Join us on Wednesday, May 19th at noon PST for a seminar about Biodiversity with presentations by Dr. Rosemary Gillespie, Professor and Schlinger Chair in Systematic Entomology at the University of California Berkeley, and Dr. Shelly Trigg, Data Science Postdoctoral Fellow at the University of Washington.
Zoom link: https://umich.zoom.us/j/98394548332
“Data Integration Across Space and Time to Infer Biodiversity Dynamics”
Abstract: The world’s ecosystems are under serious threat due to ongoing stressors of the Anthropocene, notably habitat destruction, climate change, loss of biodiversity, disease, and the spread of invasive species. Biodiversity in particular is suffering catastrophic decline and tracking and understanding the factors affecting change is a major challenge that we are currently not meeting. Unless we develop new approaches, it will take centuries to document biodiversity and identify attributes that render ecological communities robust and resilient to change, and by then it will likely be too late. Here, we examine insights we can gain into biodiversity dynamics by looking at ways that we can first assess spatial patterns of diversity, abundance, and foodwebs, and determine the response of the organisms within these communities, to the changing environments that surround them. We have piloted an environmental DNA approach to generate estimates of abundance and interactions of macroorganisms in terrestrial systems across different spatial scales. By applying various theoretical and modeling approaches to the vast amounts of genetic data, we can encapsulate the “status” of a biological community in terms of its integrity and potential resilience to change. Moreover, by analyzing these data through slices in time (months, years, decades, or longer), we can assess how the community might accommodate, adapt, or collapse in response to change. These changes include habitat transformation, climate modification, fire, or disease. The critical data challenge is to integrate data that characterize the biological community, genomic data that reveal the response of any given taxon to that change, with past, present, and modeled climate change data. We highlight the role of historic collections from museums, and the physical record they provide of past environments.
Dr. Rosemary Gillespie‘s research focuses on understanding evolutionary patterns and processes among populations and species. Her primary focus is on islands, particularly remote hotspot islands of the Pacific. Hotspot archipelagoes – in which islands emanate from a single volcanic hotspot from which they are progressively carried away by a geological plate – allow researchers to examine how communities have changed over time and thus gain insight into the nature of processes shaping communities over evolutionary time. These archipelagoes make it possible to visualize snapshots of evolutionary history. For example, the geological history of the Hawaiian archipelago is relatively well understood, with individual islands arranged linearly by age. Thus, early stages of diversification and community formation can be studied on the island of Hawaii, an island still forming, and compared to progressively later stages on the older islands of Maui, Lanai, Molokai, Oahu, and Kauai. A roughly similar chronological arrangement is found in the archipelagoes of both the Marquesas and the Societies in French Polynesia.
“Diversity in Natural Response to Environmental Change”
Abstract: How will ecosystems tolerate the climate and ocean change occurring now and predicted for the future? To begin addressing this question, we can subject different animals to different anthropogenic pressures and evaluate their responses. We can more sensitively and comprehensively assess responses by performing molecular surveys using omics technologies (e.g. genomics, proteomics, metabolomics, etc.), which allow us to more clearly see the cellular processes that underlie environmental tolerance and intolerance. This data can also help us compare between species since all species have these general molecules (DNA, proteins, metabolites) in common. I’m going to present data from different studies on marine invertebrates exposed to different environmental conditions, and describe how I used multiple data science approaches to distill large omics datasets into dominant biological pathways associated with environmental tolerance and intolerance. After summarizing responses across species and conditions, I will propose future directions and data science applications for the wealth of environmental omics data being generated.
Dr. Shelly Trigg became interested in how systems biology could be used in applied research and completed a year-long NSF Graduate Research Internship at NOAA’s Northwest Fishery Science Center using omics to investigate how physiology and genetics in marine invertebrates are affected by ocean acidification. She returned to San Diego in the summer of 2018, completing her dissertation, “High resolution molecular networks from novel ‘omics’ approaches elucidate survival strategies in organisms from land to sea,” and received her Ph.D. In the Fall of 2018, Shelly began as a Postdoctoral Researcher in Steven Roberts’ lab in the School of Aquatic and Fishery Sciences at University of Washington where she studied how the environment impacts marine animals at the physiological and molecular systems level. She conducted experiments that simulated various ocean conditions and used omics technologies (like epigenomics, proteomics, and metabolomics) in combination with physiological assays to measure animal response. In March of 2021, Shelly started her current position as a Research Scientist at Gloucester Marine Genomics Institute.
The Data Science Coast to Coast (DS C2C) seminar series is co-hosted by the eScience Institute, along with data science institutes at New York University, Rice University, Stanford University, University of California – Berkeley, University of Michigan and the Academic Data Science Alliance (ADSA).
In the first half of 2021, we will host five seminars, each featuring one faculty member and one postdoctoral fellow from two universities. Each speaker will give a 20-minute talk about ongoing projects and motivating issues, followed by 20 minutes of discussion with the audience. These seminars will be the launching point for follow-on research discussion meetings which will hopefully lead to fruitful collaborative research.