Diatoms of North America1) Genomic Insights Into the Origin of Diatoms
With some 200,000 species, diatoms are probably the most species-rich lineage of microbial eukaryotes. In sharp contrast, the sister group to diatoms (the Bolidophyceae) includes fewer than 20 species. Comparing bolidophyte genomes to those of early diverging diatoms will allow us to pinpoint the key genomic changes that took place in the common ancestor of all diatoms. We're sequencing the genomes of diatom species that bracket the earliest splits in the phylogeny and comparing them to the genomes of closely related outgroup species. These data will provide key insights into the origins of novel diatom traits, including those that may have facilitated their nearly unprecedented phylogenetic and ecological diversification.
2) The Rates, Patterns, and Roles of Cross-Kingdom HGT in Diatom Evolution
One of the biggest surprises to come out of first diatom genome projects was the presence of hundreds of genes acquired by horizontal transfer from Bacteria and Archaea. The genome of one species contains nearly 800 genes of recent bacterial origin, whereas only half of these genes were found in the other species. This points to a dynamic history of foreign gene gain and/or loss over the course of diatom evolution, a pattern that is best resolved against the backdrop of a strongly supported organismal phylogeny. We're augmenting efforts to reconstruct the diatom phylogeny using hundreds of low-copy nuclear markers, sequencing transcriptomes of >200 additional diatoms, and developing a phylogenetically based analytical pipeline for de novo detection of foreign genes. We'll then formally reconstruct the history of foreign gene gains across the phylogeny to determine whether foreign sequence acquisitions coincide with major diversification events or the origins of novel traits.
3) The Evolutionary Transition Between Marine and Fresh Waters
Freshwater colonizations are landmark events in diatom evolution, having led to the origins of perhaps tens of thousands of species. A primary goal of this research is to understand the morphological, physiological, and genetic adaptations that have allowed diatoms to diversify into freshwater environments, which present numerous obstacles to marine colonists. We're using a blend of phylogenetic, experimental, and genomic approaches to understand how diatoms have successfully, and repeatedly, conquered "the salinity barrier". This project is focused primarily on Thalassiosirales, a lineage that presents an ideal model system for several reasons: (1) most species are easily cultured; (2) the lineage includes the model species, Thalassiosira pseudonana, which offers excellent genomic resources, and; (3) there is a strongly supported phylogenetic hypothesis, laying out a rich and well-resolved historical pattern of marine–freshwater transitions. This history includes numerous successful freshwater colonizations, so nature has played out this experiment multiple times. Our goal is to determine whether these natural experiments played out in the same, or different, ways.
4) The Origins and Evolution of Non-photosynthetic Diatoms
Diatoms are prolific photosynthesizers, accounting for roughly one-fifth of global net primary production. Some pennate diatoms are mixotrophic, having the ability to also use extracellular carbon for growth. In addition, a handful of species (all in the order Bacillariales) are strictly heterotrophic. These colorless diatoms have completely abandoned photosynthesis and have an obligate need for external carbon to sustain their growth. It's not clear how many times obligate heterotrophy evolved we're addressing this question by reconstructing the phylogeny of Bacillariales using hundreds of low-copy nuclear markers. We're also assaying photosynthetic species for heterotrophic growth, in part to determine whether mixotrophy represents an intermediate evolutionary step in the transition from autotrophy to obligate heterotrophy. Finally, we're sequencing the nuclear and organelle genomes of a diverse set of autotrophic, mixotrophic, and obligately heterotrophic taxa to identify the genetic underpinnings of this complex trait and determine the origins of this novel machinery. The relict plastid genomes of heterotrophic taxa are revealing which plastid genes have functions that extend beyond photosynthesis. The plastid genomes raise several other interesting evolutionary questions that we're pursuing as well. What is the evolutionary fate of a genome whose principle function has been lost? How fast do photosynthetic genes deteriorate after the shift to heterotrophy?
