USAP-DC

{"dp_type": "Project", "free_text": "Dragonfish"}

[{"awards": "2232891 Postlethwait, John", "bounds_geometry": "POLYGON((-180 -37,-144 -37,-108 -37,-72 -37,-36 -37,0 -37,36 -37,72 -37,108 -37,144 -37,180 -37,180 -42.3,180 -47.6,180 -52.9,180 -58.2,180 -63.5,180 -68.8,180 -74.1,180 -79.4,180 -84.69999999999999,180 -90,144 -90,108 -90,72 -90,36 -90,0 -90,-36 -90,-72 -90,-108 -90,-144 -90,-180 -90,-180 -84.7,-180 -79.4,-180 -74.1,-180 -68.8,-180 -63.5,-180 -58.2,-180 -52.9,-180 -47.6,-180 -42.300000000000004,-180 -37))", "dataset_titles": null, "datasets": null, "date_created": "Mon, 14 Aug 2023 00:00:00 GMT", "description": "Antarctic animals face tremendous threats as Antarctic ice sheets melt and temperatures rise. About 34 million years ago, when Antarctica began to cool, most species of fish became locally extinct. A group called the notothenioids, however, survived due to the evolution of antifreeze. The group eventually split into over 120 species. Why did this group of Antarctic fishes evolve into so many species? One possible reason why a single population splits into two species relates to sex genes and sex chromosomes. Diverging species often have either different sex determining genes (genes that specify whether an individual\u2019s gonads become ovaries or testes) or have different sex chromosomes (chromosomes that differ between males and females within a species, like the human X and Y chromosomes). We know the sex chromosomes of only a few notothenioid species and know the genetic basis for sex determination in none of them. The aims of this research are to: 1) identify sex chromosomes in species representing every major group of Antarctic notothenioid fish; 2) discover possible sex determining genes in every major group of Antarctic notothenioid fish; and 3) find sex chromosomes and possible sex determining genes in two groups of temperate, warmer water, notothenioid fish. These warmer water fish include groups that never experienced the frigid Southern Ocean and groups that had ancestors inhabiting Antarctic oceans that later adjusted to warmer waters. This project will help explain the mechanisms that led to the division of a group of species threatened by climate change. This information is critical to conserve declining populations of Antarctic notothenioids, which are major food sources for other Antarctic species such as bird and seals. The project will offer a diverse group of undergraduates the opportunity to develop a permanent exhibit at the Eugene Science Center Museum. The exhibit will describe the Antarctic environment and explain its rapid climate change. It will also introduce the continent\u2019s bizarre fishes that live below the freezing point of water. The project will collaborate with the university\u2019s Science and Comics Initiative and students in the English Department\u2019s Comics Studies Minor to prepare short graphic novels explaining Antarctic biogeography, icefish specialties, and the science of this project as it develops. As Antarctica cooled, most species disappeared from the continent\u2019s waters, but cryonotothenioid fish radiated into a species flock. What facilitated this radiation? Coyne\u2019s \u201ctwo rules of speciation\u201d offer explanations for why species diverge: 1) the dysgenic sex in an interspecies hybrid is the one with two different sex chromosomes (i.e., in humans, it would be XY males and not XX females); and 2) \u201csex chromosomes play an outsized role in speciation\u201d. These ideas propel the project\u2019s main hypothesis: new sex chromosomes and new sex determination genes associate with cryonotothenioid speciation events. The main objective of the research is to identify notothenioid sex chromosomes and candidate sex-determination genes in many notothenioid species. The project\u2019s first aim is to identify Antarctic fish sex chromosomes, asking the question: Did new sex chromosomes accompany speciation events? Knowledge gaps include: which species have cryptic sex chromosomes; which have newly evolved sex chromosomes; and which are chromosomally XX/XY or ZZ/ZW. Methods involve population genomics (RAD-seq and Pool-seq) for more than 20 Antarctic cryonotothenioids. The prediction is frequent turnover of sex chromosomes. The project\u2019s second aim is to Identify candidate Antarctic cryonotothenioid sex-determination genes, asking the question: Did new sex-determination genes accompany