USAP-DC

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

[{"awards": "2324998 Daane, Jacob; 1955368 Daane, Jacob", "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": null, "datasets": null, "date_created": "Thu, 01 Aug 2024 00:00:00 GMT", "description": "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 \u003e120 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 \u003e250,000 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\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": "United States Of America; FISH", "locations": "United States Of America", "north": -60.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Daane, Jacob; Detrich, H. William", "platforms": null, "repositories": null, "science_programs": null, "south": -90.0, "title": "ANT LIA: Collaborative Research: Evolutionary Patterns and Mechanisms of Trait Diversification in the Antarctic Notothenioid Radiation", "uid": "p0010473", "west": -180.0}, {"awards": "1644155 Twining, Benjamin", "bounds_geometry": "POLYGON((78 -68.4,78.05 -68.4,78.1 -68.4,78.15 -68.4,78.2 -68.4,78.25 -68.4,78.3 -68.4,78.35 -68.4,78.4 -68.4,78.45 -68.4,78.5 -68.4,78.5 -68.419,78.5 -68.438,78.5 -68.457,78.5 -68.476,78.5 -68.495,78.5 -68.514,78.5 -68.533,78.5 -68.552,78.5 -68.571,78.5 -68.59,78.45 -68.59,78.4 -68.59,78.35 -68.59,78.3 -68.59,78.25 -68.59,78.2 -68.59,78.15 -68.59,78.1 -68.59,78.05 -68.59,78 -68.59,78 -68.571,78 -68.552,78 -68.533,78 -68.514,78 -68.495,78 -68.476,78 -68.457,78 -68.438,78 -68.419,78 -68.4))", "dataset_titles": "Flow cytometry enumeration of virus-like and bacteria-like abundance in Ace, Deep, \u0026 Organic lakes (Antarctica)", "datasets": [{"dataset_uid": "601626", "doi": "10.15784/601626", "keywords": "Ace Lake; Antarctica; Deep Lake; Organic Lake; Vestfold Hills", "people": "Twining, Benjamin; Martinez-Martinez, Joaquin", "repository": "USAP-DC", "science_program": null, "title": "Flow cytometry enumeration of virus-like and bacteria-like abundance in Ace, Deep, \u0026 Organic lakes (Antarctica)", "url": "https://www.usap-dc.org/view/dataset/601626"}], "date_created": "Fri, 06 Aug 2021 00:00:00 GMT", "description": "Viruses are prevalent in aquatic environments where they reach up to five hundred million virus particles in a teaspoon of water. Ongoing discovery of viruses seems to confirm current understanding that all forms of life can host and be infected by viruses and that viruses are one of the largest reservoirs of unexplored genetic diversity on Earth. This study aims to better understand interactions between specific viruses and phytoplankton hosts and determine how these viruses may affect different algal groups present within lakes of the Vestfold Hills, Antarctica. These lakes (Ace, Organic and Deep)were originally derived from the ocean and contain a broad range of saline conditions with a similarly broad range of physicochemical characteristics resulting from isolation and low external influence for thousands of years. These natural laboratories allow examination of microbial processes and interactions that would be difficult to characterize elsewhere on earth. The project will generate extensive genomic information that will be made freely available. The project will also leverage the study of viruses and the genomic approaches employed to advance the training of undergraduate students and to engage and foster an understanding of Antarctic science and studies of microbes during a structured informal education program in Maine for the benefit of high school students. By establishing the dynamics and interactions of (primarily) specific dsDNA virus groups in different habitats with different redox conditions throughout seasonal and inter annual cycles the project will learn about the biotic and abiotic factors that influence microbial community dynamics. This project does not require fieldwork in Antarctica. Instead, the investigators will leverage already collected and archived samples from three lakes that have concurrent measures of physicochemical information. Approximately 2 terabyte of Next Generation Sequencing (NGS) (including metagenomes, SSU rRNA amplicons and single virus genomes) will be generated from selected available samples through a Community Science Program (CSP) funded by the Joint Genome Institute. The investigators will employ bioinformatics to interrogate those sequence databases. In particular, they will focus on investigating the presence, phylogeny and co-occurrence of polintons, polinton-like viruses, virophages and large dsDNA phytoplankton viruses as well as of their putative eukaryotic microbial hosts. Bioinformatic analyses will be complemented with quantitative digital PCR and microbial association network analysis to detect specific virus?virus?host interactions from co-occurrence spatial and temporal patterns. Multivariate analysis and network analyses will also be performed to investigate which abiotic factors most closely correlate with phytoplankton and virus abundances, temporal dynamics, and observed virus-phytoplankton associations within the three lakes. The results of this project will improve understanding of phytoplankton and their viruses as vital components of the carbon cycle in Antarctic, marine-derived aquatic environments, and likely in any other aquatic environment. Overall, this work will advance understanding of the genetic