No description available.

In Part 1 the complex subject of biological evolution is introduced. An outline of scientific ideas on evolutionary change, concentrating on theories developed during the nineteenth and twentieth centuries, is followed by a brief biological description of heredity. In Part II a population genetics problem is examined.

The aims of this DPhil were the characterisation of major histocompatibility complex class II β loci in the amphibian species Bufo calamita, determination of fitness of four Bufo calamita populations and measurement of genetic diversity at both microsatellite loci and MHC class II β loci. The genetic diversity at microsatellite loci is considered to be neutral to selection and the genetic diversity seen at MHC loci is adaptive. Fitness in the four populations was measured using the known larval fitness traits age at metamorphosis, growth rates and survival. A 114 base pair section of MHC class II loci was characterised in this study. It was shown here that the diversity at neutral microsatellite markers was negatively correlated with adaptive MHC class II variation. No correlation was found between microsatellite HE and the larval fitness traits growth rate, survival and age at metamorphosis. However, MHC class II diversity was found to be associated with survival, and individuals that were heterozygous at both MHC loci had a significantly higher chance of survival than individuals homozygous at one or both of the two loci. A separate part of this DPhil project was the population genetics of six Irish Bufo calamita populations. The genetic structure was investigated using nine polymorphic microsatellite markers. It was found that all populations had similar and moderate levels of genetic diversity, comparable with those on the coast of north-west England. Toad populations were substantially differentiated, implying little migration between sites within historical times. Phylogenetics and estimates of divergence times supported the hypothesis that populations on the north coast of Dingle separated from those around Castlemaine Harbour many thousands of years ago, and are not recent introductions.

This study examined the hypothesis that natural selection exerts control of the human sex ratio via allelic variation in an autosomal gene that is phenotypically expressed in the male reproductive system. The hypothesis was supported by results from an analysis of a large genealogical dataset, in which inheritance of sex ratio variation by male but not female offspring was found. A series of simulations with a population genetic model showed that equality of the sex ratio may be maintained in a dynamic equilibrium by frequency dependent selection acting on such a gene. These simulations also suggest that long-term oscillations and autocorrelation between years in annual human sex ratio data may be explained by the hypothesis. A further set of simulations showed that an episode of increased male mortality - in a population with a sex ratio determined by the proposed gene - may result in a sudden increase in male births, provided the mortality is limited to a narrow cohort of males and that families with a greater tendency to have male offspring tend to be larger than those with a tendency to produce equal male and female offspring. To explore whether this could provide an explanation for significant increases in male births observed during periods of war, military service records and genealogical data were examined to determine the age structure of recruits to the British Army in the First World War and the typical age of fatherhood at the time. It was found that the cohort of men lost to the war were younger than men who typically became fathers. It was also found that families with offspring of a single sex tend to be larger than those with both sexes. As such, this work supports the hypothesis that the loss of young men in war results in a relative increase in male births, due to increased fatherhood by men from families with more male offspring (i.e. men with more brothers than sisters), because these men are most likely to have inherited a greater tendency to produce male offspring.

The role of embryology, genetics and morphology within mid twentieth century evolution theory, is discussed in the context of the growth to dominance of natural selection as the orthodox mechanism of adaptive evolution. The unification of neo-Mendelian heredity and neo-Darwinian selection theory, is descnbed as the core of modern synthetic neo-Darwinism as it emerged in 1930s mathematical population genetics. As selectionism strengthened within synthetic neo-Darwinism, embryological development was excluded from its traditional causal role in adaptive evolution within the "old synthesis" of Haeckelian recapitulation and neo-Lamarckian inheritance. A two-tier embryology was created, as embryology was understood to deal separately with the experimental analysis of ontogenetic development, and the historical descriptive analysis of phylogenetic lineages. Neither tier informed the other, or played any direct causal role in the mechanism of the creation of adaptive evolutionary novelty. That adaptive evolutionary mechanism was entirely the preside of natural selection. However, as the selectionist synthesis hardened in the 1940s, late nineteenth century Darwinists' concerns over the hereditary fixation of highly specific adaptive somatic modifications resurfaced. Consequently, the strategic defence of the synthetic theory against any resurgence of neo-Lamarckian heredity, involved an appeal to the principles of modem synthesis developmentalism; namely, the developmentalist syntheses of Waddington and Schmalhausen. The unforeseen implication of these moves by founding supporters of the synthetic theory, was that the disciplines upon which 1940s developmentalism rested--namely, Western chemical embryology and Soviet evolutionary morphology--did after all playa central and causal role in the mechanism of adaptive evolution. Attempts to characterise the alternative and developmentalist syntheses of Waddington and Schmalhausen as the "missing links" to an otherwise incomplete modem synthesis, are historically evaluated. These attempts are thought to embody either a mistaken understanding of the essential nature of synthetic neo-Darwinism, or an obfuscation of the continuing issue of its synthetic adequacy.

