Dissertation
Phylogeography and population genetics of Carex macrocephala, and the molecular evolution of Carex subgenus Vignea
Washington State University
Doctor of Philosophy (PhD), Washington State University
12/2007
DOI:
https://doi.org/10.7273/000005704
Abstract
Nuclear ribosomal DNA (nrDNA) has been used for more than a decade in species level phylogenetic analyses. While nrDNA can often be a powerful phylogenetic marker, intra-individual polymorphisms of the internal and external transcribed spacers (ITS, ETS) can lead to problems in their use for phylogeny reconstruction. Through comprehensive cloning we identified high levels of intra-individual polymorphisms and in many cases this led to the polyphyly of individuals of Car ex subgenus Vignea. We suggest that nrDNA contains multiple paralogs in many species and clades within Vignea which greatly complicates its use for phylogenetic inference and future studies in Carex need to take this into account. A drawback to phylogenetic based phylogeographic analyses is that they do not account for stochastic lineage sorting that occurs between gene divergence and lineage divergence. Gene divergence (D) begins prior to the split of the lineages (t), and the difference between D and t are not accounted for in phylogenetic analyses. In contrast, coalescent-based statistical methods have been developed which can account for the stochastic forces which drive population divergence, and can account for the lineage sorting that occurs prior to lineage divergence. We fit a molecular dataset, consisting of the rpL16 marker and 8 microsatellite loci, to the isolation with migration model as implemented in IMa to test the well-supported phylogenetic hypothesis of relationships within the Carex macrocephala species complex (Cyperaceae). By comparing the relative divergence time of the three main lineages within this group, Asian C. macrocephala, North American C. macrocephala, and C. kobomugi, we concluded the phylogenetic hypothesis is incorrect, and the divergence between these lineages occurred during the late Pleistocene epoch. Population genetic analyses of the rpL16 marker and 11 microsatellite loci suggest a high level of inbreeding, but also high levels of migration across the west coast of North America (NA). The standardized Gst value is low at 0.032, and AMOVA results show significant amount of variation across all grouping levels. A principal coordinate analysis (PCoA) suggests panmixia across the NA coast, however the high levels of inbreeding suggest this may be an artifact of metapopulation dynamics.
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Details
- Title
- Phylogeography and population genetics of Carex macrocephala, and the molecular evolution of Carex subgenus Vignea
- Creators
- Matthew George King
- Contributors
- Eric Roalson (Chair) - Washington State University, School of Biological Sciences
- Awarding Institution
- Washington State University
- Academic Unit
- School of Biological Sciences
- Theses and Dissertations
- Doctor of Philosophy (PhD), Washington State University
- Publisher
- Washington State University
- Number of pages
- 122
- Identifiers
- 99901054940001842
- Language
- English
- Resource Type
- Dissertation