This present study investigated the evolution of population genetic structure of two closely related cetacean species, bottlenose (Tursiops truncatus) and common dolphins (Delphinus spp.) within the Gulf of California (GC) and along the West Coast of Baja California. In this study, we found evidence of strong genetic differentiation in both bottlenose and common dolphin populations in the absence of physical barriers. The comparison of the patterns of population genetic differentiation found here for bottlenose and common dolphins supports the hypothesis of local habitat dependence and resource specialization at both the population and putative species level. Fine-geographic scale structure was detected in coastal bottlenose dolphins, which seemed to be strongly associated to the biogeographic subdivision of the Gulf of California and western coast of Baja California. This result suggests that gene flow among bottlenose dolphin coastal populations might be restricted by local dependence on diverse ecological conditions. In contrast, the long-beaked common dolphin genetic structure did not reflect the habitat heterogeneity of the region to the same extent. The difference in foraging specialization between coastal and offshore populations of both bottlenose and common dolphins is reflected in the pattern of genetic structure observed at a broader geographic scale. Overall, the results support the hypothesis that local habitat dependence promotes population differentiation in the absence of physical boundaries to dispersal in these highly mobile species. This study provides an unusual insight into the conditions that lead to incipient speciation in these groups. Divergence among common dolphin populations appears to be associated with changes in the paleoceanographic conditions of the region to the extent that reciprocal monophyly between the sympatric D. delphis and D. capensis forms has evolved within the Holocene timeframe.

The first part of this study examined post glacial recolonisation by UK roe. Previous studies established three main roe deer lineages exist across Europe: a western (Iberian Peninsula), an eastern (Balkan region) and a central lineage (which spans across central Europe). It was unknown which group British roe deer populations belonged. Using a 419 bp region of the mt-DNA d-loop (HVR1) amplified from ancient and modern UK samples a direct comparison was made with previously published European data. Results showed that UK populations belong to the central lineage, indicating a post glacial re-colonisation that is likely to have occurred via an eastern route. The estimation of a substitution rate, which was applied to coalescent based methods, detected a signal for divergence of UK roe from continental roe at 5,600 YBP (HPD 3,500 - 11, 200 YBP), not long after the proposed date for the land bridge split (7,500 YBP). Since post glacial re-colonisation, roe were known to have undergone severe fluctuations in population size. Perhaps the most significant fluctuation began during the medieval period, when roe suffered severe declines (bottlenecking) due to over hunting and deforestation. These declines were so severe that, by the 16th century, roe were believed to have been extirpated (locally extinct) from all southern areas of UK and considered scarce in northern areas. However, by the 19th century roe began to recover. Recovery in the south may have resulted solely from re-introductions (involving both native and non-native stocks) whilst, in the north, recovery resulted from natural re-colonisation from remnant native stocks. The second part of this study investigated the impacts of this more recent history. This was first investigated using a 750 bp of the mt-DNA d loop region (HVR), 16 microsatellite loci and 18 skull traits from modern roe from across the UK to examine structure and diversity. Results based on both DNA and morphology revealed strong differentiation. Northern roe appeared least impacted by recent events; maintaining patterns of isolation by distance (IBD) and high genetic diversity (compared to southern populations). In contrast, southern roe appeared more strongly impacted by recent events; in particular, IBD was non-significant (although this may have been due to a sample size effect) and genetic diversity was lower (compared to northern populations). The roe re-introduction records indicated that the south western population was native in origin (Perthshire). Genetic data showed that this population was, however, highly differentiated from its proposed source; which could reflect the powerful impact of genetic drift resulting from small founder populations. Alternatively, it may be that the ancestry of the south western population is more complex than previously assumed. For the other southern population (Norfolk), re-introduction records indicate a non-native (German) origin. In line with this, both genetic and morphological data implied that these roe were highly distinct. The impacts of bottlenecks (including medieval declines and founder events) on roe populations were also examined. Bottleneck analyses examined ‘signatures’ in modern populations based on 16 microsatellites. The strongest evidence of bottlenecking was detected in the Norfolk population, consistent with the small founder group size introduced into this location relatively recently. For the other populations bottleneck signatures tended to be weak and non-significant. Direct comparisons of ancient (pre-bottleneck) and modern (post –bottleneck) populations were made based on 419 bp of mt-DNA d –loop (HVR1). Results showed considerable losses in genetic diversity between time frames consistent with medieval declines. Northern populations were also found to harbour the highest number of ‘native’ haplotypes and southern populations the lowest. The southern population of Norfolk exhibited only one ‘novel’ haplotype confirming its non-native origin. The impacts of bottlenecks on populations are of concern because they have been shown to reduce population fitness and increase the risk of extinction. Therefore, fitness of roe was examined using fluctuating asymmetry (FA) of 10 skull traits as an indicator of developmental stability. Correlations of FA and genetic diversity indices were examined at the level of individuals within populations, across all populations and among populations. All correlations existed in expected directions; however, correlations tended to be weak and non-significant. Furthermore, among population level FA did not vary significantly across populations providing no indication as to whether fitness has been impacted by past population history.