underpinnings of adaptations in unique Antarctic environments.", "east": 78.5, "geometry": "POINT(78.25 -68.495)", "instruments": null, "is_usap_dc": true, "keywords": "LABORATORY; AMD; USAP-DC; VIRUSES; Vestfold Hills; Amd/Us; FIELD SURVEYS; USA/NSF", "locations": "Vestfold Hills", "north": -68.4, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Twining, Benjamin; Martinez-Martinez, Joaquin", "platforms": "LAND-BASED PLATFORMS \u003e FIELD SITES \u003e FIELD SURVEYS; OTHER \u003e PHYSICAL MODELS \u003e LABORATORY", "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -68.59, "title": "Viral control of microbial communities in Antarctic lakes", "uid": "p0010237", "west": 78.0}, {"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.)", "datasets": [{"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"}], "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": "Zenodo", "repositories": "Zenodo", "science_programs": null, "south": -90.0, "title": "Genome Evolution in Polar Fishes", "uid": "p0010200", "west": -180.0}, {"awards": "1341661 Near, Thomas", "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": "Phylogenomics of Antarctic notothenioid fishes", "datasets": [{"dataset_uid": "601264", "doi": null, "keywords": "Adaptive Radiation; Antarctica; Fish; Notothenioidei; Phylogeny; Southern Ocean; Speciation", "people": "Dornburg, Alex; Near, Thomas", "repository": "USAP-DC", "science_program": null, "title": "Phylogenomics of Antarctic notothenioid fishes", "url": "https://www.usap-dc.org/view/dataset/601264"}, {"dataset_uid": "601262", "doi": "10.15784/601262", "keywords": "Adaptive Radiation; Antarctica; Fish; Notothenioidei; Phylogeny; Southern Ocean; Speciation", "people": "Near, Thomas; Dornburg, Alex", "repository": "USAP-DC", "science_program": null, "title": "Phylogenomics of Antarctic notothenioid fishes", "url": "https://www.usap-dc.org/view/dataset/601262"}], "date_created": "Sat, 29 Feb 2020 00:00:00 GMT", "description": "Understanding how groups of organisms respond to climate change is fundamentally important to assessing the impacts of human activities as well as understanding how past climatic shifts have shaped biological diversity over deep stretches of time. The fishes occupying the near-shore marine habitats around Antarctica are dominated by one group of closely related species called notothenioids. It appears dramatic changes in Antarctic climate were important in the origin and evolutionary diversification of this economically important lineage of fishes. Deposits of fossil fishes in Antarctica that were formed when the continent was experiencing milder temperatures show that the area was home to a much more diverse array of fish lineages. Today the waters of the Southern Ocean are very cold, and often below freezing, but notothenioids fishes exhibit a number of adaptions to live in this harsh set of marine habitats, including the presence of anti-freeze proteins. This research project will collect DNA sequences from hundreds of genes to infer the genealogical relationships of nearly all 124 notothenioid species, and use mathematical techniques to estimate the ages of species and lineages. Knowledge on the timing of evolutionary divergence in notothenioids will allow investigators to assess if timing of previous major climatic shifts in Antarctica are correlated with key events in the formation of the modern Southern Ocean fish fauna. The project will also further the NSF goals of making scientific discoveries available to the general public and of training new generations of scientists. The project will support educational outreach activities to teenager groups and to the general public through a natural history museum exhibit and other public lectures. It will provide professional training opportunities for graduate students and a postdoctoral research scholar. Adaptive radiation, where lineages experience high rates of evolutionary diversification coincident with ecological divergence, is mostly studied in island ecosystems. Notothenioids dominate the fish fauna of the Southern Ocean and exhibit antifreeze glycoproteins that allow occupation of the subzero waters. Notothenioids are noted as one of the only examples of adaptive radiation among marine fishes, but the evolutionary history of diversification and radiation into different ecological habitats is poorly understood. This research will generate a species phylogeny (evolutionary history) for nearly all of the 124 recognized notothenioid species to investigate the mechanisms of adaptive radiation in this lineage. The phylogeny is inferred from approximately 350 genes sampled using next generation DNA sequencing and related techniques. Morphometric data are taken for museum specimens to investigate the tempo of morphological diversification and to determine if there are correlations between rates of lineage diversification and the origin of morphological disparity. The patterns of lineage, morphological, and ecological diversification in the notothenioid radiation will be compared to the paleoclimatic record to determine if past instances of global climate change have shaped the evolutionary diversification of this lineage of polar-adapted fishes.", "east": 180.0, "geometry": "POINT(0 -89.999)", "instruments": "NOT APPLICABLE \u003e NOT APPLICABLE \u003e NOT APPLICABLE", "is_usap_dc": true, "keywords": "FISH; Fish; AMD; USA/NSF; Southern Ocean; Amd/Us; NOT APPLICABLE; USAP-DC; MARINE ECOSYSTEMS; Notothenioidei; Phylogeny", "locations": "Southern Ocean", "north": -60.