Sea levels fluctuated following glacial cycles during the Pleistocene, reaching approximately 115-130m below current sea levels in the Indian and Pacific Oceans during the last glacial maximum 17,000 years before present. The effects of these sea level fluctuations on population structure have been shown in many near-shore marine taxa, revealing several common patterns. However, the underlying mechanisms behind these observed patterns are largely unknown. Drops in sea level affect the distribution of shallow marine biota, exposing the continental shelf on a global scale, and displacing coral reef habitat to steep slopes where shelf breaks are shallow. In these circumstances, we expect that species inhabiting lagoons should show reduced genetic diversity relative to species inhabiting more stable outer reefs. Here, I tested this expectation on the scale of an entire ocean-basin with four wrasses (genus Halichoeres): H. claudia (N=194, with ocean-wide distribution) and H. ornatissimus (N=346, a Hawaiian endemic) inhabit seaward reef slopes, whereas H. trimaculatus (N=239) and H. margaritaceus (N= 118) inhabit lagoons and shallow habitats throughout the Pacific. Two mitochondrial markers (cytochrome oxidase I and control region) were sequenced to resolve population structure and history of each species. Haplotype and nucleotide diversity were similar among all four species. The outer reef species showed significantly less population structure, consistent with longer pelagic larval durations and a historically stable population. Mismatch distributions and significant negative Fu’s F values indicate Pleistocene population expansion for all species, and (contrary to expectations) reduced genetic diversity in the outer slope species. These data indicate that lagoonal species may persist through the loss of habitat, but are restricted to isolated refugia during lower sea level stands, which may inflate genetic diversity during high sea levels. Outer reef slope species on the other hand have homogeneous and well-connected populations through their entire ranges regardless of sea level fluctuations. These findings contradict the hypothesis that shallow species are less genetically diverse as a consequence of glacial cycles. / text

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As deleterious variants continually arise in a population, they tend to be purged via purifying selection, leading to distortions in the shapes of genealogies relative to neutral expectations. In recent years, a mounting body of evidence has arisen suggesting that this can have significant implications for the patterns of diversity seen in natural populations. However, existing theory has not yet fully characterized the effects of these distortions on the structure of genealogies. The focus of this thesis is on exploring this gap, and developing an analytical description of the distortions that arise in genealogies due to purifying selection. / Physics

No description available.

The evolution of three genes from the CONSTANS-LIKE gene family is studied in Brassica nigra. We use a combination of population genetic and phylogenetic techniques in order to assess the relative importance of selection and demography on the pattern of DNA variation. The analysis is complicated by the fact that they are recent duplicates of each other and hence there is a potential redundancy factor that has to be considered. The relationship between two of the genes, COa and COb, is however much closer than between any relationship to the third gene, COL1. The three genes are all suspected to play a part in the natural variation of flowering time of B. nigra. The thesis consists of four papers. The first paper is a technical paper concerning when and if the existence of an effective population size can be assumed. More specifically, the impact of population structure and a fluctuating (census) population size on the standard coalescent is studied. The second paper is a population genetic study of B. nigra using micro-satellites and RFLP. The resulting population genetic structure is argued to reflect the early spread of agriculture in Europe. In the third paper the general evolution of the three genes is studied. We find that not all aspects of the data could be accounted for by demography or redundancy effects, but that selection most likely played a part in the evolution of these genes. The fourth paper concerns the functional status of COb, whether it is a pseudogene or not. The most likely scenario is that COb recently became non-functional due to the fixation of a deleterious mutation during a recent bottleneck.

This thesis describes a search for DNA polymorphisms at the HEXA locus as well as the characterization of three Tay-Sachs disease (TSD) mutations in the Chinese population. / No polymorphisms were detected in the HEXA gene by three different methods: (1) Southern blotting; (2) PCR amplification and restriction enzyme digestion of intronic sequences; (3) single strand conformational polymorphism (SSCP) analysis of introns. The apparent deficiency of accessible polymorphisms is a handicap in studying the origin, distribution, and frequency of mutant HEXA alleles in human populations. / I have characterized five of six infantile TSD alleles segregating in three unrelated Chinese families in which there is no known consanguinity. Two of the mutations described are novel, the third is a transition previously reported in an Italian patient (Nakano et al, 1988). / The two novel mutations occur in homozygous form in the affected individuals investigated. They are: (1) an insertion of an A at nucleotide 547 (Family 1) and (2) a T1453C transition (Family 2). (Abstract shortened by UMI.)