Numerous studies have shown that population bottlenecks result in loss of genetic diversity and as a consequence of this, it is commonly inferred that there is a loss of evolutionary potential. It is rare that circumstances are such that there should be well documented details of the founder event, such as the size and date of the bottleneck, that there should be access to subsequent demographic information and to suitable samples from both the post-bottleneck and the source populations. It is even less common for this information to be available for two separate bottlenecks that occurred in parallel in a largely unmanaged population of large mammals. The importation by whalers of two separate groups of reindeer (Rangifer tarandus tarandus) onto the island of South Georgia in the early part of the twentieth century provided precisely those circumstances. There are accurate historical records of each founder events with details of dates and numbers of reindeer. The inaccessibility and geography of the island ensures that the South Georgia reindeer herds have been isolated from immigrants and separated from each other. The aim of this study was to test hypotheses about the impact of population bottlenecks on phenotype and genetic diversity and this was achieved by making genetic and morphometric comparisons of both post- bottleneck populations with the source population in Norway. Genetic diversity was primarily measured by allele numbers and heterozygosity based on data from thirteen microsatellite loci. Morphometric comparisons included measures of developmental stability, notably fluctuating asymmetry (FA), as well as phenotypic variation and body size. Each of the post-bottleneck populations showed significant genetic differentiation from the pre-bottleneck population and showed decreased levels of heterozygosity and allelic diversity. The data was used to validate commonly used 'bottleneck signatures' and considerable variability was found in the accurate detection of the known bottlenecks by the different detection methods. Both the post-bottleneck populations showed increased FA and morphometric variation compared to the pre-bottleneck population in some of the measured traits. Both post-bottleneck populations had smaller overall skull size than the pre-bottleneck population though it is discussed that this may be due as much to a plastic environmental response as to a consequence of the genetic bottleneck. Within each population the relationship between measures of genomic diversity and indirect measures of fitness were investigated on an individual basis. Although the results were of low significance, weak associations were found to support the hypotheses that developmental stability is correlated with measures of genomic diversity even at the level of the individual.

The demographic history of humans is very complex. Populations have undergone bottlenecks, isolation, migration, admixture and expansions. All of these have added to the complexity of what makes a population and how that population has changed over time. A record of these events can be found in our DNA. This project used autosomal DNA to trace the histories and structures of human populations by using a combination of a SNP (single nucleotide polymorphism) and an STR (short tandem repeat) – SNPSTR (Mountain et al. 2002). Forensic STRs formed the basis for the SNPSTR systems because their allelic diversity is well characterised, their mutation rates have been reliably measured and they are robust in PCR amplification. Four SNPSTR systems were found, using SNPs which had been verified by HapMap and/or Perlegen and which were < 500 base pairs away from the forensic STRs. These SNPSTRs were typed on DNAs from the HapMap project, the CEPH-HGDP, Cornwall, UK African Caribbeans, Danes and Greenland Inuit. They were analysed using an ABI3100 and GeneMapper software. Data from the combined SNPSTRs allowed inferences to be made about population structures, and also enabled the calculation of the TMRCA of the derived SNPs associated with the forensic STRs. Population structure was evident in the MDS plots where rudimentary population groupings could be seen. The Americas were outliers, reflecting their later peopling some 15,000 years ago (Jobling et al. 2003). Haplogroup analysis highlighted population isolates, such as the Surui in Brazil. The STRUCTURE analysis of the SNPSTR data has also provided some insights into the admixed nature of the autosomal DNA in known admixed populations such as the Greenland Inuit and to some extent, the African Caribbeans. One SNPSTR was expanded into a larger haplotype block - a PHAX - Phylogeographically informative Haplotypes on the Autosomes and seX chromosomes, by means of a SNaPshot reaction. The preliminary data from this suggested that this would allow us to gain a more complete insight into the histories and structures of human populations.

