This study examines the evolutionary history of the cosmopolitan beaksedge tribe Rhynchosporeae (ca. 386 spp.; Cyperaceae)
using phylogenetics. Taxon sampling covers 25 of the 28 taxonomic sections proposed for the tribe. I compare a history inferred for
Rhynchosporeae using a single plastid gene (Chapter 2) with one inferred using hundreds of loci (Chapter 4). The latter involves a
sequencing methodology I develop with collaborators that can be applied across angiosperms (Chapter 3). Chapter 2 recognizes that
Rhynchosporeae has high levels of endemicity (≥ 44%) in tropical and subtropical American savannas and can provide insights into the
diversification of their biotas. Wind pollination, occupation of a savanna habitat, and a C3 photosynthetic pathway are common in the
tribe, but showy (presumably insect-pollinated) inflorescences, occupation of forest habitat, and a C4 pathway also occur. I reconstructed
a dated phylogenetic hypothesis for 79 taxa, using the trnL/F plastid region, inferring a mean crown-group age of 56 million years. Fitch
parsimony infers the most recent common ancestor (MRCA) to have occupied a savanna habitat with eight or more shifts to forest. Features
associated with insect pollination—white bracts and spikelets—were shown to evolve six or more times but were not correlated with the
shifts to forest habitat where wind pollination is likely to be less effective. I found evolutionary correlations in the pairwise
comparisons of bract color versus spikelet color and bract positioning versus bract color. Members with anatomies associated with C4,
though anatomically variable, form a clade with a crown age of 19 million years. In Chapter 3, with collaborators I develop a robust probe
design process to identify 499 low-copy nuclear regions and 18 high-copy functional genes for hybrid enrichment. We obtained >90%
enrichment success for target regions. Between 159 and 488 orthologs were retained in alignments used for phylogenetic inference at deep
and shallow levels across the angiosperms. A sampling strategy focusing on incremental removal of incongruent loci in combination with
removal of sites with high rates of change produced 196 alignments for phylogenetic inference. The phylogenetic hypotheses at each sample
level represent outcomes under different regions of parameter space. These outcomes were presented using heatmaps that depict bootstrap
support at all nodes for those 196 levels of parameter space. This provided a new approach for sensitivity analyses and for testing the
robustness of any hypotheses. A randomization methodology for hypotheses testing at specific nodes takes advantage of the heatmap
approach. Focusing on the difficult-to-resolve eudicot, monocot, Magnoliid nodes the analysis revealed that the supermatrix approach
produced a spuriously confident yet conflicting result in some regions of parameter space. With >97% of the data, supermatrix analyses
supported eudicot and Magnoliids as sister. Support switched to strongly support the eudicot and monocot sister relationship at higher
levels of data removal. In contrast the coalescent model consistently supported the latter relationship across most of the parameter
space. Overall the eudicot and monocot sister relationship is robustly favored. In Chapter 4, I reexamine beaksedge (tribe Rhynchosporeae
) diversification but employ the anchored hybrid enrichment protocols developed in Chapter 3. A dated phylogenetic hypothesis for 115 taxa
in the tribe and 11 outgroup taxa inferred a mean crown-group age for the tribe of 43.2 million years. Ancestral state reconstruction
using stochastic mapping infers an open (savanna) habitat for the MRCA. This was the common state along 77% of the total branch lengths.
However, there was an average of 22 independent shifts from open habitats into forest understory or edges in its descendants. The common
state was the typical seasonally wet savanna soils. The state associated with their occurrence in dry, well drained soils was
reconstructed for 4% of the total branch lengths, but there was an average of 11.2 transitions to that state. There were 3.7 transitions
to the state where plants typically occur in standing or flowing water. An average of 5.9 transitions from nondescript brown or green
inflorescences associated with wind pollination to those associated with insect pollination (white spikelets and/or bracts) were inferred
but these were not correlated with the shifts to forest habitat. Members with C4 anatomy formed a clade that diverged from a sister clade
containing taxa with C3 photosynthetic anatomies 26 MYA; this is earlier than previously thought. Most of the taxonomic sections described
by Shirley Gale and Georg Kükenthal for Rhynchospora and Pleurostachys were not monophyletic. I also briefly discuss the possible
significance of detecting a recently described repetitive satellite DNA element known to be associated with the centromeric protein
CENH3. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the Doctor
of Philosophy. / Fall Semester 2016. / November 14, 2016. / Anchored Phylogenomics, Angiosperms, evolution, photosynthesis, pollination, Rhynchospora / Includes bibliographical references. / Austin Mast, Professor Directing Dissertation; William Parker, University Representative; Alice
Winn, Committee Member; Scott Steppan, Committee Member; Brian Inouye, Committee Member.
| Identifer | oai:union.ndltd.org:fsu.edu/oai:fsu.digital.flvc.org:fsu_405667 |
| Contributors | Buddenhagen, Christopher E. (Christopher Evan) (authoraut), Mast, Austin R. (professor directing dissertation), Parker, William C., 1952- (university representative), Winn, Alice A. (committee member), Steppan, Scott J. (committee member), Inouye, Brian D. (committee member), Florida State University (degree granting institution), College of Arts and Sciences (degree granting college), Department of Biological Science (degree granting departmentdgg) |
| Publisher | Florida State University, Florida State University |
| Source Sets | Florida State University |
| Language | English, English |
| Detected Language | English |
| Type | Text, text |
| Format | 1 online resource (183 pages), computer, application/pdf |
| Rights | This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s). The copyright in theses and dissertations completed at Florida State University is held by the students who author them. |
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