I studied the reproductive characteristics and mating systems of a central Florida population of gopher tortoises (Gopherus polyphemus). Using x-radiography, females were monitored for stage in egg-shelling and clutch size. Eggs began to appear on x-ray photographs in the first week of May in both 2001 and 2002; however, fully shelled eggs were not found before the end of May. In total 55% of the females x-rayed were gravid. Clutch sizes ranged from 4-12 with a mean of 7.29, with a mean clutch mass of 40.9 g. Clutch size increased with an increase in mean carapace length and mean plastron length. Mean clutch mass also increased with mean carapace length of females. Hatchlings began to emerge in late August, with incubation times ranging from 83 to 96 days. 50% of the eggs hatched, with 16.2% of the eggs showing no signs of development when opened. Hatchling mass averaged 30.7 g and was positively correlated with egg mass. DNA was extracted from blood samples obtained from females and their offspring, and from the sexually mature males in the population. Nine microsatellite loci were amplified and genotypes constructed for each individual. There is evidence for promiscuous mating in gopher tortoises. Multiple paternity was detected in two of the seven clutches (28.6 %). In the clutches with multiple fathers, fertilization was highly skewed to one male, with primary male fertilizing over 70% of the clutch. Females with multiple-sired clutches were significantly smaller than females with single-sired clutches. Among the clutches assayed only one male fertilized more than one clutch, indicating that insemination of females is evenly spread among males of similar sizes. However, males assigned as fathers were significantly larger than other sampled males which may mean that larger males have an advantage in fertilization of clutches. Conservation efforts should consider the impact of the mating system on reproduction in a population, and the possible impact of the relocation of larger males on recipient populations.

Despite long-term study, the mechanism explaining the parapatric distribution of two Australian reptile ticks species, Bothriocroton hydrosauri and Amblyomma limbatum, is not understood. This project aimed to use molecular genetic data to investigate aspects of the population biology of these two tick species, such as population structure and dispersal, to gain further insights into the cause and maintenance of this parapatric boundary. I developed and subsequently tested for Mendelian inheritance a suite of B. hydrosauri and A. limbatum species-specific microsatellites markers. Pedigree analysis showed one B. hydrosauri locus and all of the A. limbatum loci to be inherited in a non-Mendelian manner. Thus I could not investigate A. limbatum population structure and focused solely on B. hydrosauri. The first part of this study tested predictions of a model formulated to explain B. hydrosauri transmission dynamics. The “ripple” model, based on detailed ecological and behavioural data on B. hydrosauri and Tiliqua rugosa, B. hydrosauri’s most common host, predicts higher relatedness among larvae than among nymphs or adults on a host, and significant spatial autocorrelation in larvae extending further than for the later life stages. The model also predicts that adult ticks are likely to encounter related partners and that this will generate inbreeding within the population. I tested those predictions using nine microsatellite loci on a sample of 848 ticks (464 larvae, 140 nymphs and 244 adults) collected from 98 T. rugosa hosts at the northern edge of B. hydrosauri’s distribution range. My data did support all of the predictions of the “ripple” model and indicated that the dynamics of transmission among hosts play an important role in parasite population structure. The second part of this project focused on investigating the population genetic structure of B. hydrosauri at the edge of its geographic range and testing the predictions of a population model derived to explain B. hydrosauri’s parapatric boundary with A. limbatum. The “ridge and trough” model suggested the tick population was organised spatially into a series of “ridges” where tick density was high and “troughs” where it was low. Genetically, the expectation was to find clusters of more closely related individuals associated with the ridges. Cluster analysis of microsatellite allele frequencies and analysis of molecular variance of mitochondrial haplotype frequencies revealed the presence of four genetic clusters within a sample of 244 B. hydrosauri adults. As the highly genetically divergent clusters had overlapping distributions, and in some cases were syntopic, the genetic population structure predicted for these ticks by the “ridge and trough” model was not observed. Several explanations were considered for the observed B. hydrosauri genetic population structure, but syntopy of the clusters suggested that assortative mating is the most likely. I speculated that the clusters have formed in allopatry, when the environment was extremely heterogeneous, such that the ticks (and their hosts) were confined to isolated patches of high-quality habitat. Given sufficient time, this could have resulted in reproductive incompatibility between ticks occupying different patches. The population structure I uncovered indicates subsequent secondary recontact of divergent groups. Although my study allowed for a better understanding of B. hydrosauri biology and population structure, the reasons for the parapatric distributions of B. hydrosauri and A. limbatum are still unclear. Further research should focus on investigating the population genetic structure of A. limbatum at the edge of its range, as well as on performing a larger-scale study of B. hydrosauri population genetic structure and a more detailed investigation of the applicability of the “ridge and trough” model to this tick species. Moreover, it will be useful to inspect the population structure of both these species within the centers of their ranges and compare these findings with population structure found at the edge of the range.