No description available.

The chromosome complement of four species phylogenetically related to man, the chimpanzee (Pan troglodytes), the pygmy chimpanzee (Pan paniscus), the gorilla (Gorilla gorilla), and the orangutan (Pongo pygmaeus) have been analysed with chromosome banding techniques and compared to the human chromosome complement. This has shown remarkable homologies between species, and presumed mechanisms of chromosome evolution have been proposed. Chromosome heteromorphisms in the great apes have been compared to those found in human populations, and most of them affected the distribution or the amount of constitutive heterochromatin and/or brilliantly fluorescent material, a situation comparable to man where such variations have been established as chromosome polymorphisms. However, a balanced polymorphic structural rearrangement involving large segments of euchromatic material has been found in two populations of orangutan. This rearrangement consisted of two pericentric inversions, one inside the other, comprising an unusual kind of chromosome polymorphism in mammalian populations. Moreover, it showed that pericentric inversions, the most probable chromosome rearrangements in the phylogeny of the chromosomes of man and the great apes, might not necessarily be restricted by infertility barriers, but may spread successfully in the population. The patterns of late replication of the chromosomes of the great apes and man have been compared, using BUdr as a thymidine substitute in the cell cycle. This has shown remarkable similarities in the patterns of late replication between species, and, as in the human chromosomes, most regions of late replication in the chromosomes of the great apes corresponded to areas of positive G-banding. Q-, C- and G-banding as methods of demonstrating chromosome homologies between these species have been analysed in relation to the content of highly repeated satellite DNAs in man and homologous sequences in the great apes. This has shown that the banding patterns are not informative about these sequences, and that they must reflect a degree of chromosome organization due to DNA packaging rather than DNA composition. Finally, the phylogeny of the chromosomes of man and the great apes has been reconstructed in view of the findings presented in this work and of previous data in the literature. In this study, man and gorilla resembled each other more closely than to any of the other species studied, a finding that is contrary to the generally held view that man and the chimpanzee are the two most closely related species. Comparative studies of the spermatozoa of the great apes and man were undertaken and showed that man was not unique in producing pleiomorphic spermatozoa, since this feature was also present in the gorilla. Moreover, the morphology of human and gorilla spermatozoa resembled each other so closely that on morphological grounds it was impossible to distinguish the spermiogram of these two species. Fluorescent ("f") bodies were detected in the spermatozoa of the African apes, although the distribution of such bodies did not resemble that of human spermatozoa, where the Y chromosome is usually visible. An analysis of the haploid DNA content of the great apes and man w®3 undertaken by estimating the total dry mass of the sperm head in these species. Man showed the lowest DNA content, whilst the gorilla showed the highest; this latter latter species also showed a higher variability in the haploid DNA content than all other species, including man. Diploid spermatozoa were also detected in the gorilla, in proportions similar to those found in man. These findings on spermatozoa are indicative of a closer relationship between man and gorilla than between man and the other hominoid apes. Moreover, the heteromorphism of spermatozoa in both human and gorilla semen samples makes it unlikely that clothing induced hyperthermia is the cause of pleiomorphic spermatozoa in man.

