Research Interests

(last updated 2012)

The evolutionary process begins with discrete changes to DNA, with consequences emerging at several levels of biological organization: the chemistry of biomolecules; the metabolism and behavior of organisms; the ecological interactions within communities; and ultimately, the survival or extinction of species.

Below are a number of topics that I am interested in. This is not to say that I am necessarily expert in them, only that I wouldn’t mind developing expertise in these topics.

My favorite bacteria

I don’t always focus on meningitis pathogens (Haemophilus influenzae, Neisseria meningitidis). Here are my favorite groups of bacteria:

The Limits of Species and Species Concepts

Humans instinctively categorize things, including living organisms. When we identify species of organisms, we hope to understand the biological processes that have produced the patterns of similarities and differences that underlie our categorization schemes. For modern biologists, our ideas about species are developed within the framework of evolutionary theory, and we largely appeal to genetics and ecology as the fundamental forces that distinguish species from each other.

I want to understand how these differences arise and the forces that cause different organisms to coexist. The topics below address various aspects of bacterial diversity.

Horizontal Gene Transfer

During reproduction, organisms provide their genomes to their offspring. In asexual organisms (such as bacteria), this “vertical inheritance” naturally leads to a set of bifurcating relationships among organisms, depicted as the Tree of Life. Sexual organisms regularly mix their genomes with those of their mates, preventing divergence among members of the same mating population. For them, only way to produce a new branch of the Tree of Life is for a portion of a mating population to stop interbreeding with the remainder of the population — thereby becoming genetically isolated and eventually forming a separate species.

In contrast to these “normal” forms of genetic transmission, there is another form called “horizontal gene transfer”. This refers to any process that transfers DNA from one organism to another organism independently from reproduction. Several processes have been identified in the laboratory: for bacteria, these include transduction and integration by bacteriophage, conjugation (often involving a plasmid), and natural transformation. In the wild, the small scale of these processes prevents direct observation, so we can only infer that they have occurred based on the patterns of similarities and differences among the DNA sequences that we recover from wild populations of bacteria. It turns out that horizontal gene transfer is pervasive; most bacterial genomes are constantly gaining and losing genes, and genes can even be transferred between the most distantly related organisms.

Despite the promiscuity of gene transfer among bacteria, there is still a bias towards exchanging genes with closely related organisms, with consequences that are in some ways analogous to the consequences of mating within species of plants and animals. Just as recombination can occur between homologous chromosomes in eukaryotes to produce chromosomes with new combinations of alleles, a bacterial chromosome can recombine with homologous DNA from a donor chromosome to generate a recombinant chromosome where a section of DNA sequence has been converted to match the donor. The rate of DNA transfer between closely related bacteria is greater than that between bacteria in general, meaning that the evolution of a particular organism’s genome is strongly influenced by the genetic diversity found among these privileged donors — much as the evolution of a plant or animal chromosome is influenced by the genetic diversity within its mating species.

Adaptation to new environments

Genome structure

Further readings