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Publication Date


Document Type

Honors Project


Biological Sciences


Bogs-Massachusetts, Fens-Masssachusetts, Biodiversity, Microorganisms, Lobosa-Variation, Species diversity, Cryptic species, Testate amoebae


Pt. 1. Microbes comprise most of the lineages in the tree of life, yet many are among the least understood organisms. Microbes include archaea, bacteria, and unicellular eukaryotes, and are important in understanding evolutionary history of life on Earth, and crucial sustaining many ecosystem processes. The morphological characters traditionally used to describe and characterize microbes, especially among lobose testate (shelled) amoebae, the focus organisms of this study, have often been found to not reflect genetic relatedness or evolutionary history. Thus, molecular analyses of gene sequences in combination with morphological descriptions are needed to assess phylogenetic and biogeographical patterns among testate amoebae within the order Arcellinda. Here, we assess (1) biogeography and distribution patterns at local sites, (2) the biodiversity within given taxa, and (3) the evolutionary relationships among the morphospecies. Our biogeographical analyses indicate there are complex distribution patterns both in terms of morphological and genetic species, including substantial short-term variability in testate community composition. In molecular analyses we use primers to target SSU-rDNA and actin genes of five morphospecies of testate amoebae. Seventy-eight individuals were used in building the SSU phylogeny (17 from Genbank, 33 from Nguyen (2011) and Lahr, unpublished, and 26 from this study). We compare reconstructions against previously published phylogenies of Arcellinda (namely, Hyalospheniidae). Our molecular results suggest that cryptic species exist within multiple Hyalospehniidae morphospecies and that morphospecies and genera are not monophyletic. Pt. 2. The perception of the bacterial and archaeal genomes as fixed within a species and throughout an individual's lifetime still dominates textbooks and much of the literature. In contrast to this view, research increasingly shows that DNA content varies dramatically within individuals in a life cycle and among closely related individuals within a bacterial or archael species. In this review, we synthesize information on five categories of dynamic genome mechanisms within bacteria and archaea: (1) ploidy level variation, (2) repair of highly fragmented genomes, (3) epigenetics and genome rearrangement, and (4) life cycle variation. Model species with dynamic genomes are found in a diverse array of lineages within archaea and bacteria. For example, Escherichia coli is rarely monoploid, Epulopiscium contains up to tens of thousands of copies of its genome and reproduces by viviparity, and Deinococcus radiodurans can repair its shattered genome in a few hours. The number of discoveries of dynamic genome features is increasing rapidly as more genome analyses are undertaken in archaeal and bacterial domains. We hypothesize that (1) archaea and bacteria have the ability to distinguish germline from somatic DNA; (2) dynamic genomes are the rule rather than the exception across the tree of life; and (3) perhaps this is representative of the last universal common ancestor (LUCA).




99 p. : ill. (some col.) Honors project-Smith College, Northampton, Mass., 2012. Includes bibliographical references (p. 61-64, 87-91)