USAP-DC

{"dp_type": "Project", "free_text": "Genome Assembly"}

[{"awards": "1645087 Catchen, Julian", "bounds_geometry": null, "dataset_titles": "Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus\u2014The Closest Ancestral Proxy of Antarctic Cryonotothenioids; Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki; Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish", "datasets": [{"dataset_uid": "200381", "doi": "", "keywords": null, "people": null, "repository": "NCBI", "science_program": null, "title": "Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus\u2014The Closest Ancestral Proxy of Antarctic Cryonotothenioids", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA917608"}, {"dataset_uid": "200380", "doi": "", "keywords": null, "people": null, "repository": "NCBI", "science_program": null, "title": "Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA857989"}, {"dataset_uid": "200331", "doi": "10.5061/dryad.ghx3ffbs3", "keywords": null, "people": null, "repository": "Dryad", "science_program": null, "title": "Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki", "url": "https://datadryad.org/stash/dataset/doi:10.5061/dryad.ghx3ffbs3"}, {"dataset_uid": "200330", "doi": "", "keywords": null, "people": null, "repository": "NCBI ", "science_program": null, "title": "Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA861284"}], "date_created": "Mon, 10 Oct 2022 00:00:00 GMT", "description": "As plate tectonics pushed Antarctica into a polar position, by ~34 million years ago, the continent and its surrounding Southern Ocean (SO) became geographically and thermally isolated by the Antarctic Circumpolar Current. Terrestrial and marine glaciation followed, resulting in extinctions as well as the survival and radiation of unique flora and fauna. The notothenioid fish survived and arose from a common ancestral stock into tax with 120 species that dominates today?s SO fish fauna. The Notothenioids evolved adaptive traits including novel antifreeze proteins for survival in extreme cold, but also suffered seemingly adverse trait loss including red blood cells in the icefish family, and the ability to mount cellular responses to mitigate heat stress ? otherwise ubiquitous across all life. This project aims to understand how the notothenoid genomes have changed and contributed to their evolution in the cold. The project will sequence, analyze and compare the genomes of two strategic pairs of notothenioid fishes representing both red-blooded and white-blooded species. Each pair will consist of one Antarctic species and one that has readapted to the temperate waters of S. America or New Zealand. The project will also compare the Antarctic species genomes to a genome of the closet non-Antarctic relative representing the temperate notothenioid ancestor. The work aims to uncover the mechanisms that enabled the adaptive evolution of this ecologically vital group of fish in the freezing Southern Ocean, and shed light on their adaptability to a warming world. The finished genomes will be made available to promote and advance Antarctic research and the project will host a symposium of Polar researchers to discuss the cutting edge developments regarding of genomic adaptations in the polar region. Despite subzero, icy conditions that are perilous to teleost fish, the fish fauna of the isolated Southern Ocean (SO) surrounding Antarctica is remarkably bountiful. A single teleost group ? the notothenioid fishes ? dominate the fauna, comprising over 120 species that arose from a common ancestor. When Antarctica became isolated and SO temperatures began to plunge in early Oligocene, the prior temperate fishes became extinct. The ancestor of Antarctic notothenioids overcame forbidding polar conditions and, absent niche competition, it diversified and filled the SO. How did notothenioids adapt to freezing environmental selection pressures and achieve such extraordinary success? And having specialized to life in chronic cold for 30 myr, can they evolve in pace with today?s warming climate to stay viable? Past studies of Antarctic notothenioid evolutionary adaptation have discovered various remarkable traits including the key, life-saving antifreeze proteins. But life specialized to cold also led to paradoxical trait changes such as the loss of the otherwise universal heat shock response, and of the O2-transporting hemoglobin and red blood cells in the icefish family. A few species interestingly regained abilities to live in temperate waters following the escape of their ancestor out of the freezing SO. This proposed project is the first major effort to advance