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The coast of South Africa is situated between the warm Indian and the cold Atlantic Oceans, resulting in an extreme intertidal temperature gradient and potentially strong opposing selection pressures between the east and west coasts. Several intertidal biogeographic divides have been identified, including one at Cape Point between the cold west coast and the temperate south coast provinces. However, few studies have investigated the effects of these opposing environments on phylogeography or gene flow in intertidal organisms. A small intertidal sea star, Parvulastra exigua, was chosen as a model organism to investigate these issues. Taxonomic confusion in this species and its systematic relationship with a related South African Parvulastra species, Parvulastra dyscrita, was resolved using nuclear (Actin intron sequences and AFLP) and mtDNA molecular markers. At least one cryptic species was identified within Parvulastra in South Africa, which occupied an extremely restricted geographic distribution and therefore may be a candidate for conservation. Molecular and morphological evidence confirmed that P. exigua and P. dyscrita are separate species. An ecological survey was conducted on P. exigua at 19 locations in South Africa covering a distance of 2500 km. P. exigua samples from each location were sequenced for mtDNA and screened for 421 AFLP loci. AFLP was also used to identify outlier loci that were potentially under selection. An 'unmottled' colour morph was distributed from the Namibian border to Cape Point and a 'mottled' morph was distributed from Cape Point to the Mozambique border, with an area of sympatry around Cape Point. The unmottled morphs were positively influenced by under boulder and bare rock habitats, but negatively affected by canopy, coralline algae and sand. Mottled morphs were positively influenced by under boulder, protected habitats, encrusting algae and bare rock, and negatively affected by algal tufts and sand. MtDNA revealed two divergent, reciprocally monophyletic clades, one comprising the east coast samples and the other encompassing the west coast samples. Both clades showed evidence for a recent, rapid population expansion. The genetic break-point was located on the south coast, but did not coincide with the divergence in colour morphs, being approximately 500 km to the east. AFLP indicated a strong isolation by distance pattern of genetic structure among sampling locations and did not recapitulate the mtDNA genetic divide. Such incongruence among data sets might be caused by a vicarance event if sea level changes separated the east and west coast populations, which expanded in isolation, followed by secondary contact, restoring present day gene flow between the coasts. Population genomic analysis revealed approximately 7% of the genome to potentially be under divergent selection, and the phenotype frequencies of the 'diverging outlier loci' revealed high directionality (spatial correlation). This suggests strong selection pressures between the east and west coasts may be acting on these loci, which could have arisen when the populations were in allopatry. The habitat and colour morph differences of P. exigua between the two coasts are potentially also influenced by selection. However, the isolation by distance pattern indicates that divergent selection pressures are not strong enough to cause reproductive isolation, or disrupt gene flow between the east and west coast populations.

Infectious disease can affect the demography of natural populations and, as a consequence, can alter the genetic variation within and between those populations. This study investigated long-term effects of rabies-induced mortality on the demography and genetic variation in two Swiss red fox populations over ten to fourteen generations. In Switzerland, the last rabies epizootic persisted from 1967 to 1999 and was continuously monitored by collecting fox carcasses throughout the country. Alongside records of rabies tests and post-mortem data, tooth samples were systematically archived for ageing. In this study, DNA from 666 individual teeth was extracted. For 279 extracts, the concentration of nuclear DNA was estimated in a quantitative PCR and found to be negatively correlated with storage time. After excluding samples with insufficient DNA concentration for reliable genotyping, 382 samples were screened using between nine and seventeen canine and red fox specific microsatellites. Tooth samples were combined with 189 modern tissue samples. By assessing the age structure continuously throughout and after the rabies epizootic for the first population, population census size and age structure were found to be altered by the high rabies-induced mortality. In contrast, no long-term trends in genetic diversity were identified although a high variation of Ho, He, F s was discovered both in short-term and longer-term. A strong isolation-by-distance pattern was revealed for the second population by comparing individual pairwise genetic with spatial distances using modern samples. Furthermore, genetic data demonstrated that dispersal was sex-biased and diverted by the topography of the landscape. When investigating isolation-by-distance patterns within the same population in 1971-73 and 1982-84 at lower population densities, density-dependant dispersal was observed. In conclusion, this study revealed no loss of genetic diversity in red foxes following a rabies epizootic despite a population bottleneck, yet highlights population density as an important factor to determine local spatial genetic structure.

This study investigates the population genetic structure of three primate species living in forest fragments of the Lower Kinabatangan Wildlife Sanctuary (LKWS), Sabah, Malaysia. The sanctuary is surrounded by oil palm plantations and human settlements but still retains high diversity of both flora and fauna. LKWS is famous for its orang-utan and proboscis monkey populations but also supports Sabah's eight other primate species. The current study investigated the effects of forest fragmentation and geographical barriers, especially the Kinabatangan River, on three species of primates with different social systems and dispersal abilities. The orang-utan is a large bodied, solitary ape that is incapable of swimming whereas the proboscis monkey and the long-tailed macaque, are smaller bodied, live in large groups and are good swimmers. Using non-invasive samples (faeces), we sequenced approximately 100 individuals from each of these three primates using the left domain (and right domain for long-tailed macaques) of the mitochondrial control region. High levels of genetic diversity were detected in the proboscis monkey and long-tailed macaque, but lower levels were detected in the orang-utan. There are four general conclusions from the current study. Firstly, non-invasive faecal samples are viable for large scale studies on these wild primate populations. Secondly, mitochondrial DNA is an informative marker for population studies due to its high levels of polymorphism over small spatial scales (with the left domain of the control region providing better resolution then the right domain). Thirdly, the social structure of primate species profoundly influences patterns of mitochondrial genetic diversity. Finally, dispersal patterns greatly influence the mitochondrial genetic structure of these populations. The implications of these findings for the future of Borneo primates and conservation of Lower Kinabatangan Wildlife Sanctuary and Sabah are discussed.

No description available.