The Wray Lab at Duke University

We participated in the analysis and annotation of the genome Strongylocentrotus purpuratus, the purple sea urchin genome. Among other findings, this study provides insights into the operation of gene regulatory networks and the origins of the vertebrate immune system.

We showed that the great white shark (Carcharodon carcharias) evolved from a group of mako sharks using morphometric analyses. This finding refutes the common claim that the great white shark is a descendent of the extinct giant sharks, such as Carcharodon megalodon.

We collaborated on a project to understand the genetic basis for lactose persistence, the ability to digest milk as an adult. This study identified cis-regulatory mutations within East African pastoral populations that show evidence of recent positive selection and that elevate the expression of lactase, the enzyme that digests milk sugar.

We identified specific cis-regulatory mutations in the PDYN gene that were fixed by positive selection during the origin of humans, and which elevate the expression of the key neuropeptide that it encodes in humans relative to chimpanzees.

We demonstrated differences in the intensity and mode of natural selection among functionally distinct cis-regulatory elements of the Endo16 gene of sea urchins. We also found that levels of genetic variation are higher in transcription factor binding sites than surrounding, putatively neutral sequences.

We found that a mutation that disrupts a repressor binding site in the cis-regulatory region of the matrix metalloproteinase MMP3 was favored by natural selection among Europeans, with consequences for the incidence of coronary heart disease.

We identified an instance of positive selection on a derived transcription factor binding site regulating the T-cell cytokine interleukin 4 in humans.

We discovered a new form of weak selection that operates to remove spurious transcription initiation sites throughout prokaryotic genomes.

We uncovered a remarkable case of evolutionary divergence in the sequences of promoters that produce a conserved transcription profile in sea urchins.

We showed that larval cloning is phylogenetically widespread in seastars, and that multiple modes of cloning take place within single species in the wild.

We discovered that the gene network underlying wing polyphenism among ant castes is evolving rapidly.

We estimated that the average human is heterozygous for variants that affect transcriptional regulation at over 40% of all loci.