USAP-DC

Part I: Nontechnical description The ecologically important notothenioid fish of the Southern Ocean surrounding Antarctica will be studied to address questions central to polar, evolutionary, and adaptational biology. The rapid diversification of the notothenioids into >120 species following a period of Antarctic glaciation and cooling of the Southern Ocean is thought to have been facilitated by key evolutionary innovations, including antifreeze glycoproteins to prevent freezing and bone reduction to increase buoyancy. In this project, a large dataset of genomic sequences will be used to evaluate the genetic mechanisms that underly the broad pattern of novel trait evolution in these fish, including traits relevant to human diseases (e.g., bone density, renal function, and anemia). The team will develop new STEM-based research and teaching modules for undergraduate education at Northeastern University. The work will provide specific research training to scholars at all levels, including a post-doctoral researcher, a graduate student, undergraduate students, and high school students. The team will also contribute to public outreach, including, in part, the develop of teaching videos in molecular evolutionary biology and accompanying educational supplements. Part II: Technical description The researchers will leverage their comprehensive notothenioid phylogenomic dataset comprising >250,000 protein-coding exons and conserved non-coding elements across 44 ingroup and 2 outgroup species to analyze the genetic origins of three iconic notothenioid traits: (1) loss of erythrocytes by the icefish clade in a cold, stable and highly-oxygenated marine environment; (2) reduction in bone mass and retention of juvenile skeletal characteristics as buoyancy mechanisms to facilitate foraging; and (3) loss of kidney glomeruli to retain energetically expensive antifreeze glycoproteins. The team will first track patterns of change in erythroid-related genes throughout the notothenioid phylogeny. They will then examine whether repetitive evolution of a pedomorphic skeleton in notothenioids is based on parallel or divergent evolution of genetic regulators of heterochrony. Third, they will determine whether there is mutational bias in the mechanisms of loss and re-emergence of kidney glomeruli. Finally, identified genetic mechanisms of evolutionary change will be validated by experimental testing using functional genomic strategies in the zebrafish model system. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Person	Role
Daane, Jacob	Investigator and contact
Detrich, H. William	Co-Investigator

Antarctic Organisms and Ecosystems	Award # 2324998
Antarctic Organisms and Ecosystems	Award # 1955368

USAP-2324998_1

None in the Database

1. Daane JM, Auvinet J, Stoebenau A, Yergeau D, Harris MP, Detrich HW 3rd. Developmental constraint shaped genome evolution and erythrocyte loss in Antarctic fishes following paleoclimate change. PLoS Genet. 2020 Oct 27;16(10):e1009173. (doi:10.1371/journal.pgen.1009173)
2. Ashique AM, Atake OJ, Ovens K, Guo R, Pratt IV, Detrich HW 3rd, Cooper DML, Desvignes T, Postlethwait JH, Eames BF. Bone microstructure and bone mineral density are not systemically different in Antarctic icefishes and related Antarctic notothenioids. J Anat. 2022 Jan;240(1):34-49. (doi:10.1111/joa.13537)
3. Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW 3rd, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021 Apr;592(7856):737-746. (doi:10.1038/s41586-021-03451-0)
4. Daane JM, Detrich HW 3rd. Adaptations and Diversity of Antarctic Fishes: A Genomic Perspective. Annu Rev Anim Biosci. 2022 Feb 15;10:39-62. (doi:10.1146/annurev-animal-081221-064325)
5. Bista I, Wood JMD, Desvignes T, McCarthy SA, Matschiner M, Ning Z, Tracey A, Torrance J, Sims Y, Chow W, Smith M, Oliver K, Haggerty L, Salzburger W, Postlethwait JH, Howe K, Clark MS, William Detrich H 3rd, Christina Cheng CH, Miska EA, Durbin R. Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun. 2023 Jun 9;14(1):3412. (doi:10.1038/s41467-023-38567-6)
6. Desvignes, T., Le François, N.R., Streeter, M. et al. Hybridization barriers between the congeneric antarctic notothenioid fish Notothenia coriiceps and Notothenia rossii. Polar Biol 47, 163–171 (2024). (doi:10.1007/s00300-023-03216-7)
7. Desvignes T, Lauridsen H, Valdivieso A, Fontenele RS, Kraberger S, Murray KN, Le François NR, Detrich HW 3rd, Kent ML, Varsani A, Postlethwait JH. A parasite outbreak in notothenioid fish in an Antarctic fjord. iScience. 2022 Jun 15;25(7):104588. (doi:10.1016/j.isci.2022.104588)