The marsh rice rat (Oryzomys palustris) is a semi-aquatic rodent endemic to the southeastern United States. Unlike most terrestrial small mammals, the marsh rice rat can easily disperse over water and has a close association with wetlands. These specialized traits have likely greatly shaped the genetic structure and diversity within this species. I studied genetic patterns within the marsh rice rat to understand how this species' specialized ecology, as well as the geologic and climatic history of the southeastern United States, affected the genetic structuring within this species. The phylogeography of many species in the southeastern United States has been studied and concordant geographic patterns of genetic variation exist among many of these species. Researchers have hypothesized that the biogeography of the southeastern United States has been influenced by the Pleistocene glacial cycles, producing similar genetic patterns within unrelated species. I first examined genetic patterns within the marsh rice rat at the macro scale of phylogenetics. This nominal species actually represents two cryptic species; populations in the eastern and western regions of its range are genetically divergent. I also identified three subspecies, in contrast to the six morphological subspecies historically recognized. The silver rice rat in the Lower Florida Keys and the Sanibel Island rice rat from Sanibel Island Florida are both subspecific taxa. Only one mainland marsh rice rat subspecies exists. I then studied the phylogeographic patterns within the marsh rice rat and determined that geographic patterns of genetic variation in this species are not concordant with the phylogeographic patterns uncovered in most other species of the southeastern United States. The genetic structuring within the marsh rice rat has been influenced not only by the geologic and climatic history of this region, but also by the species' semi-aquatic adaptation. I also studied genetic patterns at a micro scale by estimating present levels of gene flow and genetic diversity within populations. Gene flow is a contemporary factor in maintaining levels of genetic diversity within populations of the marsh rice rat. From the macro scale of phylogenetics to the micro scale of population genetics, the genetic structure of the marsh rice rat has been shaped by past climatic history and by this species' specialized ecology.

Esta tesis se propone como objetivo general comprobar la utilidad de la variación microsatélite en el manejo de poblaciones de tres especies con gran interés económico: el salmón atlántico Salmo salar L, el rodaballo Scophthalmus maximus, y el camarón blanco Litopenaeus schmitti. Los resultados obtenidos demuestran que los loci microsatélites son útiles para el manejo de reproductores en las estaciones de cultivo a través del establecimiento de pedigríes si se tienen en cuenta: un análisis previo de variabilidad en los reproductores, la posibilidad de mutaciones y alelos nulos y las relaciones genéticas existentes entre los reproductores. No se encuentra una relación alelos-caracteres de interés comercial en el cultivo, aunque si asociación entre la heterocigosidad enzimática y estos últimos mientras parece no existir ninguna relación con la heterocigosidad microsatélite. Nuestros resultados apoyan la idea de que las enzimas, a través del control del metabolismo, juegan un papel fundamental en el incremento de la eficacia biológica de los individuos. Finalmente, los loci microsatélites muestran mayores niveles de variabilidad que la enzimas en poblaciones naturales, aunque el reparto de esa variabilidad genética es similar para ambos marcadores en camarón. No obstante, la mayor variabilidad de los microsatélites permite asignar los individuos a sus poblaciones de origen, lo cual sería de gran utilidad en el manejo de poblaciones naturales y cultivadas.

