CEB Committe on Evolutionary Biology

SPOTLIGHT: Daniel Hooper (Alumnus)

Daniel Hooper (Alumnus)

Daniel Hooper, in New Zealand holding an orphaned Tui (Prosthemadera novaeseelandiae). 

Your genome has architecture. Differences in the number and copy number of chromosomes, the order and identity of genes on those chromosomes, and the accessibility of these genes to the cellular machinery are just a subset of the myriad ways in which genomic structure can vary both within and between species. How does the architecture of the genome evolve and what –if any – is the evolutionary relevance of these rearrangements? My dissertation research, as part of the Committee on Evolutionary Biology here at the University of Chicago, is focused on investigating the evolutionary significance of one class of genomic structural rearrangement: chromosome inversion.

A chromosome inversion results from a chromosome breaking at two points and the area bound by these breakpoints being repaired in the opposite orientation. Inversions are incredibly common and often observed as fixed differences between species or polymorphisms segregating within species. The pervasiveness of these rearrangements is thought to be due in large part to their ability to suppress recombination in individuals who are heterozygous for the inversion. When there is a selective advantage to maintain linkage between sets of alleles locally adapted to either the habitat or genetic background of a population an inversion may be favored if it encompasses these alleles. Indeed, empirical studies have alternately attributed to chromosome inversions a role in sex chromosome evolution, supergene formation, local adaptation, and reproductive isolation. My interest in chromosome inversions and the process of speciation led me to examine their evolutionary relevance in birds in the laboratory of Dr. Trevor Price.

Birds have a long history of use in the study of speciation and are perhaps the best-researched group of organisms with respect to how behavior and ecology contribute to population divergence but comparatively little attention has been given to the role of chromosome rearrangements to avian divergence and speciation. My research combines both a broad scale investigation into the underlying causes of rate variation in inversion evolution across the largest avian order – the Passeriformes – and a focused comparative genomics approach to examine genomic structure evolution and speciation history in a group of Australian finches in the family Estrildidae. As a graduate student in the Committee on Evolutionary Biology I have carried out field research in the Australian Outback studying a hybrid zone between subspecies of the long-tailed finch (Poephila acuticauda) – a system in which chromosome inversion polymorphism appears to be intimately linked to their divergence – and used laboratory space at the Field Museum of Natural History to prepare collected materials for sequencing. The connecting tissue of my dissertation has been a love for birds, field research, and the use of comparative genomic tools in order to better understand how and why the architecture of the genome diverges.

My research has been made possible in turn by funding from a National Geographic Young Explorers grant, an American Ornithologists’ Union student research award, two awards from the Hinds Fellowship to students in the Community on Evolutionary Biology, and a doctoral dissertation improvement grant (DDIG) from the National Science Foundation. 

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