the field from single trait studies to understanding the full spectrum of genomic and genetic responses to climatic and environmental change during notothenioid evolution, and to evaluate their adaptability to continuing climate change. To this end, the project will sequence the genomes of four key species that embody genomic responses to different thermal selection regimes during notothenioids? evolutionary history, and by comparative analyses of genomic structure, architecture and content, deduce the responding changes. Specifically, the project will (i) obtain whole genome assemblies of the red-blooded T. borchgrevinki and the S. American icefish C. esox; (ii) using the finished genomes from (i) as template, obtain assemblies of the New Zealand notothenioid N. angustata, and the white-blooded icefish C. gunnari, representing a long (11 myr) and recent (1 myr) secondarily temperate evolutionary history respectively. Genes that are under selection in the temperate environment but not in the Antarctic environment can be inferred to be directly necessary for that environment ? and the reverse is also true for genes under selection in the Antarctic but not in the temperate environment. Further, genes important for survival in temperate waters will show parallel selection between N. angustata and C. esox despite the fact that the two fish left the Antarctic at far separated time points. Finally, gene families that expanded due to strong selection within the cold Antarctic should show a degradation of duplicates in the temperate environment. The project will test these hypotheses using a number of techniques to compare the content and form of genes, the structure of the chromosomes containing those genes, and through the identification of key characters, such as selfish genetic elements, introns, and structural variants.", "east": null, "geometry": null, "instruments": null, "is_usap_dc": true, "keywords": "Genome Assembly; FISH; McMurdo Sound; Icefish; SHIPS; Notothenioid; Puerto Natales, Chile", "locations": "McMurdo Sound; Puerto Natales, Chile", "north": null, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Catchen, Julian; Cheng, Chi-Hing", "platforms": "WATER-BASED PLATFORMS \u003e VESSELS \u003e SURFACE \u003e SHIPS", "repo": "NCBI", "repositories": "Dryad; NCBI; NCBI ", "science_programs": null, "south": null, "title": "Evolutionary Genomic Responses in Antarctic Notothenioid Fishes", "uid": "p0010384", "west": null}, {"awards": "2146068 Kienle, Sarah", "bounds_geometry": null, "dataset_titles": "Data from: Individual specialization in a generalist apex predator: The leopard seal; ddRADseq leopard seal (SRR32669466); Genome assembly ASM5032014v1; Hydrurga leptonyx isolate:HLNZ013 (leopard seal); Leopard seals DDRAD", "datasets": [{"dataset_uid": "200550", "doi": "10.3389/fgene.2025.1561273", "keywords": null, "people": null, "repository": "NCBI Genbank", "science_program": null, "title": "Genome assembly ASM5032014v1", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_050320145.1/"}, {"dataset_uid": "200548", "doi": "", "keywords": null, "people": null, "repository": "Github", "science_program": null, "title": "Leopard seals DDRAD", "url": "https://github.com/DavidVendrami/LeopardSeals_ddRAD"}, {"dataset_uid": "200552", "doi": "10.1038/s41598-025-25641-w", "keywords": null, "people": null, "repository": "SRA (NCBI)", "science_program": null, "title": "ddRADseq leopard seal (SRR32669466)", "url": "https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP569941\u0026o=acc_s%3Aa"}, {"dataset_uid": "200551", "doi": "10.3389/fgene.2025.1561273", "keywords": null, "people": null, "repository": "NCBI (BioProject)", "science_program": null, "title": "Hydrurga leptonyx isolate:HLNZ013 (leopard seal)", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1194539/"}, {"dataset_uid": "200549", "doi": "10.5061/dryad.f4qrfj75k", "keywords": null, "people": null, "repository": "Dryad", "science_program": null, "title": "Data from: Individual specialization in a generalist apex predator: The leopard seal", "url": "https://datadryad.org/dataset/doi:10.5061/dryad.f4qrfj75k"}], "date_created": "Mon, 12 Sep 2022 00:00:00 GMT", "description": "The leopard seal (Hydrurga leptonyx) is an enigmatic apex predator in the rapidly changing Southern Ocean. As top predators, leopard seals play a disproportionately large role in ecosystem functioning and act as sentinel species that can track habitat changes. How leopard seals respond to a warming environment depends on their adaptive capacity, that is a species\u2019 ability to cope with environmental change. However, leopard