Brian J. Knaus

Population genetics, evolutionary biology and genome biology.

Research

Population genetics

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The study of the structure and demographics of populations}{Inference of subdivision, effective size and migration are central topics to understanding the dynamics of populations. My research has sought to infer the structure and demographic processes which may have led to the structure we observe in populations.

We sequenced the mitochondrial genomes (~16 kbp) of 34 fishers (Martes pennanti). Through the use of existing softwares and custom tools developed in perl and R we've begun to bring genomic information to population and conservation biology. Although this group appears to have less molecular diversity than Native American humans (estimated to have arrived in the New World ~40 thousand years ago), we have managed to infer evolutionary relationships with unprecedented precision. Some of these relationships are very recent, perhaps as recent as 500 years ago. Because this predates Euro-American settlement it suggests that these lineages predate modern land management decisions. This information is of great importance to conservationists whom have recently considered the Californian populations (M.p. pacifica) as candidates for listing as protected organisms.


Evolutionary biology

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A number of organismal groups have been identified by biologists as groups which have experienced a recent and rapid evolutionary radiation. These groups are characterized as containing exceptional amounts of diversity (genetic, phenotypic, or otherwise). Examples include the Hawaiian Silversword alliance, Cichlids and others. Biologists study these exceptionally diverse groups in an attempt to better understand the process of speciation.

The legume genus Astragalus is the most species rich genus of vascular plant on the planet, containing approxiametly 2,500 species. Notable within the genus is the species A. lentiginosus, which contains more taxa (taxonomic varieties) than any other species in the U.S. flora. My Ph.D. dissertation sought to characterize this infra-specific diversity from a morphologic and molecular context, as well as propose mechanisms to explain this diversity. Through the study of diverse groups such as this, and the integration of theory and empiricism, we can begin to better describe the diversity we observe on this wonderful planet, and begin to understand the processes which have led to it.


Genome biology

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The union of biology, computer science and statistics. As the cost of genome scale sequencing has plummeted the practicality of assaying these genomes has become increasingly feasible. While the current technologies are rapidly changing, there are many long term perspective. For example, mamalian genomes average three billion nucleotides. Even model organisms typically have genomes on the order of hundreds of millions of nucleotides. This means that future biologists will need not just the quantitative skills to analyze these data, but computational skills to deal with large data sets. With these skills in hand genomes can be efficiently assembled, annotated and analyzed to feed into applications such as population genetics, evolutionary biology and others.



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