Working groups formed in the 2019 Synthesis Workshop

Genome-informed approaches and insights for characterizing targets of selection across complex life cycles in eukaryotes

Authors (currently in alphabetical order, authorship order not determined): Molly Albecker, Sam Bashevkin, Matthew Hahn, Matthew Hare, Holly Kindsvater, Stacy Krueger-Hadfield, Katie Lotterhos, Adam Reitzel, Mary Sewell, Laetitia Wilkins

Overview: Our goal is to develop and write a perspective article on the use of genome-focused approaches to characterize the mechanisms of selection across the life cycle. We have organized this article by summarizing current studies using single-generation studies paired with genomic analyses, comparing how genomic approaches complement other approaches (life history modeling, quantitative genetics), and listing recommendations for experimental design based on simulation studies. Marine organisms are ideally suited for studies quantifying how selection at different life cycle stages impacts genome-wide variation due to comparatively wide life cycle diversity, large numbers of propagules/offspring, feasibility of family designs in small research spaces, and the availability of genomic and experimental resources.

Fluctuating Selection

Mark Bitter, Scott Burgess, Hans Dam, Groves Dixon, Sarah Donelan, Santiago Herrera, Lee Karp-Boss, Carly Kenkel, Lisa Komoroske, Katie Lotterhos, Kerry Nickols, Emily Rivest, Juliet Wong

Goals: The overarching goal of our working group is to provide a single, synthetic article in which we accomplish the following:

  • Provide a novel synthesis of theoretical literature exploring evolutionary dynamics under different regimes of fluctuating selection pressures. -Highlight attributes of marine systems that make them ideal for testing these theoretical predictions. -Review empirical studies that have effectively tested theoretical predictions in a marine setting, and highlight those theoretical predictions that still warrant substantial practical corroboration. -Provide perspective regarding how adaptation to various regimes of contemporary/historic variability may influence adaptation to climate change.

Surf and Turf - Comparing intraspecific differences in thermal limits between marine and terrestrial habitats

Matthew Sasaki, Brian Cheng*, Sarah Gignoux-Wolfsohn, Cynthia Hays, Morgan Kelly, Seema Sheth, Jordanna Barley, Alysha Putnam, Andrew Villenueve

Our group has two primary goals: To explore intra-specific differences in thermal limits in marine, intertidal, freshwater, and terrestrial taxa, and to compare the scaling of those differences between realms, using geographic distance and environmental differences as our moderators. To date, we have surveyed the literature on adaptive divergence of upper and lower thermal limits, and compiled a list of papers that meet our requirements for inclusion. We have made significant progress towards extracting data from the complete collection of >60 papers (currently ~75% complete). We have generated code that calculates geographic distance between populations, extracts environmental data for each site from commonly used temperature databases, and analyzes/visualizes the data.

Modeling evolution in marine systems

Amanda Xuereb, Peter Tiffin, Huijie Xue, Megan Phifer-Rixey

Goals: One challenge of modelling evolution in marine taxa is incorporating the effects of pelagic life stages that impact population structure and connectivity. This group will review the use of eco-evolutionary marine models and discuss the impact of factors such as larval dispersal, larval settlement, and sharp clines in environmental conditions on local adaptation. They will demonstrate how spatial complexities in the marine environment can be incorporated into evolutionary models and evaluate the outcomes of spatially explicit models using SLiM3.

Blinded by the Wright? Prevalence of adaptive divergence in phenotypic traits at microgeographic scales

Dan Bolnick, Wes Dowd, Atsushi Fujimura, Cameron Ghalambor, Torrance Hanley*, Randall Hughes, Erik Sotka, Phil Yund

Goals: Evolutionary biologists are increasingly aware of the potential for organisms to exhibit putatively adaptive differentiation over surprisingly small spatial scales, even those well within the dispersal range of a species. For example, even marine species with long-lived, highly dispersive, pelagic larvae may exhibit fine-grained local adaptation. These observations appear to contradict conclusions of the classic Wright migration-selection balance model. Motivated by a need to more comprehensively evaluate the prevalence of this phenomenon, we are conducting a meta-analysis with two objectives: 1. to quantify the strength of trait-environment correlations across spatial scales, and 2. to assess whether these scale-dependent patterns might vary across taxa (e.g., plant, invertebrate) or ecosystem (e.g., terrestrial, marine). We are focusing on studies that included common garden and/or reciprocal transplant evaluations of phenotypic traits across environments. If prevalent, microgeographic scales of adaptation demand refined approaches to evolutionary biology and conservation biology, with possible implications for a variety of other fields.

Predicting Diversity and Divergence in the Sea

Gideon Bradburd*, Reid Brennan, Joanna Kelley, Misha Matz, Jamie Pringle, Cynthia Riginos, Rachel Toczydlowski, John Wares

Working group goals: The goal of the working group is to quantify patterns of genetic diversity and divergence in marine organisms and understand the biotic and abiotic processes that drive them. To accomplish this goal, we are taking a data synthesis approach, aggregating publicly available, georeferenced, next-generation sequence datasets for marine species, as well as biotic trait data for those species and oceanographic data for the areas in which they were sampled. Taken together, these data will allow us to integrate across scales both temporally (micro- to macroevolution) – and spatially (local to global) to test hypotheses about what biotic and abiotic factors predict genomic diversity and divergence in marine ecosystems.

Since the working group formation in August, we have kept to a monthly meeting schedule to ensure that we are holding ourselves accountable for progress. In that time, we have created a reproducible pipeline aggregating the next-generation sequence datasets this project requires. Specifically, this pipeline cross-references individuals in the NCBI Short Read Archive (SRA) database with those in the NCBI BioProject database to identify all individuals with georeferenced locations and genomic data (a tricky step, as not all BioProject individuals have the appropriate data in the SRA, and not all SRA individuals are georeferenced). This pipeline further automates the identification of all marine species in that dataset, and culls by sampling requirements (e.g., more than 10 individuals per species). Having identified an initial set of datasets that fit our needs, we are beginning to aggregate biotic trait data (e.g., body size, trophic position, life history traits including larval dispersal mode) and abiotic data (mean and variance in ocean temperature, mean current speed and direction) for these species. We are also beginning to establish the bioinformatic pipeline we will use to analyze the available raw sequence read data, and identify the computational resources we will need to execute the necessary analyses.