seals are one of the least studied apex predators on Earth, hindering our ability to predict how the species is responding to polar environmental changes. Investigating the adaptability of Antarctic biota in a changing system aligns with NSF\u2019s Strategic Vision for Investments in Antarctic and Southern Ocean Research. This research, which is tightly integrated with educational and outreach activities, will increase diversity in STEM and Antarctic science by recruiting students from historically underrepresented groups in STEM and providing training, mentoring, and educational opportunities at an emerging Hispanic Serving Institution and a Historically Black Colleges and Universities campus. This project will improve STEM education and science literacy via museum collaborations, creation of informational videos and original artwork depicting the research. The proposal supports data and sample reuse in polar research and long-term reuse of scientific data, thereby maximizing NSF\u2019s investment in previous field research and reducing operational costs. The researchers will investigate leopard seals adaptive capacity to the warming Southern Ocean by quantifying their ability to move (dispersal ability), adapt (genetic diversity), and change (plasticity). Aim 1 of the research will determine leopard seals\u2019 dispersal ability by assessing their distribution and movement patterns. Aim 2 will quantify genetic diversity by analyzing genetic variability and population structure and Aim 3 will examine phenotypic plasticity by evaluating changes in their ecological niche and physiological responses. The international, multidisciplinary team will analyze existing data (e.g., photographs, census data, life history data, tissue samples, body morphometrics) collected from leopard seals across the Southern Ocean over the last decade. Additionally, land- and ship-based field efforts will generate comparable data from unsampled regions in the Southern Ocean. The research project will analyze these historical and contemporary datasets to evaluate the adaptive capacity of leopard seals against the rapidly warming Southern Ocean. This research is significant because changes in the distribution, genetic diversity, and ecophysiology of leopard seals can dramatically restructure polar and subpolar communities. Further, the research will expand understanding of leopard seals\u2019 ecological role, likely characterizing the species as flexible polar and subpolar predators throughout the Southern Hemisphere. The findings of this research will be relevant for use in ecosystem-based management decisions\u2014including the design of Marine Protected Areas\u2014 across three continents. This study will highlight intrinsic traits that determine species\u2019 adaptive capacity, as well as showcase the dynamic links between polar and subpolar ecosystems. 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": null, "geometry": null, "instruments": null, "is_usap_dc": true, "keywords": "Foraging Ecology; Sub-Antarctic; Ecophysiology; Population Genetics; FIELD SURVEYS; SPECIES/POPULATION INTERACTIONS; Livingston Island; Adaptation; Leopard Seal; MARINE ECOSYSTEMS; Movement Data; MAMMALS; ; Antarctica; Chile; Southern Ocean", "locations": "Southern Ocean; Chile; ; Antarctica; Sub-Antarctic; Livingston Island", "north": null, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Kienle, Sarah; Bonin, Carolina; Borras-Chavez, Renato", "platforms": "LAND-BASED PLATFORMS \u003e FIELD SITES \u003e FIELD SURVEYS", "repo": "NCBI Genbank", "repositories": "Dryad; Github; NCBI (BioProject); NCBI Genbank; SRA (NCBI)", "science_programs": null, "south": null, "title": "Move, Adapt, or Change: Examining the Adaptive Capacity of a Southern Ocean Apex Predator, the Leopard Seal", "uid": "p0010375", "west": null}, {"awards": "1643825 Bucklin, Ann", "bounds_geometry": "POLYGON((-74.57 -60.9,-72.487 -60.9,-70.404 -60.9,-68.321 -60.9,-66.238 -60.9,-64.155 -60.9,-62.072 -60.9,-59.989 -60.9,-57.906 -60.9,-55.823 -60.9,-53.74 -60.9,-53.74 -61.537,-53.74 -62.174,-53.74 -62.811,-53.74 -63.448,-53.74 -64.085,-53.74 -64.722,-53.74 -65.359,-53.74 -65.996,-53.74 -66.633,-53.74 -67.27,-55.823 -67.27,-57.906 -67.27,-59.989 -67.27,-62.072 -67.27,-64.155 -67.27,-66.238 -67.27,-68.321 -67.27,-70.404 -67.27,-72.487 -67.27,-74.57 -67.27,-74.57 -66.633,-74.57 -65.996,-74.57 -65.359,-74.57 -64.722,-74.57 -64.085,-74.57 -63.448,-74.57 -62.811,-74.57 -62.174,-74.57 -61.537,-74.57 -60.9))", "dataset_titles": "Alongtrack data collected continuously by the ship\u0027s underway acquisition system from ARSV Laurence M. Gould