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Near, Thomas", "platforms": "OTHER \u003e NOT APPLICABLE \u003e NOT APPLICABLE", "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -90.0, "title": "Phylogenomic Study of Adaptive Radiation in Antarctic Fishes", "uid": "p0010087", "west": -180.0}, {"awards": "1040945 Place, Sean; 1040957 Sarmiento, Jorge; 1447291 Place, Sean", "bounds_geometry": "POLYGON((-180 90,-144 90,-108 90,-72 90,-36 90,0 90,36 90,72 90,108 90,144 90,180 90,180 72,180 54,180 36,180 18,180 0,180 -18,180 -36,180 -54,180 -72,180 -90,144 -90,108 -90,72 -90,36 -90,0 -90,-36 -90,-72 -90,-108 -90,-144 -90,-180 -90,-180 -72,-180 -54,-180 -36,-180 -18,-180 0,-180 18,-180 36,-180 54,-180 72,-180 90))", "dataset_titles": "Does the strength of the carbonate pump change with ocean stratification and acidification and how? Project data; NCBI GenBank RNA sequences, Pagothenia borchgrevinki; NCBI GenBank RNA sequences, Trematomus bernacchii; NCBI GenBank RNA sequences, Trematomus newnesi; NCBI links to BioProjects of total RNA isolated from Trematomus bernacchii gill tissues acclimated to elevated temperature and pCO2, July 2015", "datasets": [{"dataset_uid": "000166", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "NCBI links to BioProjects of total RNA isolated from Trematomus bernacchii gill tissues acclimated to elevated temperature and pCO2, July 2015", "url": "http://www.bco-dmo.org/dataset/665853"}, {"dataset_uid": "000164", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "NCBI GenBank RNA sequences, Pagothenia borchgrevinki", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294774"}, {"dataset_uid": "000163", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "NCBI GenBank RNA sequences, Trematomus bernacchii", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA289753"}, {"dataset_uid": "000184", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "NCBI GenBank RNA sequences, Trematomus bernacchii", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA289753"}, {"dataset_uid": "000219", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "Does the strength of the carbonate pump change with ocean stratification and acidification and how? Project data", "url": "http://www.bco-dmo.org/project/521216"}, {"dataset_uid": "000186", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "NCBI GenBank RNA sequences, Trematomus newnesi", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294787"}, {"dataset_uid": "000185", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "NCBI GenBank RNA sequences, Pagothenia borchgrevinki", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294774"}, {"dataset_uid": "000165", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "NCBI GenBank RNA sequences, Trematomus newnesi", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294787"}], "date_created": "Mon, 12 Jan 2015 00:00:00 GMT", "description": "The proposed research will investigate the interacting and potentially synergistic influence of two oceanographic features - ocean acidification and the projected rise in mean sea surface temperature - on the performance of Notothenioids, the dominant fish of the Antarctic marine ecosystem. Understanding the joint effects of acidification and temperature rise on these fish is a vital component of predicting the resilience of coastal marine ecosystems. Notothenioids have repeatedly displayed a narrow window of physiological tolerances when subjected to abiotic stresses. Given that evolutionary adaptation may have led to finely-tuned traits with narrow physiological limits in these organisms, this system provides a unique opportunity to examine physiological trade-offs associated with acclimation to the multi-stressor environment expected from future atmospheric CO2 projections. Understanding these trade-offs will provide valuable insight into the capacity species have for responses to climate change via phenotypic plasticity. As an extension to functional measurements, this study will use evolutionary approaches to map variation in physiological responses onto the phylogeny of these fishes and the genetic diversity within species. These approaches offer insight into the historical constraints and future potential for evolutionary optimization. The research will significantly expand the genomic resources available to polar researchers and will support the training of graduate students and a post doc at an EPSCoR institution. Research outcomes will be incorporated into classroom curriculum.", "east": 180.0, "geometry": "POINT(0 -89.999)", "instruments": null, "is_usap_dc": true, "keywords": "Not provided", "locations": null, "north": 90.0, "nsf_funding_programs": "Antarctic Integrated System Science; Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Place, Sean; Sarmiento, Jorge; Dudycha, Jeffry; Kwon, Eun-Young", "platforms": "Not provided", "repo": "BCO-DMO", "repositories": "BCO-DMO; NCBI GenBank", "science_programs": null, "south": -90.0, "title": "Ocean Acidification Category 1: Identifying Adaptive Responses of Polar Fishes in a Vulnerable Ecosystem", "uid": "p0000006", "west": -180.0}]

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