The biology of the sub-aquatic lichen, Dermatocarpon luridum, was investigated. This lichen is sparsely distributed within the temperate climatic zones around the world, colonizing rock along watercourses that regularly experience water level fluctuations. Specimens collected from Canada and Austria were cultured using standard growth media. Brightfield microscopy was used for algal species identification, while fungal ITS, algal ITS and algal actin gene sequences were used for phylogenetic and population genetic evaluation. Results were: 1) axenic cultures of the photobiont were successful, while those of the mycobiont were not successful; 2) Diplosphaera chodatii is the photobiont associated with D. luridum var. luridum and allies, suggesting algal sharing between mycobiont species; 3) genetic diversity is high, and gene flow was high within local populations, but low between continental populations. Diplosphaera chodatii may be a keystone species contributing to the survival of D. luridum var. luridum along with other sub-aquatic, aquatic and terrestrial lichens.

Natural hybrid zones provide opportunities to study a range of evolutionary phenomena from speciation to the genetic basis of fitness-related traits. Additionally, investing the structure of hybrid zones can provide valuable insight in the ecology and evolution of species. The present dissertation approaches the investigation of natural hybrid zones between Xiphophorus birchmanni and X. malinche from a population genetics perspective. The goal of the chapters herein are to investigate the genetic structure of these natural hybrid zones overall and the genetic structure of the populations within them in an effort to better understand the factors producing and maintaining spatial genetic patterns among this species pair and their hybrids. Using informative single nucleotide polymorphisms (SNPs) in one mitochondrial and three nuclear intron loci, I show that hybrid zones occur in replicated fashion in multiple stream reaches along a gradient from high to low elevation. Tests of FIS and linkage disequilibrium (LD) revealed significant genetic structure within a small subset of populations. Specifically, parentals and hybrids all three occur in some locations while other locations appear to be hybrid swarms. I then investigated a behavioral mechanism of reproductive isolation - social association, which might affect population structure. In clean water, individuals shoaled significantly more closely with conspecifics. Additionally, genotyping of females and their embryos revealed signatures of non-random mating in structured populations. Taken together, assortative social grouping, which may translate to assortative female mate choice, likely plays a role in maintaining population structure. Finally, I show that fluctuating asymmetry is significantly higher in unstructured than structure populations. This is a further indication that some form of non-random mating occurs in structured populations and has effects on male phenotypes.

Ancient DNA (aDNA) was isolated from the bones of 290 individuals and four species of extinct New Zealand moa. All sampled bones had been recovered from a small geographic area (~10 km radius) near Waikari in North Canterbury. A total of 217 specimens were 14C-AMS dated, providing a temporal framework for the genetic analyses and an unprecedented opportunity to study extinct megafauna at the population level. Taxon and sex were determined for each individual, using aDNA technology. This revealed a large excess of females (overall ♂:♀ = 1:5.1), and significant compositional differences for the moa assemblages between fossil sites. Balanced sex ratios were observed among juvenile moa, suggesting that a gender-bias developed as the birds matured, probably as a result of higher male mortality. Female territoriality and ecological niche-separation are discussed in this context. Mitochondrial DNA (mtDNA), amplified using a quantitative PCR procedure, provided a measure of DNA preservation in each radiocarbon-dated fossil. This assessment showed that DNA degrades over thousands of years according to an exponential decay model, and the average molecular half-life for the here targeted DNA fragment was estimated to be 521 years. By using high-throughput sequencing, six polymorphic moa microsatellite markers were identified and characterised. These are the first microsatellite primers developed exclusively for extinct taxa. A high-resolution genetic study of the four sympatric moa populations was carried out, combining information from mtDNA, microsatellites, sex-identification, and radiocarbon age. Genetic diversity, past demography, kinship, and other aspects of moa biology were analysed. The populations showed a remarkable extent of genetic stability throughout the 3000-4000 years preceding their extinction, suggesting that they were large and viable before suddenly disappearing. The results represent significant advances in aDNA research and thanks to the high resolution in microsatellite markers, moa have here been studied, almost as if they were still alive.

Pattern of Linkage Disequilibrium (LD) is a major factor largely determining the power of association mapping studies. Along with nucleotide diversities and DNA polymorphism, knowledge of patterns of LD along the genome needs to be to known to effectively design association mapping studies. In this study, patterns of nucleotide diversity, population structure, LD was estimated in Norway spruce (Picea abies). The data used for this were 23 nuclear loci sequenced in around 90 individuals originating from natural populations of Norway spruce throughout the current distribution range in Sweden and Finland. The observed levels of nucleotide diversity are variable among loci varying between 0.002 and 0.008 if measured by average pairwise nucleotide diversity. Despite the samples stretching large part of Finland and Sweden there were no evidence for strong population structure. As in earlier studies LD decays fast with distance and the average pattern of the squared correlation of allele frequencies drops to less than 0.2 within 100bp. In order to put the data in perspective previously generated data sets were re-analyzed and compared to the inferred results.