Research

Genetic/genomic basis of adaptive morphological (co)variation

Developing a mechanistic understanding of the genetic and genomic basis of complex traits, including the craniofacial skeleton, has been called one of the greatest challenges in modern biology. While mutagenesis screens in model systems have made key inroads in identifying the genes and mechanisms that underlie early patterning of the skull, the extent to which these factors contribute to variation in craniofacial shape is unclear. Genome-wide association studies (GWAS) can complement mutagenesis screens by identifying loci that contribute to variation in complex traits; however, genes implicated in early craniofacial development via mutagenesis are conspicuously absent from GWAS data sets. Moreover, these association studies have only been able to explain a small percentage of the heritable variation in facial traits. Thus, there remain many open questions in the field with respect to the genetic mechanisms that contribute to craniofacial variation, including, but not limited to:

  1. How do environmental variables influence the genotype-phenotype (G-P) map?

  2. Does the G-P map change over ontogeny?

  3. Are loci that contribute to phenotypic variation the same as those that regulate covariation?

Ongoing research in the lab is providing some answers, as well as new questions to follow up in future studies.

Evolution mutant models to study development, disease and evolution

There is a fine line between adaptation and disease, and in many instances the distinction between the two is a matter of lineage. Certain Antarctic icefish species have osteopenia, blind cavefish are insulin resistant, and many squamate reptiles undergo heterotopic ossification. In each of these cases, the phenotype is adaptive, but mimics a maladaptive human condition. Much of our research leverages the utility of these on these “evolutionary mutant models”.


The genetic basis of phenotypic plasticity

Phenotypic plasticity is the capacity of an organism’s phenotype to vary in distinct environments. The ability of an individual to change its phenotype in different environments may increase its fitness in changing and/or fluctuating environments, which suggests that developmental plasticity may be adaptive and therefore subject to selection itself. While sufficient levels of genetic variation have been documented for plasticity to respond to selection, a proximate genetic basis for this trait has remained elusive. We have developed a set of foraging challenges to generate a "plasticity axis" within species in the lab (see below). Experimental fishes may then be subjected to a suite of anatomical, genetic, and genomic analyses. These data may be used to identify novel molecules involved in mechanosensing as well as inform theory related to the intersection of phenotypic plasticity and evolution.

Contemporary evolution of cichlids in response to rapid anthropogenic change

Humans are changing their environment in ever rapid and extensive ways. Indeed, few environments remain untouched by human disturbance, and so it is rarely a matter of if but rather the degree to which humans have altered the environment. A particularly sensitive region is the amazon basin, with major culprits being deforestation and the damming of rivers. The outcome is often the extirpation of local flora and fauna. However, species may also be able to adapt to local environmental changes. We have recently begun to explore this idea in cichlids in and around the Tucuruí reservoir, Pará, Brazil. The reservoir was created in the early 1980’s resulting in a large (2,850km2) body of water, with a complex coast line. Ancestrally riverine cichlids from the Tocantins River are now found in a lake environment. Using a combination of anatomical and genetic/genomic tools, we intend to test two (non-mutually exclusive) hypotheses: (1) Local adaptation to a lake environment is due to phenotypic plasticity in response to novel foraging habitats; (2) Local adaptation to a lake environment is due to the non-random assortment of ancestral alleles in reservoir populations.

Evolution and genetic basis of locomotor activity patterns among Lake Malawi cichlids: Exploring a novel mechanism of habitat partitioning

The circadian timing of activity is critical for organismal fitness, and species across the Animal Kingdom exhibit diversity in the timing of activity that ranges from strongly diurnal to strongly nocturnal. While the neural and molecular basis through which animals maintain a 24-hour circadian clock is well-studied, much less is known about how the timing of activity evolves. Identifying the ecological and genetic factors associated with variation in activity patterns would therefore address a critical gap in our knowledge. This proposal investigates these open questions by applying high-throughput behavioral analyses in Lake Malawi cichlid fishes – an iconic and powerful model system for ecology and evolutionary research. Malawi cichlids exhibit unparalleled diversity in an array of phenotypes, including behavioral traits. While these fishes have long been presumed to be largely diurnal, our preliminary investigations identified a nocturnal species. Furthermore, we documented a surprisingly high magnitude of variation in locomotor activity patterns among species, offering a unique opportunity to investigate its evolution and genetic basis.