The brown rat, Rattus norvegicus is a relatively recent addition to the English fauna. However it is currently one of the most important vertebrate pest species. Anticoagulant rodenticides are the major control method used for the last 50 years. Widespread use of the rodenticide has led to evolution of resistance leading to problems controlling brown rat populations. One thus far ignored aspect of resistance biology is the population structure of the brown rat. In this research mitochondrial DNA and microsatellite DNA were used to elucidate the population structure of the brown rat at different scales in the English countryside. I also report on the type and the distribution of different warfarin resistant mutations in the English rural population.;Mitochondrial DNA data suggests a structured population at county level and the English brown rat population as a whole appears not to be at equilibrium. The relative lack of diversity in the mitochondrial DNA sequences examined can be explained by a founder effect and a subsequent spatial expansion. However, the microsatellite data shows much more mixing of populations at county level, even more clearly at the farm level. I discuss two possible explanations for this discrepancy; small effective population size of mitochondrial genomes and the greater movement of males compared to female rats.;Through mutation analysis we found 3 types of mutations in the exon 3 region of the VKORC1 gene among our brown rat populations. One mutation type is almost ubiquitous being found in almost all counties. We also found a geographical pattern to the different mutation distribution. As these mutations are also found in other parts of Europe, we suggest that they have entered England through different ports from different parts of the Continent which would explain the geographical structure of the mutations.

No description available.

The thesis is composed of two parts that are related by the theme of genetic markers. The first part involves the application of genetic markers to investigate the mating system, population genetic structure, and evolutionary relationship of the three Chinese larch taxa: <I>Larix gmelinii, L. olgensis </I>and <I>L. principis-rupprechtii. </I>Seventeen populations of the <I>Larix</I> taxa listed above were analysed using eight polymorphic allozyme markers. Results indicated that mating system was variable among taxa and among natural populations within taxa. Population differentiation of each taxa was very small, showing that less than 2% of total genetic variation occurred among populations. Spatial distribution of genetic variation of <I>L. gmelinii </I>was random, but a weak pattern of isolation by distance was detected in <I>L. olgensis. </I>The genetic relationship among the three taxa elucidated by allozyme markers indicated that the genetic distances were very low between them. Based on morphological traits and the results obtained by allozyme and cpDNA sequence markers, it is reasonable to consider <I>L. olgensis </I>and <I>L. principis-rupprechtii</I> to be two varieties of <I>L. gmelinii </I>rather than two separate <I>Larix </I>species. In the second part of this thesis, theories of plant population genetic structure were developed to incorporate biparentally, paternally, and maternally inherited genes into a variety of models. Population differentiation for each of the three plant genomes was formulated in the island, stepping stone and isolation by distance models of population structure. The results showed that maternally inherited organelle genes maintain larger differentiation than paternally inherited organelle genes, which in turn maintain larger differentiation than biparentally inherited nuclear genes. In the stepping-stone model, differences in genetic correlation with distance among the differently inherited genomes were conditional on the values of long and short distance migration for pollen and seeds. The relative contribution to migration of seed and pollen flow can be estimated in terms of gene frequency data or DNA sequence data.

This thesis presents theoretical results on the number of junctions on chromosomes in partially inbred populations, and addresses problems posed by locating these junctions using markers in both simulated populations and recombinant inbred lines (RILs). Chapter 1 presents a general introduction to the concept of junctions, and reviews previous work on the theory. Chapter 2 confirms by simulation some of the results presented in chapter 1, and shows that in a population of size <i>N</i> where selfing is excluded, but otherwise mating at random, the expected number of junctions per Morgan on a chromosome is linearly related to the inbreeding coefficient of that population, until complete inbreeding where 2(<i>N</i>+1) junctions are expected. Chapter 2 investigates the efficiency of using markers to detect junctions in inbred populations. Even with a highly dense map of fully informative markers, not all of the junctions present are detected, with the actual detection rate lower than expected if junctions were distributed at random. An approximate expression for the proportion of junctions detected 1/(1+1.4γ), where γ = <i>J/B</i>, the ratio of junctions to marker brackets Chapter 3 applies the theory of junctions to RILs. Theoretical analysis suggests a density of 4 junctions per Morgan in a RIL. The observed counts of junctions detected using microsatellite markers in multiple RILs are found to be slightly lower than this expectation. In the analysis of junctions detected, “cross” and “line” were found to have significant effects in the analysis. Chapter 5 attempts to further elucidate the factors affecting observed junction counts in RILs by looking at the effects of individual markers on the junction count to locate specific regions of the genome that affect junction formation.