cruise LMG1110 in the Southern Ocean in 2011 ; Bucklin, A., R.J. O\u0027Neill, D. Payne (2018) Antarctic salp genome and RNAseq transcriptome from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean. Biological and Chemical Oceanography Data Management Office (BCO-DMO). ; Bucklin, A., R.J. O\u0027Neill, D. Payne (2018) Salp specimen log for genomic and transcriptomic study collected from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2. Biological and Chemical Oceanography Data Management Office (BCO-DMO).; CTD data from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from November to December 2011 (Salp_Antarctic project) ; CTD data from MOCNESS tows taken in the Antarctic in 2011 from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from November to December 2011 (Salp_Antarctic project) ; Scientific sampling event log from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from Nov. 2011 (Salp_Antarctic project) ", "datasets": [{"dataset_uid": "200227", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "Bucklin, A., R.J. O\u0027Neill, D. Payne (2018) Salp specimen log for genomic and transcriptomic study collected from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2. Biological and Chemical Oceanography Data Management Office (BCO-DMO).", "url": "https://www.bco-dmo.org/dataset/672600"}, {"dataset_uid": "200228", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "Bucklin, A., R.J. O\u0027Neill, D. Payne (2018) Antarctic salp genome and RNAseq transcriptome from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean. Biological and Chemical Oceanography Data Management Office (BCO-DMO). ", "url": "https://www.bco-dmo.org/dataset/675040/data"}, {"dataset_uid": "200229", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "CTD data from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from November to December 2011 (Salp_Antarctic project) ", "url": "https://www.bco-dmo.org/dataset/559174/data"}, {"dataset_uid": "200230", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "Scientific sampling event log from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from Nov. 2011 (Salp_Antarctic project) ", "url": "https://www.bco-dmo.org/dataset/3565/data"}, {"dataset_uid": "200231", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "Alongtrack data collected continuously by the ship\u0027s underway acquisition system from ARSV Laurence M. Gould cruise LMG1110 in the Southern Ocean in 2011 ", "url": "https://www.bco-dmo.org/dataset/3636/data"}, {"dataset_uid": "200232", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "CTD data from MOCNESS tows taken in the Antarctic in 2011 from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from November to December 2011 (Salp_Antarctic project) ", "url": "https://www.bco-dmo.org/dataset/488871/data"}], "date_created": "Sat, 03 Jul 2021 00:00:00 GMT", "description": "The Antarctic salp, Salpa thompsoni, is a gelatinous zooplankton that is an important member in the Southern Ocean pelagic ecosystem. Field studies have documented rapid population growth under favorable environmental conditions, resulting in dense blooms of salps that substantially change the pelagic ecosystem in regards to both structure and processes. Because this zooplankton can proliferate rapidly and it is not readily consumed by upper trophic levels, its periodic dominance has the potential to drastically chance ecosystem energetics as well as change material export to the deep ocean. Completion of a comprehensive reference genome for the Antarctic salp will enable the identification of genes and gene networks underlying physiological responses and allow detection of potential processes driving natural selection and the species? adaptation strategies to the Antarctic Environment. Comparative genomic analysis will add the dimension of time to inferences about organismal adaptation and allow consideration of their potential to adapt to future environmental changes, and will allow examination of novel aspects of genomic evolution found only in the invertebrate class Tunicata. The completed salp reference genome will provide a valuable foundational resource for other scientists working on this species as well as the genomic basis for function and adaptation in the Antarctic. The primary goal of this effort is to examine the rapid genome evolution characteristic of this tunicate species and examine the genomic bases of the species? potential for adaptation, and specifically the role of flexible gene networks for successful responses to changing environmental conditions. The primary hypothesis driving this research is that