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Figure 1.  A seasonal killifish pool in the Ribeira de Iguape region of São Paulo, Brazil.  The annual fish species Leptopanchax aureoguttatus was collected at this locality. 

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Figure 2.  A phylogeny of annual killifishes and their relatives.  Photos by Anthony Terceira.  Annual species are highlighted in red.

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Developmental Genomics

of "Ancient Fishes":

Most fishes, like killifishes, are decendents from a common ancestor that underwent whole genome duplication.  Consequently, they possess highly diverged paralogous genes that have sub- or neo functionalized.  However, some slowly evolving "Living Fossil" fishes diverged before this genome duplication.  By using living fossils like Bowfin (Amia calva) and Spotted Gar (Lepisosteus oculatus), I am studying the deep homology of vertebrate developmental phenotypes and the evolutionary consequences of gene and genome duplication. Importantly, the slowly evolving gar and bowfin genomes can be used as stepping stones to find homologous genetic elements between humans and rapidly evolving biomedical fish models like killifishes. I have recently been the lead author on the Bowfin (Amia calva) genome published in Nature Genetics. We used Bowfin to identify the gene regulatory elements responsible for a number of vertebrate developmental phenotypes. Bowfin solidifies our stepping stone comparative approach into a "Holostean Bridge" using all major living holostean fish lineages (gars and bowfins) to bridge the gap between humans and other fishes.

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Research Themes: 

 

I am an evolutionary biologist studying evolutionary, ecological, and developmental genomics. My research investigates the genetic basis of developmental adaptations in extreme environments. I integrate molecular phylogenetics, models of molecular evolution, comparative genomics, and functional genomic tools in an Eco-Evo-Devo framework, specifically using tropical killifishes and “ancient” fishes as my primary model systems. My central aims are to explore:

 

1.) How do underlying, deeply homologous genetic and developmental processes contribute to the evolvability of complex and convergent phenotypes in response to extreme environmental change? 

 

2.) How do gene duplicates and gene regulatory networks evolve to create developmental plasticity and adaptive resilience to perturbations of “normal" physiology and development?

Eco-Evo-Devo of Annual Killifishes:

Killifishes are emerging research models for evolution, development, behavior, cancer, developmental perturbations, and aging. This is because annual killifishes have dormant (diapausing) embryos that withstand seasonal habitat (Figure 1) desiccation which results in death of the entire parental population. This annual life history includes the independent, convergent evolution (Figure 2) of rapid aging and embryonic dormancy among distantly related lineages of killifishes. I am using annual killifishes and their relatives as a model clade to explore the evolution of developmental phenotypes in extreme environments. 

Ongoing Research Projects:

 

Figure 3.  "Living Fossils" like this Bowfin  illuminate vertebrate evolution with their slowly-evolving, ancestrally unduplicated genomes.  

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Figure 4.  This Longnose Gar (Lepisosteus osseus) is one representative of only seven living species of gar.  Gars together with one species of Bowfin make up Holostei, a once diverse group of fishes, now mostly extinct with the exception of these eight "living fossil" species.