Genetic analyses of two endangered species of mammals in the Lower Keys of Florida (Lower Keys marsh rabbit, LKMR, Sylvilagus palustris hefneri; silver rice rat, SRR, Oryzomys palustris natator) were performed to evaluate the genetic structure of their populations. Mitochondrial sequence data (control region; 763 base pairs (bp), LKMR; 788 bp, SRR) were used to explore patterns of genetic variation within and among island populations in both species. Analysis of the SRR also included 8 polymorphic nuclear microsatellite loci (9 to 16 alleles). Phylogenetic analyses of mitochondrial sequence data for both species revealed two main lineages corresponding to eastern and western localities, with high levels of genetic structuring (LKMR FST = 0.982, SRR ΦST = 0.916). The two species differed in the level of sequence divergence between eastern and western populations (LKMR, 19 bp; SRR 4 bp). In addition to an overall similar pattern of genetic subdivision, populations of both species possessed low levels of mtDNA variation (haplotypic diversity in the LKMR = 66.1%, SRR = 58.6%). Microsatellite analyses of the SRR revealed subdivision between eastern and western regions. Although less pronounced than the structure observed in mtDNA, the overall pattern was still apparent. Additional examination of divergence between mainland and Lower Keys rice rats revealed a genetic division that indicated a lack of recent gene exchange between the regions (i.e. no shared haplotypes, the presence of private alleles, and distinctive separation in numerous analyses). Although this degree of division does not warrant species designation, the levels and patterns of divergence, both morphological and genetic, do suggest genetic isolation of mainland and island forms. This fact, along with restricted gene flow between the Lower Keys and the Everglades, suggests that the SRR is on an evolutionary trajectory separate from its mainland counterparts and validates its identification as a separate subspecies, Oryzomys palustris natator. Finally, the genetic division between eastern and western populations of the SRR and LKMR suggests that populations of both species in these two regions of the Lower Keys should be treated as separate management units, especially when considering the enhancement of populations via translocations.

Thesis (M.S.)--West Virginia University, 2001. / Title from document title page. Document formatted into pages; contains vii, 78 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references (p. 52-62).

Norway spruce is one of two dominating species in Swedish forestry and the most economically important tree species in Sweden. In order to preserve the ability to adapt to a changing environment and to keep populations healthy, genetic diversity has to be preserved. When choosing a small number of individuals from a natural stand to establish a seed orchard the population size decrease. With only a small number of genetically different individuals the risk of inbreeding increase. Furthermore if many clones of the same tree are used in one seed orchard there is also an increased risk selfing. The aim of this study was therefore to investigate whether genetic diversity in Norway spruce differs between age groups and if this can be attributed to forestry practices. All sampling was done from a single location in Västerbotten, Sweden and the different age groups were chosen to represent stands not affected by the modern forest industry to recently planted forests. The chosen age groups are young (12-18 years), intermediate (30-45 years), and old (above 85 years). From each age group 150 individuals were sampled. With genomic microsatellite markers each individual was genotyped at eight simple sequence repeat (SSR) loci. Results show an overall high genetic diversity with an average expected heterozygosity (He) at 0.842 and low genetic differentiation with an average fixation index among populations (FST) of 0.003. The genetic diversity of each age group was also high (He 0.832 to 0.843) and the inbreeding coefficient ranged from 0.061 in the old group to 0.078 in the intermediate group. The pairwise FST value was highest between the old group and the young group but the differentiation was only 0.005 (P=0.001). An analysis of molecular variance also showed that only 0.34% of the total genetic variance was explained by differences among age groups. This study found little evidence for a decrease in genetic diversity due to forestry practices and revealed high genetic diversity and low differentiation between the age groups, indicating a healthy population.