predicted S. thompsoni orthologs (i.e., genes of the same function that share a common ancestor) that show evidence of rapid evolution are indicative of positive selection, and further that these genes and associated gene networks provide the basis for rapid adaptation of the Antarctic salp to environmental variation associated with a changing ocean. The proposed genome assembly strategy will allow further refinements and scaffolding of the current, highly fragmented genome assembly using the methods developed during previous work. Specimens of S. thompsoni now archived at UConn will be analyzed to improve the salp genome assembly, increasing overall scaffold length, and decreasing the number of total contigs. High-quality reference assemblies will be obtained with two high-output paired-end sequencing runs (Illumina) on a single individual, coupled with three runs on the Oxford Nanopore long-read sequencer. The same sequencing strategy will be performed on a sub-sampling of tissues from the same specimen to produce a very high quality reference transcriptome, which will allow for high quality gene models and near-complete gene predictions in the genome assembly. Comparisons with available genomic data for Urochordate and Cephalochordate species will increase the number of orthologs analyzed. Orthologous genes will be tested for evidence of rapid selection in the salp lineage, and the results will be compared to published expression profiles and ontology functions for the salp. All data will be made publicly available via existing web portals; a project website will be developed to disseminate research results for access by the both research and educational communities. Website design will use a local instance of jbrowse that will offer annotations, downloadable data files, and tracts of previously-published datasets.", "east": -53.74, "geometry": "POINT(-64.155 -64.085)", "instruments": null, "is_usap_dc": true, "keywords": "SHIPS; PELAGIC; Southern Ocean", "locations": "Southern Ocean", "north": -60.9, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Bucklin, Ann; O\u0027Neill, Rachel J", "platforms": "WATER-BASED PLATFORMS \u003e VESSELS \u003e SURFACE \u003e SHIPS", "repo": "BCO-DMO", "repositories": "BCO-DMO", "science_programs": null, "south": -67.27, "title": "Genome Assembly and Analysis of the Bloom Forming Southern Ocean Salp, Salpa thompsoni", "uid": "p0010224", "west": -74.57}, {"awards": "1906015 Kelley, Joanna", "bounds_geometry": "POLYGON((-180 -60,-144 -60,-108 -60,-72 -60,-36 -60,0 -60,36 -60,72 -60,108 -60,144 -60,180 -60,180 -63,180 -66,180 -69,180 -72,180 -75,180 -78,180 -81,180 -84,180 -87,180 -90,144 -90,108 -90,72 -90,36 -90,0 -90,-36 -90,-72 -90,-108 -90,-144 -90,-180 -90,-180 -87,-180 -84,-180 -81,-180 -78,-180 -75,-180 -72,-180 -69,-180 -66,-180 -63,-180 -60))", "dataset_titles": "Data, Code, and Results for the Zoarcoidei Phylogeny (Hotaling et al.); Genome assembly ASM2452992v1; Genome assembly ASM5057508v1; Genome assembly ASM5057547v1; Genome assembly ASM5057549v1; Genome assembly ASM5057553v1; Genome assembly ASM5057805v1; Genome assembly of Zoarcoidei fishes", "datasets": [{"dataset_uid": "200556", "doi": "GCA_050575475.1", "keywords": null, "people": null, "repository": "NCBI", "science_program": null, "title": "Genome assembly ASM5057547v1", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_050575475.1/"}, {"dataset_uid": "200221", "doi": "10.5281/zenodo.4306092).", "keywords": null, "people": null, "repository": "Zenodo", "science_program": null, "title": "Data, Code, and Results for the Zoarcoidei Phylogeny (Hotaling et al.)", "url": "https://doi.org/10.5281/zenodo.4306092"}, {"dataset_uid": "200559", "doi": "PRJNA1236397", "keywords": null, "people": null, "repository": "SRA", "science_program": null, "title": "Genome assembly of Zoarcoidei fishes", "url": "https://www.ncbi.nlm.nih.gov/bioproject/1236397"}, {"dataset_uid": "200553", "doi": "GCF_050575085.1", "keywords": null, "people": null, "repository": "NCBI", "science_program": null, "title": "Genome assembly ASM5057508v1", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_050575085.1/"}, {"dataset_uid": "200558", "doi": "GCA_050575535.1", "keywords": null, "people": null, "repository": "NCBI", "science_program": null, "title": "Genome assembly ASM5057553v1", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_050575535.1/"}, {"dataset_uid": "200557", "doi": "GCA_024529925.1", "keywords": null, "people": null, "repository": "NCBI", "science_program": null, "title": "Genome assembly