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Alternative Title

Biodiversity of testate amoebae based on analyses of single-cell transcriptomes

Publication Date


First Advisor

Laura A. Katz

Document Type

Honors Project

Degree Name

Bachelor of Arts


Biological Sciences


Testate amoeba, Single-cell transcriptomics, Genetic diversity, Phylogenetic tree, Arcellinida, Hyalosphenia, Eukaryotic microbes, SSU rDNA, Cryptic species


Despite the astounding prevalence of eukaryotic microbes in the biosphere, we know relatively little about most protists (Katz, 2012). We are only just starting to discover the incredible importance of testate amoebae to geology and ecology. Testate amoebae are single-celled eukaryotic microorganisms that move using projections of their cytoplasm, or pseudopods, and have shells – or tests – composed of a variety of materials (Meisterfeld & Mitchell, 2008). This study looks into the Arcellinida clade of testate amoebae, which are found on Sphagnum mosses in peatlands and wetlands around the world (Meisterfeld & Mitchell, 2008). Peatlands are known for their ability to absorb atmospheric carbon, and these tiny testate amoebae play a huge role in this carbon cycling (Jassey et al., 2015). In this study, I investigate the population structure of protein-coding genes from populations of Hyalosphenia papilio and Hyalosphenia elegans testate amoebae from four New England bogs: Hawley Bog, Harvard Forest, Orono Bog, and Acadia National Park. Given the relatively large distance between the four bogs (two in Massachusetts, two in Maine), I expect to see some degree of speciation by geographic separation, or allopatry. Additionally, this project involved the development of phylogenetic trees using SSU sequences from cells putatively identified as H. papilio and H. elegans through morphological means in order to confirm the identity of the cells. Results from the investigation into the population structure of protein-coding genes showed an overall low level of diversity between the populations, with some patterns of variation that may indicate the presence or formation of cryptic species, or species that are morphologically identical but genetically distinct. Although these cryptic species do not seem to be diverging across geographical boundaries (i.e. are not separated by bog), they may be diverging based on ecological microhabitat, which has been seen in Arcellinida species (Lamentowicz et al., 2005). A lack of genetic diversity across multiple geographic locations may lower testate amoebae resilience to disasters and can drastically decrease the amount of carbon the peatlands are able to absorb. The phylogeny of H. papilio and H. elegans cells allowed us to confirm the identity of H. papilio and H. elegans cells. This project is a first look into population structure and genetic diversity of these vital eukaryotic microorganisms.


©2021 Clara Rojan Malekshahi Access limited to the Smith College community and other researchers while on campus. Smith College community members also may access from off-campus using a Smith College log-in. Other off-campus researchers may request a copy through Interlibrary Loan for personal




77 pages : color illustrations. Includes bibliographical references (pages 50-57)