Antarctic cryonotothenioid speciation events? A knowledge gap is the identity of sex determination genes in any notothenioid. Preliminary data show that three sex-linked loci are in or adjacent to three different candidate sex determination genes: 1) a duplicate of bmpr1ba in blackfin icefish; 2) a tandem duplicate of gsdf in South Georgia icefish; and 3) a transposed duplicate of gsdf in striped notothen. Methods involve annotating the genomic neighborhoods of cryonotothenioid sex linked loci for anomalies in candidate sex genes, sequencing sex chromosomes, and testing sex gene variants by CRISPR mutagenesis in zebrafish. The prediction is frequent turnover of sex determination genes. The project\u2019s third aim is to identify sex chromosomes and sex-determination genes in temperate notothenioids. Basally diverging temperate notothenioids (\u2018basals\u2019) lack identifiable sex chromosomes, consistent with temperature-cued sex determination, and one \u2018basal\u2019 species is a hermaphrodite. The constantly cold Southern Ocean rules out temperature, a common sex determination cue in many temperate fish, favoring genetic sex determination. Some cryonotothenioids re-invaded temperate waters (\u2018returnees\u2019). Knowledge gaps include whether basals and returnees have strong sex determination genes. Methods employ pool-seq. The prediction is that genetic sex determination is weak in basals and that returnees have the same, but weaker, sex-linked loci as their Antarctic sister clade. A permanent exhibit will be established at the Eugene Science Center Museum tentatively entitled: The Antarctic: its fishes and climate change. Thousands of visitors, especially school children will be exposed, to the science of Antarctic ecosystems and the impacts of climate change. The research team will collaborate with the university\u2019s Science and Comics Initiative to produce short graphic novels explaining Antarctic biogeography, icefish specialties, and this project. This award reflects NSF\u0027s statutory mission and has been deemed worthy of support through evaluation using the Foundation\u0027s intellectual merit and broader impacts review criteria.", "east": 180.0, "geometry": "POINT(0 -89.999)", "instruments": null, "is_usap_dc": true, "keywords": "Speciation; Southern Ocean; Dragonfish; Antarctica; Plunderfish; Fish; Notothenioid; FISH; Eleginopsioidea; Icefish; MARINE ECOSYSTEMS; Cryonotothenioid; Sub-Antarctic", "locations": "Antarctica; Southern Ocean; Sub-Antarctic", "north": -37.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Postlethwait, John; Desvignes, Thomas", "platforms": null, "repositories": null, "science_programs": null, "south": -90.0, "title": "ANT LIA: The Role of Sex Determination in the Radiation of Antarctic Notothenioid Fish", "uid": "p0010431", "west": -180.0}, {"awards": "1543383 Postlethwait, John; 1947040 Postlethwait, John; 2232891 Postlethwait, John", "bounds_geometry": "POLYGON((-180 -37,-144 -37,-108 -37,-72 -37,-36 -37,0 -37,36 -37,72 -37,108 -37,144 -37,180 -37,180 -42.3,180 -47.6,180 -52.9,180 -58.2,180 -63.5,180 -68.8,180 -74.1,180 -79.4,180 -84.69999999999999,180 -90,144 -90,108 -90,72 -90,36 -90,0 -90,-36 -90,-72 -90,-108 -90,-144 -90,-180 -90,-180 -84.7,-180 -79.4,-180 -74.1,-180 -68.8,-180 -63.5,-180 -58.2,-180 -52.9,-180 -47.6,-180 -42.300000000000004,-180 -37))", "dataset_titles": "aBSREL tests for episodic diversifying selection on hemoglobin genes in notothenioids.; MEME tests of sites evolving under episodic diversifying selection in notothenioid hemoglobin genes.; Notothenioid hemoglobin protein 3D modeling.; Notothenioid species tree used in the study.; Phylogenetic trees of hemoglobin proteins in notothenioids.; Rates of hemoglobin evolution among genes and across notothenioid species.; RELAX tests for pervasive changes in strength of natural selection on hemoglobin genes in notothenioids.", "datasets": [{"dataset_uid": "601732", "doi": "10.15784/601732", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Genetic Analysis; Hemoglobin; Icefish; Notothenioid; Notothenioid Fishes; Plunderfish; Sub-Antarctic", "people": "Postlethwait, John; Desvignes, Thomas", "repository": "USAP-DC", "science_program": null, "title": "Notothenioid hemoglobin protein 3D modeling.", "url": "https://www.usap-dc.org/view/dataset/601732"}, {"dataset_uid": "601721", "doi": "10.15784/601721", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Gene; Hemoglobin; Icefish; Notothenioid; Plunderfish; Sub-Antarctic", "people": "Desvignes, Thomas; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "Notothenioid