Zachary Hyde's Research Interests
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I am interested in a few overlapping subjects that we can study using gene sequence. The exponentially growing amount of gene sequence that is available
makes possible many new analyses of life at the molecular level.
Molecular Systematics Call it phylogenetics if you want. I use whole-genome data sets with Bayesian and Maximum Likelihood
methods on parallel process computers to resolve nodes deep in the tree of life.
Molecular Evolution I am using sequences from the 13 mitochondrial
protein-coding genes to generate a matrix of amino acid substitution rates (see Dayhoff etal. 1978 for an example). I hypothesize that the amino
acid substitution process is not reversible, and that we can find statistical evidence for a direction in the evolution of protein composition.
Genome Architecture Why does the mitochondrial genome have almost no non-coding DNA, while our chromosomes are mostly so-called "junk" DNA? Is it
really junk? How can we systematically use gene arrangements for phylogenetic inference? How can we automate the annotation of gene sequence and the
creation of gene order maps from that data? I am interested in developing analytical methods that treat gene rearrangements and other such markers as
'hard' data in phylogenetics.