Comprehensive systematic approaches to understanding species diversity: a case study utilizing a non-model group of sedges, Carex sect. Acrocystis (Cyperaceae)
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Poindexter, Derick Bret. Comprehensive Systematic Approaches to Understanding Species Diversity: a Case Study Utilizing a Non-model Group of Sedges, Carex Sect. Acrocystis (cyperaceae). 2019. https://doi.org/10.17615/nkz2-9v93APA
Poindexter, D. (2019). Comprehensive systematic approaches to understanding species diversity: a case study utilizing a non-model group of sedges, Carex sect. Acrocystis (Cyperaceae). https://doi.org/10.17615/nkz2-9v93Chicago
Poindexter, Derick Bret. 2019. Comprehensive Systematic Approaches to Understanding Species Diversity: a Case Study Utilizing a Non-Model Group of Sedges, Carex Sect. Acrocystis (cyperaceae). https://doi.org/10.17615/nkz2-9v93- Creator
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Poindexter, Derick Bret
- Affiliation: College of Arts and Sciences, Department of Biology
- Abstract
- For nearly two and half millennia we have struggled to characterize life on earth. In the face of our current global extinction crisis, this effort attains even greater urgency. While methods to characterize significant biological units naturally began with morphology, hinging on the evolutionarily derived innate computational capabilities of the brain based on visual cues, our cognitive growth and technological advancements have provided us with new tools and also caused us to consider more complex paradigms as to what constitutes a species. Phylogenetic tools aiding this process of biodiversity exploration are in the midst of an adaptive radiation. While massive datasets derived from whole genome sampling have become a mainstay, rapid cost-effective SNP-based methods of inquiry are being explored using various approaches to examine their resolving potential. For many non-model groups in larger and taxonomically difficult clades, these applications are paramount, as determination of interspecific relationships remains untenable utilizing traditional Sanger Sequencing methods. SNP-based methods serve as a practical alternative to examine broader variation with greater accuracy than ever before. Despite these emerging capabilities, ideal taxonomic decisions are contingent upon an “all available evidence” approach to minimize subjectivity and to generate informed hypotheses with all forms of data in tandem. These lines of evidence are the cornerstone of a General Lineage Concept of species. In this dissertation I apply multiple lines of evidence to disarticulate species units within a plant group, Carex section Acrocystis (Cyperaceae), a clade largely endemic to North America. I first generated an initial understanding of species concepts by examining type specimens and ca. 6000 specimens loaned from numerous herbaria. In Chapter 2, I explore chromosomal diversity within this section. While largely lacking in this group, basic cytogenetic data is of elevated importance in Carex due to the presence of holocentric centromeres and subsequent symploidy and agmatoploidy that alter chromosome number within species, often without appreciable changes in total genomic content. I made 158 new counts for this group to evaluate variation and taxonomic utility of this data. In Chapter 3, I examine species relationships with section Acrocystis using a Next Generation Sequencing approach. Whole genomic DNA were extracted from all available representatives of the section, as well as outgroups. NextRAD sequencing was performed to gather SNP-based loci and then utilized for de novo reference library construction and sample alignments. Clade reconstruction beginning with a total inclusive analysis (i.e., including the most removed outgroup members) was conducted, followed by successive de novo reference generation and subclade analyses selected from the most well-supported preceding dichotomies gauged with standard Maximum Likelihood Bootstrap values and Bayesian Posterior Probabilities. This iterative approach was followed until the terminal-most clades were mostly resolved. The results of this method were compared to previous studies to demonstrate efficacy. Several taxa demonstrated topological fluidity based on successive analyses, likely attributable to hybrid speciation. In Chapter 4, I narrow my focus on a group of closely related and mostly undescribed species. I initially identified clades containing putative novel taxa based on the large-scale phylogenetic analyses described above. A single clade of interest, the Carex novae-angliae Species Complex, was selected for exhaustive interrogation. I selected a subset of the multitude of recently developed SNP-based methods for examining potential short-comings in tree topology inference (SVD-Quartets), as well as a procedure for evaluating directional historic and contemporary introgression (DFOIL) based on a five-taxon tree. I incorporated morphometric analyses and PCA of micro- and macromorphological features, chromosome data, biogeographic distributions, and descriptive ecology to further support the taxonomic recognition of 4 new species. Lastly, in Chapter 5, I reevaluate the taxonomy and nomenclature of section Acrocystis as informed by all available evidence. To facilitate future taxonomic efforts and nomenclatural organization, I assessed ca. 242 names for members of this group, located most type material, provided necessary lectotypifications, and synthesized this information.
- Date of publication
- 2019
- Keyword
- DOI
- Resource type
- Advisor
- Weakley, Alan S.
- Gabrielson, Paul W.
- Naczi, Robert F.C.
- Peet, Robert K.
- Vision, Todd J.
- Degree
- Doctor of Philosophy
- Degree granting institution
- University of North Carolina at Chapel Hill Graduate School
- Graduation year
- 2020
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