IMAGiNE: Testing multi-level controls on an aridity tolerance phenotype over time through physio-genomic data integration

Project: Research project

Project Details

Description

Overview
Adapting to environmental challenges is central to an organisms survival and to the diversity of behaviors and traits manifested across life. However, the factors contributing to any given adaptive phenotype are diverse and occur through specific biological mechanisms that operate over different timescales. These include long-term deterministic mechanisms such as coding and regulatory genomic changes, as well as shorter-term plastic responses such as epigenomic, transcriptomic, and behavioral modifications. Understanding the relative importance of these mechanisms, their interplay, and how their roles vary over the time since the phenotype diverged are critical to how organisms respond to novel environmental conditions and therefore to accurately predict their ability to accommodate the impacts of rapidly changing environmental conditions.
Here, we propose to integrate whole-genome, epigenome, and transcriptome sequencing with behavioral and physiological data to quantify the direct and indirect contributions these different control mechanisms have on tolerance to prolonged water limitation in three rattlesnake lineages, as well as to understand to what extent the degree of phenotype divergence influences the relative contribution of these mechanisms. Integrative statistical analysis using structural equation modeling will enable us to compare the relative controls across the different lineages as well as data from wild and common garden experiments.
Intellectual Merit
Previous research has established relationships in which genotypic, epigenomic, transcription, and behavioral changes each individually underlie phenotypic adaptations. However, rarely are multiple phenotypic controls considered together when studying organismal adaptations and the potential for adaptive responses to cope with varying environmental conditions. Therefore, we will use a comparative phylogenetic framework to examine the genomic, epigenomic, transcriptomic, behavioral and physiological responses of three lineages of rattlesnake that inhabit the entirety of a xeric environment that, across its range, has a strong late summer precipitation gradient. The divergence time between populations at each end of the gradient varies among the lineages, providing the opportunity to also examine the influence of time on the relative roles of the various mechanisms of adaptations. To account for the complexity associated with confounding variable in field studies and to ground-truth the structural equation models, we will also conduct a common garden experiment where individuals from all 6 populations (each of the 3 lineages represented by an east and a west population) will be housed under identical conditions and subjected to extended, but ecologically relevant, water deprivation. We will compare physiological, epigenomic, and transcriptomic responses of the individuals over time as well as among populations and lineages. Combined, this work will provide an unprecedented examination of the interplay of mechanisms of adaptation, and thereby provide new insight into the rate at which species can adapt to spatially or temporally changing environmental conditions, a topic of great importance given the rapid environmental changes occurring as a result of anthropogenic disturbances. It furthermore offers an approach to quantitatively evaluate hierarchical controls on a complex phenotype that is broadly applicable to other settings.
Broader Impacts
In addition to the exceptional interdisciplinary research experience and education this study will provide to participating undergraduate and graduate students, we will expand the impact of this work by developing a series of data manipulation and interpretation modules that utilize the large, diverse data sets produced by this study. The modules will vary in complexity so that they can be incorporated into courses ranging from introductory biology through upper-division and graduate courses, and they will be employable in both in-person and online courses, thus widely implementable beyond Arizona State University (ASU). By experiencing learning modules built from a single large, integrative dataset over the course of their education, students will progressively develop their ability to address broad biological concepts and relationships through an examination of the complexity of organisms and the multitude of processes by which the organism copes with environmental challenge, as well as how to statistically integrate data.
To achieve an even broader impact, we will work with ASUs award-winning Ask A Biologist program, a web-based STEM program that, in 2020, is expected to provide enriching online educational experiences to 25 million site visitors of all ages from across the globe. We will work with their popular game designers to create an online interactive drought survival game that, at differing complexity levels, will require the gamer to assign genomic and behavioral strategies to rattlesnakes as they enter a time of drought. The use of different strategies for different challenges will result in more or less of the population surviving. The game will bring attention to the varied survival strategies of organisms and the basics of evolution.
StatusActive
Effective start/end date9/1/218/31/24

Funding

  • National Science Foundation (NSF): $869,404.00

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