Andrew David Foote

• Garroway, Colin J.; de Greef, Evelien; Lefort, Kyle J.; Thorstensen, Matt J.; Foote, Andrew David & Matthews, Cory J. D. [Show all 13 contributors for this article] (2024). Climate change introduces threatened killer whale populations and conservation challenges to the Arctic. Global Change Biology. ISSN 1354-1013. 30(6). doi: 10.1111/gcb.17352.
• Jourdain, Eve Marie; Karoliussen, Richard; Fordyce Martin, Sarah L.; Langangen, Øystein Ole Gahr; Robeck, Todd & Borgå, Katrine [Show all 8 contributors for this article] (2024). Social and genetic connectivity despite ecological variation in a killer whale network. Proceedings of the Royal Society of London. Biological Sciences. ISSN 0962-8452. 291(2021). doi: 10.1098/rspb.2024.0524.
• Laine, Jan Tapio; Mak, Sarah S.T.; Martins, Nuno F.G.; Chen, Xihan; Gilbert, Marcus Thomas Pius & Jones, Felicity C. [Show all 9 contributors for this article] (2024). Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation. Current Biology. ISSN 0960-9822. 34(5), p. 1142–1147.e6. doi: 10.1016/j.cub.2024.01.056.
• Meyer, Laura; Barry, Pierre; Riquet, Florentine; Foote, Andrew David; Der Sarkissian, Clio & Cunha, Regina L. [Show all 13 contributors for this article] (2024). Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long-snouted seahorse. Molecular Ecology. ISSN 0962-1083. doi: 10.1111/mec.17277.
• Reeves, Isabella; Totterdell, John A.; Betty, Emma; Donnelly, David M.; George, Angela & Holmes, Steven [Show all 11 contributors for this article] (2023). Ancestry testing of "Old Tom," a killer whale central to mutualistic interactions with human whalers. Journal of Heredity. ISSN 0022-1503. 114(6), p. 598–611. doi: 10.1093/jhered/esad058. Full text in Research Archive
• Louis, Marie; Korlević, Petra; Nykänen, Milaja; Archer, Frederick; Berrow, Simon & Brownlow, Andrew [Show all 18 contributors for this article] (2023). Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. Nature Communications. ISSN 2041-1723. 14(1). doi: 10.1038/s41467-023-39532-z. Full text in Research Archive
• Foote, Andrew David; Alexander, Alana; Ballance, Lisa T.; Constantine, Rochelle; Galletti Vernazzani Muñoz, Bárbara & Guinet, Christophe [Show all 15 contributors for this article] (2023). "Type D" killer whale genomes reveal long-term small population size and low genetic diversity. Journal of Heredity. ISSN 0022-1503. 114(2), p. 94–109. doi: 10.1093/jhered/esac070.
• Foote, Andrew; Bunskoek, Paulien & Sanger, Wellcome (2022). The genome sequence of the killer whale, Orcinus orca (Linnaeus, 1758). Wellcome Open Research. ISSN 2398-502X. 7. doi: 10.12688/wellcomeopenres.18278.1. Full text in Research Archive
• Louis, Marie; Korlević, Petra; Nykänen, Milaja; Archer, Frederick I.; Berrow, Simon & Brownlow, Andrew [Show all 18 contributors for this article] (2022). Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. bioRxiv. ISSN 2692-8205. doi: 10.1101/2022.11.03.515020.
• Foote, Andrew; Gilbert, Marcus Thomas Pius; Gopalakrishnan, Shyam; Louis, Marie; Martin, Michael David & Morin, Phillip A. [Show all 9 contributors for this article] (2021). Evidence of long-term purging of mutation load in killer whale genomes. bioRxiv. ISSN 2692-8205. doi: 10.1101/2021.08.21.457186.
• Louis, Marie; Galimberti, Marco; Archer, Frederick; Berrow, Simon; Brownlow, Andrew & Fallon, Ramon [Show all 15 contributors for this article] (2021). Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. Science Advances. ISSN 2375-2548. 7(44). doi: 10.1126/sciadv.abg1245. Full text in Research Archive
• Foote, Andrew; Hooper, Rebecca; Alexander, Alana; Baird, Robin; Baker, Charles Scott & Ballance, Lisa [Show all 34 contributors for this article] (2021). Runs of homozygosity in killer whale genomes provide a global record of demographic histories. Molecular Ecology. ISSN 0962-1083. 30(23), p. 6162–6177. doi: 10.1111/mec.16137. Full text in Research Archive Show summary

  Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigate whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global dataset of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstruct demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We find a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.

