The transition from cross-fertilization to predominant self-fertilization is considered the most common evolutionary transition in flowering plants. This change in mating system has profound influences on the amounts and patterns of genetic diversity within and among populations, and on key genetic and demographic processes. The main goal of my thesis is to determine the molecular population genetic consequences of this transition in the annual neotropical aquatic plant Eichhornia paniculata (Pontederiaceae) using DNA sequence from individuals sampled from throughout the species’ geographic range. Populations exhibit a wide range of mating patterns associated the evolutionary breakdown of tristyly facilitating specific contrasts between outcrossing and selfing populations. Analysis of molecular variation supported the hypothesis of multiple origins of selfing, including the evolution of two morphologically distinct selfing variants from Central America and the Caribbean. A survey of 10 nuclear loci from 225 individuals sampled from 25 populations demonstrated the joint influence of mating system, population size and demographic bottlenecks in affecting patterns of nucleotide variation. Small selfing populations exhibited significantly lower genetic diversity compared with larger outcrossing and mixed mating populations. There was also evidence for higher population differentiation and a slower decay of linkage disequilibrium in predominately selfing populations from the Caribbean region. Coalescent simulations of the sequence data indicated a bottleneck associated with colonization of the Caribbean from Brazil ∼125,000 years ago. To investigate the consequences of transitions from outcrossing to selfing across the genome, I used high-throughput, short-read sequencing to assemble ~27,000 ESTs representing ∼24Mbp of sequence. Characterization of floral transcriptomes from this dataset identified 269 genes associated with floral development, 22 of which were differentially expressed in three independently derived selfing lineages compared to an outcrossing genotype. Evidence for relaxed selection in selfing lineages was obtained from an analysis of a subset of ~8000 orthologous sequences from each genotype, as predicted by theory. Selfing genomes showed an increase in the proportion of nonsynonymous to synonymous changes and relaxation of selection for codon usage bias. My thesis represents the most detailed investigation to date of the molecular population genetic consequences of intraspecific variation in the mating systems of plants.

2 PDF files included one for title page and one for main document Title from title page PDF (University of Missouri--St. Louis, viewed February 8, 2010). Includes bibliographical references.

Thesis (Ph. D.)--University of Texas at Austin, 2001. / Vita. Includes bibliographical references. Available also from UMI Company.

Thesis (Ph. D.)--University of Chicago, Committee on Evolutionary Biology, August 2003. / Includes bibliographical references. Also available on the Internet.

Not available / text

Barramundi (Lates calcarifer) is a centropomid teleost with a wide distribution across the Indo Pacific. In Australia, barramundi are native to the tropical zone from Exmouth Gulf in Western Australia, across the northern part of the continent, to the Mary River in Queensland. Barramundi are protandrous hermaphrodites, and are euryhaline, with a catadromous life history. Barramundi are a valuable Australian resource, with important commercial and recreational fisheries and aquaculture production to the value of $11 million dollars per year. Recent declines in the availability of the fish in some rivers has led to an interest in the possibility of restocking rivers with barramundi from other areas. Determining the genetic structure of barramundi populations in Australia is important for understanding biogeographic history, and appropriate management practices for both aquaculture and recreational and commercial fishing. Previous studies have concentrated on the east coast of Australia, and have largely ignored the western populations. In this study, I obtained DNA data from barramundi populations across the Australian range of the species, as well as populations from Papua New Guinea and Indonesia. The aims of this study were to use the genetic data to determine: 1. if populations in Western Australia show genetic differences between geographic regions 2. if these populations show an ancestral split from populations in the east of Australia and 3. the ancestral origins of Australian barramundi. Previous studies of DNA data from barramundi have discovered an east/west split occurring at the Torres Strait that was assumed to be caused by the closing of the strait during lowered sea levels. However, these studies suffered from a bias in sampling area, concentrating either on the eastern half of the range of barramundi, or on the western tip of the range. Data from these studies were combined and reanalyzed. Two major clades were discovered, with considerable biogeographic structuring, but their geographic locations did not coincide with the reported vicariance event at the Torres Strait. Instead, historical divisions among freshwater drainage systems appeared to have driven the evolutionary history of barramundi in Australia. In order to investigate these historical divisions further, a 290 bp section of the mitochondrial DNA control region was sequenced in 284 barramundi from seven populations across the Australian geographic range of the species and from one population in Papua New Guinea and one population in Indonesia. Analyses of molecular variance within and among populations showed significant geographic structuring, based on biogeographical provinces and drainage divisions. Nested clade analyses indicated that these geographical associations were the result of restricted gene flow, range expansion, and past fragmentation events. I hypothesise that the Ord River area in the west of the continent was the ancestral source population for the rest of the species’ range across Australia, with Indonesia being the most likely origin of this source. Populations of barramundi from the Pilbara region are genetically distinct and geographically isolated, with strong evidence of an ancestral divide along geographical barriers to dispersal. There is a strong association between Papua New Guinea and Australia, although further investigations using the cytochrome b region of mitochondrial DNA indicated a more ancestral divide between the two than is currently evident, which could reflect an ancient geographical divide between the two, or could be evidence of a secondary migration route to Australia. For a more detailed study of evolutionary processes acting on populations of barramundi in Western Australia, allelic diversity was examined at five microsatellite loci. All loci were polymorphic and genotypic frequencies conformed to Hardy-Weinberg expectations, with no significant linkage between loci evident in any population. Measures of within population diversity were significantly related to latitude, suggesting southerly migration from a northern source population. The Ord River was the most genetically diverse population, and the most likely ancestral migration source to the area, with diversity decreasing down the west coast. Although there were significant differences among populations, the nuclear microsatellite data do not indicate the same degree of genetic structuring as is evident in the mitochondrial data. This may be a consequence of rapid evolutionary change at microsatellite loci, with past separations or population differences masked by recombination and back mutation of the microsatellite alleles. However, the nature of nuclear and mitochondrial inheritance may also indicate life history differences between the sexes, where significant genetic contribution to gene flow by males and limited female gene flow may lead to preservation of maternally inherited population substructure. The principal findings from this study are: • There is no genetic evidence for an east/west division of barramundi populations in Australia, as suggested by previous research. • Despite barramundi’s catadromous life history, and ability to disperse through marine waters, the present genetic structure indicates a division principally among river drainages. From a population genetic viewpoint, the species can be regarded as freshwater, rather than marine. • The most likely origin of barramundi in Australia is the Ord River region, with Indonesia as the route of migration. • Differences in the population structure demonstrated by nuclear and mitochondrial data indicate possible life history differences between the sexes. • Barramundi populations in different biogeographical provinces may have been substantially isolated over a long period of time, and may therefore represent independently evolving populations. This has important implications for fishery management and translocation issues for restocking rivers.

Thesis (Ph. D.)--University of Canterbury, 2009. / Typescript (photocopy). Includes bibliographical references (p. 139-143) and index. Also available via the World Wide Web.

Thesis (Ph.D.)--Michigan State University. Genetics, 2008. / Title from PDF t.p. (viewed on July 13, 2009) Includes bibliographical references (p. 90-103). Also issued in print.

Thesis (Ph. D.)--University of Chicago, Committee on Developmental Biology, March 2003. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of Chicago, Committee on Evolutionary Biology, December 2000. / Includes bibliographical references. Also available on the Internet.