Metastasis is the main cause of cancer morbidity and mortality. Despite its clinical significance, several fundamental questions about the metastatic process in humans remain unsolved. Does metastasis occur early or late in cancer progression? Do metastases emanate directly from the primary tumor or give rise to each other? How does heterogeneity in the primary tumor relate to the genetic composition of secondary lesions? Addressing these questions in representative patient populations is crucial, but has been difficult so far. Here we present a simple, scalable PCR assay that enables the tracing of tumor lineage in patient tissue specimens. Our methodology relies on somatic variation in highly mutable polyguanine (poly-G) repeats located in non-coding genomic regions. We show that poly-G mutations are present in a variety of human cancers. Using colon carcinoma as an example, we demonstrate an association between patient age at diagnosis and tumor mutational burden, suggesting that poly-G variants accumulate during normal division in colonic stem cells. We further show that poorly differentiated colon carcinomas have fewer mutations than well-differentiated tumors, possibly indicating a shorter mitotic history of the founder cell in these cancers. We collect multiple spatially separated samples from primary carcinomas and their metastases and use poly-G fingerprints to build well-supported phylogenetic trees that illuminate each patient's path of progression. Our results imply that levels of intra-tumor heterogeneity vary significantly among patients.

The spatial scale at which populations are genetically structured is of immense interest for the understanding of a species’ ecology and evolutionary biology. This can have important implications for management of resources as well as predicting responses to future change. Rainbow smelt (Osmerus mordax) is an anadromous species with a relatively short freshwater residence time compared to other species with similar life-history strategies. Therefore, while they offer the opportunity to sample distinct spawning aggregations, they also offer an insight into the relative roles of contemporary and historical factors shaping connectivity among marine populations, an area of great interest, and for which further understanding is required. With the use of both mitochondrial DNA and nuclear microsatellite markers, I explored the historical and contemporary factors influencing population structure in smelt. While previous phylogeographic work on this species has resolved two mtDNA lineages dating back to previous glacial episodes, I document the discovery of a zone of contact between these lineages in Newfoundland. This is in addition to the established contact zone in the St. Lawrence estuary, and results in a longitudinal distribution of the races with one race predominating on opposite ends of the species distribution, while the other race is geographically intermediate. Patterns of nuclear genetic variation largely mirror the phylogeographic signals in Newfoundland and suggest a more recent colonization of the Avalon Peninsula as well as implicating a remnant historical signal of colonization of the west coast of Newfoundland from the mainland. In addition, contrasting patterns of genetic diversity and levels of differentiation were apparent between the mainland and Newfoundland and suggest differing scales of dispersal within this species. While the population structure within Newfoundland is most consistent with dispersal restricted to within bays, larger scale biogeographic regions were identified in the mainland range, suggesting dispersal is more common and widespread. In addition, sampling of different run times (i.e. ‘early’ vs. ‘late’) demonstrated the potential for isolation by time when spawning events are separated by a break in activity. Overall, these results shed light into the possible roles of both historical and contemporary factors shaping the dynamics and connectivity among populations.

Rhinoceroses are arguably the most endangered of all large mammal taxa. In order for ongoing conservation of this species to be successful, it is crucial to accurately characterize the remaining genetic diversity for all rhinoceros species. To do this, I optimized a standard suite of 24 taxon-specific rhinoceros microsatellite loci. These loci have the power to provide the most comprehensive estimate of comparative microsatellite genetic diversity within and among the four extant African and Asian rhinoceros genera. These loci were further used to evaluate the comparative influences of rhinoceros species versus microsatellite taxonomic origin as predictors of rhino microsatellite diversity, and finally to examine the evolutionary relationships between extant rhino taxa. The African black michaeli rhino subspecies had the highest level of microsatellite genetic variability of all available rhinos, while southern white and Indian rhinos were the least variable rhinos. These findings also suggested that species and taxonomic origin of microsatellite loci were both significant predictors of microsatellite heterozygosity in rhinoceroses. A weak association between the Sumatran and black rhinos was found with a DLR neighbour-joining tree. The standard loci were able to assign unique genotypes to all available rhinos as well as differentiate between all rhino species by correctly assigning individual rhinos back to their respective populations. / Thesis (Master, Biology) -- Queen's University, 2008-07-02 23:01:32.553