species tree used in the study.", "url": "https://www.usap-dc.org/view/dataset/601721"}, {"dataset_uid": "601722", "doi": "10.15784/601722", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Gene; Hemoglobin; Icefish; Notothenioid; Plunderfish; Sub-Antarctic", "people": "Postlethwait, John; Desvignes, Thomas", "repository": "USAP-DC", "science_program": null, "title": "Phylogenetic trees of hemoglobin proteins in notothenioids.", "url": "https://www.usap-dc.org/view/dataset/601722"}, {"dataset_uid": "601728", "doi": "10.15784/601728", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Gene; Genetic Analysis; Hemoglobin; Icefish; Notothenioid; Notothenioid Fishes; Plunderfish; Sub-Antarctic", "people": "Desvignes, Thomas; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "aBSREL tests for episodic diversifying selection on hemoglobin genes in notothenioids.", "url": "https://www.usap-dc.org/view/dataset/601728"}, {"dataset_uid": "601729", "doi": "10.15784/601729", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Genetic Analysis; Hemoglobin; Icefish; Notothenioid; Notothenioid Fishes; Plunderfish; Sub-Antarctic", "people": "Desvignes, Thomas; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "Rates of hemoglobin evolution among genes and across notothenioid species.", "url": "https://www.usap-dc.org/view/dataset/601729"}, {"dataset_uid": "601730", "doi": "10.15784/601730", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Genetic Analysis; Hemoglobin; Icefish; Notothenioid; Notothenioid Fishes; Plunderfish; Sub-Antarctic", "people": "Postlethwait, John; Desvignes, Thomas", "repository": "USAP-DC", "science_program": null, "title": "MEME tests of sites evolving under episodic diversifying selection in notothenioid hemoglobin genes.", "url": "https://www.usap-dc.org/view/dataset/601730"}, {"dataset_uid": "601731", "doi": "10.15784/601731", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Genetic Analysis; Hemoglobin; Icefish; Notothenioid; Notothenioid Fishes; Plunderfish; Sub-Antarctic", "people": "Postlethwait, John; Desvignes, Thomas", "repository": "USAP-DC", "science_program": null, "title": "RELAX tests for pervasive changes in strength of natural selection on hemoglobin genes in notothenioids.", "url": "https://www.usap-dc.org/view/dataset/601731"}], "date_created": "Wed, 03 May 2023 00:00:00 GMT", "description": "Antarctic notothenioid fishes, also known as cryonotothenioids, inhabit the icy and highly oxygenated waters surrounding the Antarctic continent after diverging from notothenioids inhabiting more temperate waters. Notothenioid hemoglobin and blood parameters are known to have evolved along with the establishment of stable polar conditions, and among Antarctic notothenioids, icefishes are evolutionary oddities living without hemoglobin following the deletion of all functional hemoglobin genes from their genomes. In this project, we investigate the evolution of hemoglobin genes and gene clusters across the notothenioid radiation until their loss in the icefish ancestor after its divergence from the dragonfish lineage to understand the forces, mechanisms, and potential causes for hemoglobin gene loss in the icefish ancestor.", "east": 180.0, "geometry": "POINT(0 -89.999)", "instruments": null, "is_usap_dc": true, "keywords": "FISH; Icefish; Cryonotothenioid; Gene; Plunderfish; Eleginopsioidea; AQUATIC ECOSYSTEMS; Dragonfish; Sub-Antarctic; Notothenioid; Blood; Hemoglobin", "locations": "Sub-Antarctic", "north": -37.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Desvignes, Thomas; Postlethwait, John", "platforms": null, "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -90.0, "title": "Evolution of hemoglobin genes in notothenioid fishes", "uid": "p0010417", "west": -180.0}, {"awards": "1142122 Miller, Nathan", "bounds_geometry": "POLYGON((166.163 -76.665,166.2635 -76.665,166.364 -76.665,166.4645 -76.665,166.565 -76.665,166.6655 -76.665,166.766 -76.665,166.8665 -76.665,166.967 -76.665,167.0675 -76.665,167.168 -76.665,167.168 -76.782,167.168 -76.899,167.168 -77.016,167.168 -77.133,167.168 -77.25,167.168 -77.367,167.168 -77.484,167.168 -77.601,167.168 -77.718,167.168 -77.835,167.0675 -77.835,166.967 -77.835,166.8665 -77.835,166.766 -77.835,166.6655 -77.835,166.565 -77.835,166.4645 -77.835,166.364 -77.835,166.2635 -77.835,166.163 -77.835,166.163 -77.718,166.163 -77.601,166.163 -77.484,166.163 -77.367,166.163 -77.25,166.163 -77.133,166.163 -77.016,166.163 -76.899,166.163 -76.782,166.163 -76.665))", "dataset_titles": "Antarctic emerald rockcod have the capacity to compensate for warming when uncoupled from CO2-acidification; Physiological and biochemical measurements on Antarctic dragonfish (Gymnodraco acuticeps) from McMurdo Sound; Physiological and biochemical measurements on juvenile Antarctic rockcod (Trematomus bernacchii) from McMurdo Sound; Thermal windows and metabolic performance curves in a developing Antarctic fish", "datasets": [{"dataset_uid": "601025", "doi": "10.15784/601025", "keywords": "Antarctica; Biota; Fish; McMurdo Sound; Oceans; Ross Sea; Southern Ocean", "people": "Flynn, Erin; Davis, Brittany; Todgham, Anne; Miller, Nathan", "repository": "USAP-DC", "science_program": null, "title": "Physiological and biochemical measurements on juvenile Antarctic rockcod (Trematomus bernacchii) from McMurdo Sound", "url": "https://www.usap-dc.org/view/dataset/601025"}, {"dataset_uid": "601040", "doi": "10.15784/601040", "keywords": "Antarctica; Biota; Fish; McMurdo Sound; Oceans; Ross Sea; Sample/collection Description; Sample/Collection Description; Southern Ocean", "people": "Miller, Nathan; Todgham, Anne", "repository": "USAP-DC", "science_program": null, "title": "Thermal windows and metabolic performance curves in a developing Antarctic fish", "url": "https://www.usap-dc.org/view/dataset/601040"}, {"dataset_uid": "601039", "doi": "10.15784/601039", "keywords": "Antarctica; Biota; Chemistry:fluid; Chemistry:Fluid; CTD Data; Fish; McMurdo Sound; Ocean Acidification; Oceans; Physical Oceanography; Ross Sea; Southern Ocean", "people": "Todgham, Anne; Miller, Nathan", "repository": "USAP-DC", "science_program": null, "title": "Antarctic emerald rockcod have the capacity to compensate for warming when uncoupled from CO2-acidification", "url": "https://www.usap-dc.org/view/dataset/601039"}, {"dataset_uid": "601026", "doi": "10.15784/601026", "keywords": "Antarctica; Biota; Chemistry:fluid; Chemistry:Fluid; CTD Data; Fish; McMurdo Sound; Ocean Acidification; Oceans; Physical Oceanography; Ross Sea; Southern Ocean", "people": "Davis, Brittany; Flynn, Erin; Todgham, Anne; Miller, Nathan", "repository": "USAP-DC", "science_program": null, "title": "Physiological and biochemical measurements on Antarctic dragonfish (Gymnodraco acuticeps) from McMurdo Sound", "url": "https://www.usap-dc.org/view/dataset/601026"}], "date_created": "Tue, 15 Aug 2017 00:00:00 GMT", "description": "Ocean acidification and increased temperatures are projected to be the primary impacts of global climate change on polar marine ecosystems over the next century. While recent research has focused on the effects of these drivers on calcifying organisms, less is known about how these changes may affect vertebrates. This research will focus on two Antarctic fishes, Trematomus bernacchii and Pagothenia borchgrevinki. Fish eggs and larvae will be collected in McMurdo Sound and reared under different temperature and pH regimes. Modern techniques will be used to examine subsequent changes in physiology, growth, development and gene expression over both short and long timescales. The results will fill a missing gap in our knowledge about the response of non-calcifying organisms to projected changes in pH and temperature. Results will be widely disseminated through publications as well as through presentations at national and international meetings; raw data will also be made available through open-access, web-based databases. This project will support the research and training of three graduate and three undergraduate students. As well, this project will foster the development of two modules on climate change and ocean acidification for an Introduction to Biology course.", "east": 167.168, "geometry": "POINT(166.6655 -77.25)", "instruments": null, "is_usap_dc": true, "keywords": "Not provided", "locations": null, "north": -76.665, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Miller, Nathan; Todgham, Anne", "platforms": "Not provided", "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -77.835, "title": "RUI: Synergistic effects of Ocean Acidification and Warming on Larval Development in Antarctic Fishes", "uid": "p0000411", "west": 166.163}]

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