Evolutionary Ecology and Genomics


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Selected Publications

Eco-evolutionary dynamics will play a critical role in determining species’ fates as climatic conditions change. Unfortunately, we have little understanding of how rapid evolutionary responses to climate play out when species are embedded in the competitive communities that they inhabit in nature. We tested the effects of rapid evolution in response to interspecific competition on subsequent ecological and evolutionary trajectories in a seasonally changing climate using a field-based evolution experiment with Drosophila melanogaster. Populations of D. melanogaster were either exposed, or not exposed, to interspecific competition with an invasive competitor, Zaprionus indianus, over the summer. We then quantified these populations’ ecological trajectories (abundances) and evolutionary trajectories (heritable phenotypic change) when exposed to a cooling fall climate. We found that competition with Z. indianus in the summer affected the subsequent evolutionary trajectory of D. melanogaster populations in the fall, after all interspecific competition had ceased. Specifically, flies with a history of interspecific competition evolved under fall conditions to be larger and have lower cold fecundity and faster development than flies without a history of interspecific competition. Surprisingly, this divergent fall evolutionary trajectory occurred in the absence of any detectible effect of the summer competitive environment on phenotypic evolution over the summer or population dynamics in the fall. This study demonstrates that competitive interactions can leave a legacy that shapes evolutionary responses to climate even after competition has ceased, and more broadly, that evolution in response to one selective pressure can fundamentally alter evolution in response to subsequent agents of selection.
Proceedings of the National Academy of Sciences, 2021.

Population genomic data has revealed patterns of genetic variation associated with adaptation in many taxa. Yet understanding the adaptive process that drives such patterns is challenging; it requires disentangling the ecological agents of selection, determining the relevant timescales over which evolution occurs, and elucidating the genetic architecture of adaptation. Doing so for the adaptation of hosts to their microbiome is of particular interest with growing recognition of the importance and complexity of host–microbe interactions. Here, we track the pace and genomic architecture of adaptation to an experimental microbiome manipulation in replicate populations of Drosophila melanogaster in field mesocosms. Shifts in microbiome composition altered population dynamics and led to divergence between treatments in allele frequencies, with regions showing strong divergence found on all chromosomes. Moreover, at divergent loci previously associated with adaptation across natural populations, we found that the more common allele in fly populations experimentally enriched for a certain microbial group was also more common in natural populations with high relative abundance of that microbial group. These results suggest that microbiomes may be an agent of selection that shapes the pattern and process of adaptation and, more broadly, that variation in a single ecological factor within a complex environment can drive rapid, polygenic adaptation over short timescales.
Proceedings of the National Academy of Sciences, 2019.

Evidence that organisms evolve rapidly enough to alter ecological dynamics necessitates investigation of the reciprocal links between ecology and evolution. Data that link genotype to phenotype to ecology are needed to understand both the process and ecological consequences of rapid evolution. Here, we quantified the suite of elements in individuals (i.e., ionome) and differences in the fluxes of key nutrients across populations of threespine stickleback. We find that allelic variation associated with freshwater adaptation that controls bony plating is associated with changes in the ionome and nutrient recycling. More broadly, we find that adaptation of marine stickleback to freshwater conditions shifts the ionomes of natural populations and populations raised in common gardens. In both cases ionomic divergence between populations was primarily driven by differences in trace elements rather than elements typically associated with bone. These findings demonstrate the utility of ecological stoichiometry and the importance of ionome‐wide data in understanding eco‐evolutionary dynamics.
Ecology Letters, 2019.

Evolution can occur quickly; sometimes quickly enough to cause changes in ecological communities. Yet, our understanding of how, when, and why rapid evolution shapes ecology is still very rudimentary. Genomic data has greatly advanced many areas of study in biology and in this paper we discuss ways to apply genomic data to enhance research on the interplay between rapid evolution and ecology. We focus on using genomics to detect selection, estimate heritabilities of key traits, uncover phenotypes that are rapidly evolving, and determine the predictability of some ecological dynamics. When combined with experimental and observational datasets we believe that genomics can provide additional insight into the study of rapid evolution and ecology.
Nature Ecology & Evolution, 2018.

A tremendous body of research has demonstrated that when species are lost the function of ecosystems is altered. All of these studies model the process of extinction by demographic decline, where species decline until they are extirpated. The ecological effects of extinction by reverse speciation, where previously separate species interbreed leading to a single hybrid population, were largely unknown. Using a case of reverse speciation in threespine stickleback in a replicated experiment and field study we demonstrated that this type of extinction can have profound effects on aquatic ecosystems-altering the benthic invertebrate community, the breakdown of organic matter, and the emergence of insects from the aquatic environment into the terrestrial. These ecological effects were largely predictable based on the morphological evolution that had resulted from reverse speciation. As such, our study provides a guideline for predicting how reverse speciation may effect ecology in many ecosystems.
Current Biology, 2016.

