Molecular Phylogeny and Evolution of Dogwoods
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2004-02-04
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Abstract
Dogwoods consist of morphologically diverse plants, and taxonomic circumscription and phylogenetic relationships of dogwoods have long been controversial. My dissertation study has two major goals: 1) elucidate phylogenetic relationships in the dogwoods group using nuclear DNA sequences, and 2) investigate the sequence evolution and its morphological link of the myc-like anthocyanin regulatory gene and explore the phylogenetic utility of the gene in dogwoods. Phylogenetic relationships within Cornus and Cornales (Cornus and related genera and families) were previously investigated using chloroplast DNA sequence data in several studies, but these still remained incompletely resolved. I used nuclear 26S rDNA sequences to further elucidate relationships within the group and to corroborate previously published phylogenetic hypotheses based on cpDNA and morphological data. Phylogenetic analyses of 26S rDNA sequence data (~3.4 kb) in combination with sequences of chloroplast genes rbcL and matK, suggest that the aquatic enigmatic genus, Hydrostachys from southern Africa, is sister to the remainder of Cornales among which Cornus and Alangium are sisters, nyssoids (Nyssa, Camptotheca, and Davidia) and mastixioids (Mastixia and Diplopanax) are sisters, and Hydrangeaceae and Loasaceae are sisters. These relationships, except the placement of Hydrostachys, are consistent with previous findings from analyses of matK-rbcL sequence data. Within Cornus, the dwarf dogwoods (subg. Arctocrania) are the sister of the big-bracted dogwoods (subg. Cynoxylon and subg. Syncarpea). This clade is, in turn, sister to the cornelian cherries (subg. Cornus and subg. Afrocrania). This large red-fruited clade is sister to a clade consisting of the blue- or white-fruited species (subg. Mesomora, subg. Kraniopsis, and subg. Yinquania). Within latter clade, C. oblonga (subg. Yinquania) is sister to the remainder, and subg. Mesomora is sister to subg. Kraniopsis. These relationships are congruent with those suggested by cpDNA sequences data, but with greater statistical support when the cpDNA data are combined with nuclear DNA sequences.
To accomplish the second goal, the entire sequences (~4 kb) of the myc-like anthocyanin regulatory gene were sequenced for nine species of Cornus representing all four major clades of the genus and 47 samples of the dwarf dogwood species complex. Our phylogenetic analyses of sequences indicate that the myc-like anthocyanin regulatory gene is phylogenetically useful at different taxonomic levels depending on the data set (nucleotide vs. protein sequences) and regions (exons vs. introns) applied. Amino acid sequences are useful to resolve relationships among families of flowering plants, whereas nucleotide sequences from the coding region are useful to resolve relationships among subgroups of Cornus and DNA sequences of the entire gene are informative among closely related species within subgroups of Cornus. Sequence evolution of the gene was examined using a codon-based substitution model and population genetic methods. All results indicate accelerated sequence evolution of this gene at both interspecific and intraspecific levels. Mosaic evolution and heterogeneous rates in DNA sequence were detected among the four functional domains and among sites. The interaction domain, involving an important function, has the lowest ratio of nonsynonymous and synonymous substitution rate, suggesting the strongest evolutionary constraint. The acidic domain evolves most rapidly among four domains. In the bHLH domain, the key residues are conserved among all species examined, although its evolutionary rate is faster than that of the interaction domain. Most changes in this domain occur in loop region and among amino acids with similar chemical features. Furthermore, sites under positive selection were detected. Nucleotide diversity and neutrality tests of DNA sequences suggested that an excess of low-frequency polymorphisms and an excess of replacement substitutions exist within the dwarf dogwoods complex. Positive selection and/or recent, rapid population expansion are the main forces acting on the accelerated gene evolution and result in an excess of low-frequency polymorphism. Significant correlation between petal color and amino acid sequence variation in the dwarf dogwoods complex was detected by ANOVA analyses using GLM model. Substitutions at three amino acid sites are significantly associated with petal color, which suggests that the mutation at these sites may result in changes of protein function, and are thus responsible for the color change in flowers. Extensive gene flow, gene recombination, and introgression were also detected within the dwarf dogwoods complex, suggesting a dynamic evolutionary process within the dwarf dogwoods.
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Molecular evolution, 26S rDNA, Cornale, Cornus, Molecular phylogeny, myc-like anthocyanin regulatory gene, Positive selection
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Degree
PhD
Discipline
Botany