ASM2452992v1", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_024529925.1/"}, {"dataset_uid": "200555", "doi": "GCA_050575495.1", "keywords": null, "people": null, "repository": "NCBI", "science_program": null, "title": "Genome assembly ASM5057549v1", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_050575495.1/"}, {"dataset_uid": "200554", "doi": "GCA_050578055.1", "keywords": null, "people": null, "repository": "NCBI", "science_program": null, "title": "Genome assembly ASM5057805v1", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_050578055.1/"}], "date_created": "Fri, 25 Jun 2021 00:00:00 GMT", "description": "Fish that reside in the harsh, subfreezing waters of the Antarctic and Arctic provide fascinating examples of adaptation to extreme environments. Species at both poles have independently evolved ways to deal with constant cold temperature, including the evolution of antifreeze proteins. Under freezing conditions, these compounds attach to ice crystals and prevent their growth. This lowers the tissue freezing point and reduces the chance the animal will be injured or killed. While it might seem that the need for unique adaptations to survive in polar waters would reduce species diversity in these habitats, recent evidence showed higher speciation rates in fishes from polar environments as compared to those found in warmer waters. This is despite the fact cold temperatures slow cellular processes, which had been expected to lower rates of molecular evolution in these species. To determine how rates of speciation and molecular evolution are linked in marine fishes, this project will compare the genomes of multiple polar and non-polar fishes. By doing so, it will (1) clarify how rates of evolution vary in polar environments, (2) identify general trends that shape the adaptive trajectories of polar fishes, and (3) determine how functional differences shape the evolution of novel compounds such as the antifreeze proteins some polar fishes rely upon to survive. In addition to training a new generation of scientists, the project will develop curriculum and outreach activities for elementary and undergraduate science courses. Materials will be delivered in classrooms across the western United States, with a focus on rural schools as part of a network for promoting evolutionary education in rural communities. To better understand the biology of polar fishes and the evolution of antifreeze proteins (AFPs), this research will compare the evolutionary histories of cold-adapted organisms to those of related non-polar species from both a genotypic and phenotypic context. In doing so, this research will test whether evolutionary rates are slowed in polar environments, perhaps due to constraints on cellular processes. It will also evaluate the effects of positive selection and the relaxation of selection on genes and pathways, both of which appear to be key adaptive strategies involved in the adaptation to polar environments. To address specific mechanisms by which extreme adaptation occurs, researchers will determine how global gradients of temperature and dissolved oxygen shape genome variation and influence adaptive trajectories among multiple species of eelpouts (family Zoarcidae). An in-vitro experimental approach will then be used to test functional hypotheses about the role of copy number variation in AFP evolution, and how and why multiple antifreeze protein isoforms have evolved. By comparing the genomes of multiple polar and non-polar fishes, the project will clarify how rates of evolution vary in polar environments, identify general trends that shape the adaptive trajectories of cold-adapted marine fishes, and determine how functional differences shape the evolution of novel proteins. This project addresses the strategic programmatic aim to provide a better understanding of the genetic underpinnings of organismal adaptations to their current environment and ways in which polar fishes may respond to changing conditions over different evolutionary time scales. The project is jointly funded by the Antarctic Organisms and Ecosystems Program in the Office of Polar Programs of the Geosciences Directorate, and the Molecular Biophysics Program of the Division of Molecular and Cellular Biosciences in the Biological Sciences Directorate. 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": "Antarctica; FISH; MARINE ECOSYSTEMS; LABORATORY; AMD; USAP-DC; Amd/Us; USA/NSF", "locations": "Antarctica", "north": -60.