Over the past decade it has become clear that variation between individuals of the same species (called intraspecific variation) can have profound effects on ecological communities. Variation between genotypes of the same species in key functional traits, like plant phenology or predator feeding morphology, can cascade to alter community structure and ecosystem functions. For this study we used a factorial experiment to assess how variation in two species within the same ecosystem, a primary producer and top predator, interact to shape the ecological community and ecosystem functions. We uncovered interactive effects, whereby the combinations of genotypes from these two species had notable effects on the the ecological community. The results from this paper highlight that the true importance of intraspecific variation in ecology may be underappreciated, as few studies have assessed the effects of this variation in multiple co-occurring species.
Proc. R. Soc. B, 2015.

Genetic data has become crucial to many areas of ecology, but whole genome data has not proven particularly beneficial. In this study we used an experiment to determine whether we could track the influence of individual alleles on metrics of community and ecosystem ecology in an outdoor aquatic experiment. Previous work has demonstrated that allelic variation at loci that control mendelian phenotypes of keystone species can have incredibly strong effects on the wider community. In our experiment we used naturally occurring genotypes of a dominant tree species that had tremendous genetic variation for many ecologically important traits (phenology, leaf chemistry, productivity). Yet this genetic variation was underlied by many independent loci. In our experiment we observed tremendously strong and pervasive effects of intraspecific diversity on ecological parameters. However, these effects were underlied by a variation in several traits and the variation in these traits was controlled by numerous genes. As such, the influence of any individual locus on any ecological response variable was miniscule. Our study modulates the expectations of these ‘genes-to-ecosystems’ approaches and suggests that other uses for genomic data in ecology may be more fruitful.
Molecular Ecology, 2014.

Recent Publications

More Publications

. Competitive history shapes rapid evolution in a seasonal climate. Proceedings of the National Academy of Sciences, 2021.

Project DOI

. Stoichiometric Traits Vary Widely Within Species: A Meta-Analysis of Common Garden Experiments. Frontiers in Ecology and Evolution, 2019.

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. Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster. Proceedings of the National Academy of Sciences, 2019.

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. Genetics of adaptation: Experimental test of a biotic mechanism driving divergence in traits and genes. Evolutionary Letters, 2019.

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. Detecting the macroevolutionary signal of species interactions. Journal of Evolutionary Biology, 2019.

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. Ionome and elemental transport kinetics shaped by parallel evolution in threespine stickleback. Ecology Letters, 2019.

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Recent Posts

Post Doctoral Researcher, Department of Biology, University of Pennsylvania (2016 – present).

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Assistant Professor, School of Biological Sciences, Washington State University (2021 – present).

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Projects

Trophic ecology, physiology, and ecosystem services in freshwater ecosystems

A part of my research in this area has focused on understanding population level-variation in fish physiology. Understanding the extent and pace over which Intraspecific variation in physiology evolves is crucial to being able to predict the pace of evolution and population persistence in the populations that are often isolated. An extension of my interest in this area is in quantifying the contribution of rapid evolution to ecosystem services in freshwater ecosystems. From local adaptation in salmonids to rapid evolution of Daphnia that leads to remediation of algal blooms there is a wealth of suggestive evidence of the benefits that we derive from rapid evolution. These ‘evosystem services’ present an avenue to manage ecosystems to ensure ecosystem services are maintained for future generations.

Eco-evolutionary Dynamics

Ecologist have studied the factors that regulate populations and shape ecological communities for over a century. One factor that was NOT traditionally considered is that rapid evolution could shape ecological dynamics. Many lab-based experiments have demonstrated that rapid evolution can dictate population dynamics, but there is little know about how common in natural ecosystems. My research in this area seeks to add ecological realism to understand when and how rapid evolution shapes ecology

The ecological and evolutionary implications of host-microbiome interactions

Bacteria play a crucial role in the physiology, ecology, and evolution of animals even if they are not transmitted or acquired across generations and the composition of affiliated microbial communities can impact host performance and relative fitness. Do microbiomes affect the evolutionary trajectories of host populations? Do host genotypes shape microbiome composition? How do these interactions influence the phenotypes, population dynamics, and evolutionary trajectories of host populations?

Using genomics to understand ecological processes

Some of the most pressing questions in biology are at the intersection of ecology, evolution, and genetics. To what extent will climate change and environmental degradation drive extinction? What role will rapid adaptation play and can this be enhanced?

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