Presented By: Ecology and Evolutionary Biology
EEB Tuesday Seminar Series -- Four Lightning Talks
Abrianna Soule, Madelyn Foulkes, Will Weaver, Ben Nicholas
This event is part of our ongoing Tuesday Seminar Series.
-- Abrianna Soule, PhD Candidate
Talk title: How do Differences in Metabolomics Methods Influence Assessments of Latitudinal Gradients in Plant Chemical Defense?
Summary: The Latitudinal Biotic Interactions Hypothesis posits that investment in traits which mediate species interactions, such as plant chemical defense against herbivores, should increase towards the equator in alignment with species density and diversity gradients. Empirical evidence for this hypothesis as it relates to plant chemical defense has been mixed, and several confounding variables have been suggested to contribute to the inconsistency of results. For example, because there is no established ‘standard’ method for the quantification or comparison of plant chemicals, there is substantial methodological variation introduced between studies. In this study, we disentangle the potentially confounding impacts of chemical methodology as well as plant life history traits on the relationship between chemical defense and latitude using meta-analysis.
http://www.theweberlab.com/
https://bioio.org/
-- Madelyn Foulkes, EEB Undergraduate student
Talk title: How Is Competitive Success Determined between Heterotrophic Bacteria in the Algal Microbiome?
Summary: Chlorella sorokiniana is a crucial pillar of the Laurentian Great Lakes food web and a critical component of water filtration and biogeochemical cycling. Recently there has been an increased interest in studying Chlorella growth by examining interactions in the external microbiome, which comprises the microbes in the phycosphere that interact with a host organism that can consequently alter host behavior, fitness, and enrichment of heterotrophic bacteria. However, the mechanism behind these interactions has yet to be understood. This project seeks to compare unidirectional and bidirectional relationships between host Chlorella and phycosphere-dwelling bacteria to understand why these species live together, how competitive success in the microbiome is established, and the molecular underpinnings that foster these relationships.
-- Will Weaver, PhD Candidate, Smith Lab, GSCA for the Michigan Herbarium
Talk title: Building an automated specimen label transcription workflow with large language models
Summary: A major challenge in making natural history specimen vouchers findable and accessible is the slow process of manual label transcription. To address this, VoucherVision automates the extraction and transcription process using OCR, handwriting recognition, and vision-based large language models (v-LLMs), producing formatted JSON for collections databases. By fine-tuning LLMs and using a system of collaborating agents, we significantly enhance transcription accuracy and customization for institutional needs. Additionally, our editing interface helps reduce human-induced errors, ensuring high-quality transcriptions by preventing issues like hallucinations or omissions.
https://huggingface.co/spaces/phyloforfun/VoucherVision
https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/ajb2.16256
https://michigan.it.umich.edu/news/2024/10/11/digitizing-1-7-million-specimens-at-the-u-m-herbarium-with-ai/
-- Ben Nicholas, PhD Candidate, EEB
Talk title: Shadows of radiations past: did early divergence of the pharyngeal jaw apparatus set the stage for trophic diversification of modern Neotropical cichlids?
Summary: Understanding how continental assemblages have diversified can be difficult as they are products of extinction, biogeographic rearrangements, and changing environments over millions of years. Much of our knowledge of adaptive radiations stems from relatively recent, insular-like systems. However, increasing evidence supports the idea that adaptive radiations have a major role in hyper diverse continental radiations like Neotropical cichlids. This primarily riverine group has undergone adaptive diversification in many into ecologically, morphologically, and behaviorally complex lineages. Surprisingly, the macroevolutionary patterns of the entire pharyngeal jaw is relatively understudied in Neotropical cichlids. In this study we use µCT scans to characterize the morphological diversity of the entire pharyngeal system across Neotropical cichlids and test for signatures of adaptive radiation.
-- Abrianna Soule, PhD Candidate
Talk title: How do Differences in Metabolomics Methods Influence Assessments of Latitudinal Gradients in Plant Chemical Defense?
Summary: The Latitudinal Biotic Interactions Hypothesis posits that investment in traits which mediate species interactions, such as plant chemical defense against herbivores, should increase towards the equator in alignment with species density and diversity gradients. Empirical evidence for this hypothesis as it relates to plant chemical defense has been mixed, and several confounding variables have been suggested to contribute to the inconsistency of results. For example, because there is no established ‘standard’ method for the quantification or comparison of plant chemicals, there is substantial methodological variation introduced between studies. In this study, we disentangle the potentially confounding impacts of chemical methodology as well as plant life history traits on the relationship between chemical defense and latitude using meta-analysis.
http://www.theweberlab.com/
https://bioio.org/
-- Madelyn Foulkes, EEB Undergraduate student
Talk title: How Is Competitive Success Determined between Heterotrophic Bacteria in the Algal Microbiome?
Summary: Chlorella sorokiniana is a crucial pillar of the Laurentian Great Lakes food web and a critical component of water filtration and biogeochemical cycling. Recently there has been an increased interest in studying Chlorella growth by examining interactions in the external microbiome, which comprises the microbes in the phycosphere that interact with a host organism that can consequently alter host behavior, fitness, and enrichment of heterotrophic bacteria. However, the mechanism behind these interactions has yet to be understood. This project seeks to compare unidirectional and bidirectional relationships between host Chlorella and phycosphere-dwelling bacteria to understand why these species live together, how competitive success in the microbiome is established, and the molecular underpinnings that foster these relationships.
-- Will Weaver, PhD Candidate, Smith Lab, GSCA for the Michigan Herbarium
Talk title: Building an automated specimen label transcription workflow with large language models
Summary: A major challenge in making natural history specimen vouchers findable and accessible is the slow process of manual label transcription. To address this, VoucherVision automates the extraction and transcription process using OCR, handwriting recognition, and vision-based large language models (v-LLMs), producing formatted JSON for collections databases. By fine-tuning LLMs and using a system of collaborating agents, we significantly enhance transcription accuracy and customization for institutional needs. Additionally, our editing interface helps reduce human-induced errors, ensuring high-quality transcriptions by preventing issues like hallucinations or omissions.
https://huggingface.co/spaces/phyloforfun/VoucherVision
https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/ajb2.16256
https://michigan.it.umich.edu/news/2024/10/11/digitizing-1-7-million-specimens-at-the-u-m-herbarium-with-ai/
-- Ben Nicholas, PhD Candidate, EEB
Talk title: Shadows of radiations past: did early divergence of the pharyngeal jaw apparatus set the stage for trophic diversification of modern Neotropical cichlids?
Summary: Understanding how continental assemblages have diversified can be difficult as they are products of extinction, biogeographic rearrangements, and changing environments over millions of years. Much of our knowledge of adaptive radiations stems from relatively recent, insular-like systems. However, increasing evidence supports the idea that adaptive radiations have a major role in hyper diverse continental radiations like Neotropical cichlids. This primarily riverine group has undergone adaptive diversification in many into ecologically, morphologically, and behaviorally complex lineages. Surprisingly, the macroevolutionary patterns of the entire pharyngeal jaw is relatively understudied in Neotropical cichlids. In this study we use µCT scans to characterize the morphological diversity of the entire pharyngeal system across Neotropical cichlids and test for signatures of adaptive radiation.
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