• Papadopulos, Alexander; Helmstetter, A.; Osborne, Owen; Comeault, Aaron; Wood, Daniel & Straw, Edward [Show all 13 contributors for this article] (2021). Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution . Molecular Biology and Evolution (MBE). ISSN 0737-4038. 38(9), p. 3724–3736. doi: 10.1093/molbev/msab141. Full text in Research Archive
• Kirch, Melanie; Romundset, Anders; Gilbert, Marcus Thomas Pius; Jones, Felicity C. & Foote, Andrew (2021). Ancient and modern stickleback genomes reveal the demographic constraints on adaptation. Current Biology. ISSN 0960-9822. 31, p. 2027–2036. doi: 10.1016/j.cub.2021.02.027. Full text in Research Archive Show summary

  Adaptation is typically studied by comparing modern populations with contrasting environments. Individuals persisting in the ancestral habitat are typically used to represent the ancestral founding population; however, it has been questioned whether these individuals are good proxies for the actual ancestors.1 To address this, we applied a paleogenomics approach2 to directly access the ancestral genepool: partially sequencing the genomes of two 11- to 13,000-year-old stickleback recovered from the transitionary layer between marine and freshwater sediments of two Norwegian isolation lakes3 and comparing them with 30 modern stickleback genomes from the same lakes and adjacent marine fjord, in addition to a global dataset of 20 genomes.4 The ancient stickleback shared genome-wide ancestry with the modern fjord population, whereas modern lake populations have lost substantial ancestral variation following founder effects, and subsequent drift and selection. Freshwater-adaptive alleles found in one ancient stickleback genome have not risen to high frequency in the present-day population from the same lake. Comparison to the global dataset suggested incomplete adaptation to freshwater in our modern lake populations. Our findings reveal the impact of population bottlenecks in constraining adaptation due to reduced efficacy of selection on standing variation present in founder populations.

• Morin, Phillip A.; Alexander, Alana; Blaxter, Mark; Caballero, Susana; Fedrigo, Olivier & Fontaine, Michaël C. [Show all 16 contributors for this article] (2020). Building genomic infrastructure: Sequencing platinum-standard reference-quality genomes of all cetacean species. Marine mammal science. ISSN 0824-0469. 36(4), p. 1356–1366. doi: 10.1111/mms.12721. Full text in Research Archive
• Hosegood, Jane; Humble, Emily; Ogden, Rob; de Bruyn, Mark; Creer, Simon & Stevens, Guy [Show all 25 contributors for this article] (2020). Phylogenomics and species delimitation for effective conservation of manta and devil rays. Molecular Ecology. ISSN 0962-1083. 29(24), p. 4783–4796. doi: 10.1111/mec.15683. Full text in Research Archive
• Dehasque, Marianne; Ávila-Arcos, María C; Díez-del-Molino, David; Fumagalli, Matteo; Guschanski, Katerina & Lorenzen, Eline D. [Show all 15 contributors for this article] (2020). Inference of natural selection from ancient DNA. Evolution Letters. ISSN 2056-3744. 4(2), p. 94–108. doi: 10.1002/evl3.165. Full text in Research Archive

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• Foote, Andrew (2022). Are “Type 2” killer whales long in the tooth? A critical reflection on the discrete categorization of Northeast Atlantic killer whales. Marine mammal science. ISSN 0824-0469. doi: 10.1111/mms.12964.
• Taylor, Rebecca S.; Jensen, Evelyn L.; Coltman, David; Foote, Andrew & Lamichhaney, Sangeet (2021). Seeing the whole picture: What molecular ecology is gaining from whole genomes. Molecular Ecology. ISSN 0962-1083. 30(23), p. 5917–5922. doi: 10.1111/mec.16282.
• Taylor, Rebecca S.; Jensen, Evelyn L.; Coltman, David; Foote, Andrew & Lamichhaney, Sangeet (2021). Seeing the whole picture: What molecular ecology is gaining from whole genomes. Molecular Ecology. ISSN 0962-1083. 30, p. 5917–5922. doi: 10.1111/mec.16282.
• Tiller, Kristin; Ellingsen, Ellen J. Grav; Ekrem, Torbjørn; Alsli, Lise Mariann Bolstad; Austrheim, Gunnar & Bendiksby, Mika [Show all 26 contributors for this article] (2019). (Dis)Harmoni i hjemlandet – Masterplan for Nye Hovedutstillinger ved NTNU Vitenskapsmuseet.

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