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Kelley, Joanna", "platforms": "OTHER \u003e PHYSICAL MODELS \u003e LABORATORY", "repo": "NCBI", "repositories": "NCBI; SRA; Zenodo", "science_programs": null, "south": -90.0, "title": "Genome Evolution in Polar Fishes", "uid": "p0010200", "west": -180.0}, {"awards": "1921491 Hindle, Allyson; 1443554 Buys, Emmanuel", "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": "Biosamples and observations from Weddell Seal colonies in McMurdo Sound during the 2015-2016 Antarctic field season", "datasets": [{"dataset_uid": "601028", "doi": "10.15784/601028", "keywords": "Antarctica; Biota; McMurdo Sound; Ross Sea; Sample/collection Description; Sample/Collection Description; Seals", "people": "Buys, Emmanuel; Hindle, Allyson", "repository": "USAP-DC", "science_program": null, "title": "Biosamples and observations from Weddell Seal colonies in McMurdo Sound during the 2015-2016 Antarctic field season", "url": "https://www.usap-dc.org/view/dataset/601028"}], "date_created": "Fri, 26 May 2017 00:00:00 GMT", "description": "The Weddell seal is a champion diving mammal. The physiology that permits these animals to sustain extended breath-hold periods and survive the extreme pressure of diving deep allows them to thrive in icy Antarctic waters. Key elements of their physiological specializations to breath-hold diving are their ability for remarkable adjustment of their heart and blood vessel system, coordinating blood pressure and flow to specific body regions based on their metabolic requirements, and their ability to sustain periods without oxygen. Identifying the details of these strategies has tremendous potential to better inform human medicine, helping us to develop novel therapies for cardiovascular trauma (e.g. stroke, heart attack) and diseases associated with blunted oxygen delivery to tissues (e.g. pneumonia, sepsis, or cancer). The goal of this project is to document specific genes that control these cardiovascular adjustments in seals, and to compare their abundance and activity with humans. Specifically, the investigators will study a signaling pathway that coordinates local blood flow. They will also use tissue samples to generate cultured cells from Weddell seals that can be used to study the molecular effects of low oxygen conditions in the laboratory. The project will further the NSF goals of training new generations of scientists and of making scientific discoveries available to the general public. The project will train a pre-veterinary student researcher will conduct public outreach via a center for community health improvement, a multicultural affairs office, and a public aquarium. The goal of this study is to unravel the molecular mechanisms underlying the dive response. A hallmark of the dive response is tissue-specific vascular system regulation, likely resulting from variation in both nerve inputs and in production of local signaling molecules produced by blood vessel cells. The investigators will use emerging genomic information to begin to unravel the genetics underlying redistribution of the circulation during diving. They will also directly test the hypothesis that modifications in the signaling system prevent local blood vessel changes under low oxygen conditions, thereby allowing the centrally mediated diving reflex to override local physiological responses and to control the constriction of blood vessel walls in Weddell seals. They will perform RNA-sequencing of Weddell seal tissues and use the resulting sequence, along with information from other mammals such as dog, to obtain a full annotation (identifying all genes based on named features of reference genomes) of the existing genome assembly for the Weddell seal, facilitating comparative and species-specific genomic research. They will also generate a Weddell seal pluripotent stem cell line which should be a valuable research tool for cell biologists, molecular biologists and physiologists that will allow them to further test their hypotheses. It is expected that the proposed studies will advance our knowledge of the biochemical and physiological adaptations that allow the Weddell seal to thrive in the Antarctic environment.", "east": 167.168, "geometry": "POINT(166.6655 -77.25)", "instruments": null, "is_usap_dc": true, "keywords": "MAMMALS; McMurdo Sound", "locations": "McMurdo Sound", "north": -76.665, "nsf_funding_programs": "Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Hindle, Allyson; Hindle, Allyson; Costa, Daniel; Zapol, Warren", "platforms": null, "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -77.835, "title": "Unraveling the Genomic and Molecular Basis of the Dive Response: Nitric Oxide Signaling and Vasoregulation in the Weddell Seal", "uid": "p0000072", "west": 166.163}]

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