Evolutionary Ecology and Genomics


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Selected Publications

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

. 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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. Differential predation alters pigmentation in threespine stickleback (Gasterosteus aculeatus). Journal of Evolutionary Biology, 2018.

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. What genomic data can reveal about eco-evolutionary dynamics. Nature Ecology & Evolution, 2018.

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Recent Posts

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

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Projects

Trophic ecology, physiology, and ecosystem services in freshwater ecosystems

Having grown up in the great lakes region I am motivated to understand the rapid evolution, ecology, and physiology of freshwater organisms. I mainly work in lakes, where populations are often discrete and eco-evolutionary processes occur in parallel in multiple locations within a landscape.

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

Many fields of biology have tremendously benefitted from the increasing availability of whole genome data. Genetic data has become crucial to many areas of ecology, but whole genome data has not proven particularly beneficial. In this area of my research I seek to use whole genome data as a tool to increase the predictability of community ecology.

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