Date of Completion


Embargo Period



Haloarchaea, speciation, biogeography, temporal stability, MLSA, genome fingerprinting, recombination, 16S rRNA, bacteriorhodopsin, rpoB

Major Advisor

Dr. R Thane Papke

Associate Advisor

Dr. J Peter Gogarten

Associate Advisor

Dr. Spencer Nyholm

Associate Advisor

Dr. Dan Gage

Associate Advisor

Dr. Kent Holsinger

Field of Study

Genetics and Genomics


Doctor of Philosophy

Open Access

Open Access


This dissertation discusses a working model for species genesis in Haloarchaea based on evidence obtained from multiscale analyses of Haloarchaeal communities and populations. First, a spatial distribution analysis of the haloarchaeal communities using both PCR amplified environmental gene marker as well as metagenomic comparisons reveal unique haloarchaeal communities in geographically distant hypersaline environments. Similar to eukaryotes, endemism is apparent in haloarchaea. However, unlike the eukaryotes, there is neither a distance-decay relationship nor is there a similarity in haloarchaeal communities based on whether they are from lakes or salterns. Second, temporal analysis on one haloarchaeal community reveals stability in the community at the genus level. Stable environmental conditions provided by the hypersaline environments ensure stability in the community with only fluctuations in the relative abundances with respect to salinity. Third, comparing individuals within a community showed widespread genomic variations between isolates. Comparing a multi gene concatenated phylogeny and whole genome fingerprinting exposed that even isolates that were identical at each locus tested had varying genome patterns. This happens at a rate much greater than the accumulation of third codon substitutions. Finally, assaying two highly conserved genes from 109 haloarchaeal genomes evidenced the existence of extensive recombination at predicted rates far greater than the rate of mutation in haloarchaea. Based on all this data, it can be hypothesized that frequent recombination occurs within the community members at each geographically distant site, homogenizing them, and maintaining endemic populations while often forming stable chimaeras that could become new species.