 Molecular phylogeny of sharks. We are
exploring the nature of the molecular evolutionary process
within the context of shark phylogeny. Sharks lend themselves
well to the problem because they exhibit a tremendous range of
adaptations, are well represented by modern forms (more than
370 species identified), and have an excellent and reasonably
continuous fossil record. Indeed, they may represent one of
very few groups for which both the patterns of diversification (their
evolutionary relationships) and the timing of the various
cladogenic events can be accurately estimated.
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 Lamniform sharks whole mitochondrial genome.
Under construction
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 Morphometric study of sharks teeth.
Under construction
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 Gene expression in cranial development of
sharks. Advances in the genetics and embryology in the
chick and the mouse have uncovered a wealth of genes and
regulatory elements that are involved in cranial development.
At present, it is unclear whether the patterns of similar gene
expression seen in chicks and mice represent novel pathways
that are uniquely associated with higher vertebrates or are
merely patterns that are common to all vertebrates. In this
project, we aim to contrast gene expression in the head of
higher vertebrates with that of a suite of basal vertebrates
over the course of their early development. We will survey
expression patterns in bamboo shark, chain dog-fish, little skate,
and sturgeon.
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 Phylogeny and population genetics of
Pristis.
Link to
Vicente Faria web page
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 Chromosomal evolution among Esocoid
fishes.
Link
to Andres Lopez web page
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 Protein structure/function effects on DNA
substitutional pattern.
Under
construction
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 Understanding phylogenetic signal in DNA
sequences. Several forces are known to affect molecular
evolutionary change. Many of these leave their "fingerprints"
in the patterns of DNA sequence variation observed among
organisms. In our lab we are interested in discriminating
between the patterns of sequence variation that are due to
phylogenetic history and those that are due to other
influences. We are exploring the utility of filters for
distinguishing between patterns of character state variation at
different scales.
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 Sequencing by hybridization. We are exploring
the possibilities of designing a gene-specific sequencing-by-hybridization chip to facilitate high-throughput sequencing
for phylogenetic systematics.
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 Morphometry of protein structure. Geometric
morphometric methods will be used to construct a "protein
shape space," in which clusters of similarly-structured
proteins can be identified. Because of the correlation between
protein structure and function, this space should serve as a tool for identifying the "functional phenotype" of an uncharacterized
protein.
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 Reconstructing fossil myoglobins. We are
surveying extant variation in myoglobin sequences in
conjunction with a well-established phylogeny of vertebrates to
estimate ancestral myoglobin sequences. We will synthesize
these estimated ancestral sequences, express them in vitro,
determine their structures, and contrast their functional
properties with those of extant sequences using a series of
functional biochemical assays. This process will allow us to estimate
the genotype-phenotype map for an ancestral protein and give
us insight into both ancestral properties of the molecule and
how its g-p map has evolved over time.
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 Investigating evolutionary lines of least
resistance using the inverse protein-folding problem.
Under construction
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