heavily studied so-called ‘model’ organisms such as humans or Drosophila. Despite this, recent technological advances have become available that combine so-called ‘reduced representation genome sequencing’ with the power of high-throughput sequencing platforms, and as such in the near future we can expect that genome-scale datasets will have the potential to be a widely adopted and powerful tool for application to evolutionary, conservation and population genetics questions in a broad range of species. Given this, it is of current great general scientific interest to apply their use to a range of other organisms, in particular those that, while non-model, are sufficiently well-described so as to enable both method validation, and to present testable hypotheses of wide general interest.The objective of this project was to apply the latest groundbreaking techniques in the area, to a long-lived, globally distributed and partially- characterised non-model organism, the killer whale (Orcinus orca) – a polymorphic species for which there has been a long-standing debate as to its taxonomic status. Killer whales are apex predators found in all the world’ s oceans, and while currently considered a single species, local variation in a number of characteristics, including body size, colour patterning, social structure, vocalization pattern and foraging behaviour has led to the recognition of several named killer whale types.The project progressed well and the research and training objectives set out in the application were met, and even surpassed.In addition to producing the genome wide scan data using a global dataset of killer whales, we have sequenced, assembled and annotated the whole genome of a killer whale, the first complete high coverage genome of a marine mammal.This therefore accomplished two important scientific goals - the first information on adaptation of the mammalian genome to the marine environment, and an understanding of how regions of the genome diverge during the speciation process in our model system.We are currently writing up two papers based on this work: first an intra-specific comparison of the genomic architecture of speciation between a global dataset of killer whale ecotypes; second, an investigation of adaptation of the mammalian genome to the aquatic environment (for this we have also denovo sequenced the walrus and bottlenose dolphin genomes). Further, I have worked on additional projects during the two years and a number of publications have arisen from these:Foote AD, Morin PA, Durban JW, Willerslev E, Orlando L, Gilbert MTP (2011) Out of the Pacific and back again: the matrilineal history of Pacific killer whale ecotypes. PLoS ONE 6:e24980Foote AD, Hofreiter M, Morin PA (2012) Ancient DNA and marine mammals: Studying long-lived species over ecological and evolutionary timescales. Annals of Anatomy 194. 112-120Foote AD (2012) Investigating ecological speciation in non-model organisms: a case study on killer whale ecotypes. Evolutionary Ecology Research 14, 447-465Foote AD, Thomsen PF, Sveegaard S, et al. (2012) Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS ONE 7: e41781Foote AD, Vester H, Vikingsson GA, Newton J (2012) Dietary variation within and between populations of northeast Atlantic killer whales Orcinus orca inferred from d13C and d15N analyses. Marine Mammal Science 28, E472-E485Sinding MHS, Gilbert MTP, Grønnow B, Gulløv HC, Toft PA, Foote AD (2012) Non-destructive DNA extraction from archaeological artifacts made from whale baleen. Journal of Archaeological Science 39, 3750-3753Foote AD, Morin PA, Pitman RL, et al. (2013) Mitogenomic insights into a recently described and rarely observed killer whale morphotype. Polar Biology 36, in pressFoote AD, Kaschner K, Schultze S, et al. (2013) Habitat tracking by Arctic whales during climate change. Nature Communications 4:1677Foote AD, Newton J, Ávila-Arcos MC, et al. (2013) Tracking niche variation over millennial timescales in sympatric killer whale lineages. Proceedings of the Royal Society, B 280: 20131481Beck S, Foote AD, Kötter S et al. (2014) Using opportunistic photo-identifications to detect a population decline of killer whales (Orcinus orca) in British and Irish waters. Journal of Marine Biological Association UK (special issue on North Atlantic killer whales) in pressFoote AD, Kuningas S, Sammara FIP (Guest Editors) (2014) North Atlantic killer whale research: past, present and future (Foreword for special issue on North Atlantic killer whales). Journal of Marine Biological Association UK in pressTervo OM, Christoffersen M, Foote AD, et al. Female bowhead whales sing: phylogenetic insights in to the evolution of whale song. Proceedings of the Royal Society, B in reviewMartin M, Zimmer E, Olsen M, Foote AD, Gilbert MTP. A temporal shift in phylogeographic structure of common ragweed during massive disturbance of its native range. Molecular Ecology in reviewBank C, Boughman JW, Brännström Å, Brelsford A, Butlin RK, Clarkson C, Eroukhmanoff F, Feder JL, Fischer M, Foote AD, Franchini P, Hohenlohe PA, Jiggins CD, Jones FC, Keller I, Lindholm AK, Lucek K, Maan ME, Marques DA, Martin SH, Matthews B, Meier JI, Möst M, Nachman MW, Nonaka E, Peichel CL, Rennison DJ, Saetre G-P, Schwarzer J, Seehausen O, Wagner CE, Watson ET, Westram AM, Widmer A (in review) Genome-scale data and the genetics of speciation. Nature Reviews Genetics in review.I have attended and presented at several conferences and workshops including: The European Cetacean Society conference 2011, 2012 (oral presentations and a poster, plus hosted a workshop at the 2012 conference); IUCN ASCOBANS meeting 2011 (invited presentation); Oceans conference, Salt Lake City 2012 (oral presentation); ESF FROSPECTS workshop, Hungary (oral presentation); Invited presentations include Genomics workshop, Society for Marine Mammalogy Bienniel Conference, New Zealand (2013); Departmental seminar, EAWAG, University of Bern, Lake Lucerne (2013); Advances in Ecological Speciation meeting, CIBIO, Vairão, Portugal (2013); One of fifteen early career researchers selected to attend a ESF Frospects Network workshop, which resulted in the Nature Reviews Genetics synthesis (2013); Departmental seminar, Scripps Oceanographic Institute, San Diego (2013); Departmental seminar, Evolutionary Biology Centre, Uppsala University (2012); Genetic Monitoring of Marine Mammal Populations Workshop, Society for Marine Mammalogy, Tampa, Florida, USA (2011)The training at Copenhagen on molecular laboratory techniques and bioinformatics has been at a level sufficient to complete the project and allow me to progress with my career by becoming further specialised in genomics. Further training has been undertaken at Cornell University and at the Leibniz Institute for Zoology, Berlin.