Hybridization and speciation–hybridization has multiple and varied effects on the speciation process and can be used as a tool to study this process. For example, hybridization and introgression can prevent, slow or reverse population divergence, or be the source of novel combinations of adaptive alleles that might facilitate rapid hybrid speciation. Moreover, segregating variation in hybrid zones can be used to map traits that differ between species, including those that constitute inherent barriers to gene flow. We are interested in hybridization for all of these reasons, and recent or ongoing studies in the lab investigate:

• the genetic basis and evolution of barriers to gene flow in Lycaeides butterflies (read more, and more, and even more)
• the nature and repeatability of homoploid hybrid speciation in alpine butterflies (read more)
• speciation (and the failure of speciation) with gene flow in Timema stick insects
• We have also written recent review articles on this hybridization as a tool and important evolutionary process, including reviews in Evolutionary Applications and the Annual Review of Ecology, Evolution, and Systematics.

photo by L. Lucas

Contemporary evolution and fluctuating selection–Evolution can be rapid and relentless. Rapid adaptation can prevent extinction when populations are exposed to extremely marginal or stressful environments. But despite strong selection, directional evolutionary change might be limited if the nature and intensity of selection vary (i.e., fluctuate) across space and time. Along these lines, a number of projects in the lab analyze evolution on ecological time-scales. We aim to better understand the causes and consequences of rapid/contemporary evolution. We are especially interested in:

• how strong, negative-frequency dependent selection on Timema cristinae color pattern morphs causes predictable evolutionary dynamics and maintains variation in nature (read more)
• the genomic basis and evolutionary dynamics of evolutionary rescue in Callosobruchus maculatus seed beetles feeding on a novel, stressful host plant (read more)
• the causes and consequences of spatial and temporal variation in the nature, direction, and magnitude of selection in Lycaeides butterflies (read more)

drawings by R. Rubias

Patterns of genetic diversity and the structure of biodiversity— Understanding what factors determine levels of genetic variation within populations and species and the distribution of genetic variants among populations is central to evolutionary biology and might be important for biodiversity conservation. Related to this is the question of how the combination of gene flow, selection, and reproductive isolation structure biodiversity in nature, including whether (or rather when) these processes give rise to discrete units we think of as species versus a continuum of variation. Along these lines, we are particularly interested in:

• how selection shapes variation in genetic diversity levels in nature
• the organization of genetic and phenotypic diversity into species (or not) in Lycaeides butterflies (read more)
• patterns of population genetic structure and their consequences of conservation biology (conservation genetics) (past work has focused on spring endemics and Lycaeides butterflies, ongoing work focuses on Hayden’s ringlet)

photo by L. Lucas

Genetics of adaptation and the evolution of interactions–Considerable uncertainty remains about the genetic basis of adaptation in nature. We still do not know whether adaptation most often occurs from new mutations or standing genetic variation, involves changes at a few or many loci, or involves the same genetic variants in different populations. We are using multiple systems and approaches to advance understanding of the genetic basis of complex adaptive traits and components of fitness, including those that underlie the establishment of novel interactions (i.e., use of a new host plant), by, for example:

• applying genome-wide association mapping and genomic prediction methods to ecologically important traits in natural populations (e.g., butterfly wing patterns)
• comparing SNP-fitness associations in lab experiments to patterns of genetic variation in natural populations to understand host adaptation in Lycaeides melissa (read more)
• testing for genetic trade-offs that could constrain host plant adaptation in seed beetles using quasi-natural selection lines and population genomics (read more)
• deciphering the genetic basis of color variation across multiple Timema stick insect species
• determining the extent to which genetic variants in both an herbivore and its host plant affect of the outcome of the interaction (the plant being eaten and the caterpillars surviving or not) (see this initial paper from the project)

Statistical models and computational biology–Large-scale genome sequencing and resequencing is now possible for many organisms, but making sense of these data requires computational tools and advanced statistical models. More work in this area is needed. In particular, we need models that are sufficiently complex to incorporate multiple evolutionary processes and linkage among variants, but also computationally efficient. We have developed hierarchical Bayesian models to quantify genetic differentiation and introgression using high-througput DNA sequence data (check out our software and software page). Similarly, we have studied several of these models or other aspects of population genomic inference using computer simulations. Current and ongoing work in our lab will develop and evaluate models and software to:

• test for fluctuating selection using population genomic time series data (see this paper, and my talk)
• quantifying selection on (many correlated) genes/genetic loci from selection experiments (read more)
• quantifying ancestry frequencies in partially stabilized hybrid lineages (read more)