Neotoma micropus from Jack County, Texas, were studied over a 9-month period. Loci from blood and saliva were used to determine genetic variation within the population. Deviations from Hardy-Weinberg equilibrium were found at one locus. The average temporal F over all seven loci was 0.040. Genetic structuring was subtle, fluctuated on a seasonal basis, and was due to differential migration or predation on genotypes. Heterozygotes tended to move more than homozygotes, and a greater proportion of heterozygotes were lost from the population during each season. Genetic variation was maintained in the population by immigrant individuals. This differential in dispersal of genotypes fits current models of reorganization within the genome of populations.

The inter- and intraspecific taxonomy of the genus Lepus is highly controversial. Since these animals play an important ecological role as prey species, their conservation is of high priority. A prerequisite for adequate management strategies is the precise knowledge of taxonomic borders and geographic distributions of the taxa in question. Especially in African hares the clear delimitations of the species and subspecies are still unresolved. In an attempt to obtain a clearer understanding of the evolutionary history, the phylogenetic relationships and the detection of conservation relevant units in African hares, a molecular investigation using mitochondrial DNA sequence data and information from six microsatellite loci was initiated. In this study, the phylogenetic analyses of DNA sequence data of the mitochondrial control region and the cytochrome b gene identified 2 major maternal lineages within South African hares that were further subdivided into two clusters each. The nuclear genetic structure revealed by six dedicated microsatellite loci confirmed this subdivision. While the mitochondrial diversity was characterized by high sequence divergences and haplotype diversities, the nuclear variation seemed more moderate with relatively low FST and RST values. Using the information content of the six microsatellite loci developed for this project, the results of assignment tests strongly supported the validity of the four genetic lineages. The levels of of cytochrome b sequence divergences among the four clusters suggested that they may warrant distinct species status (applying the phylogenetic species concept). The data are suggestive of two species groups consisting of two sister species each: A "saxatilis" group with Lepus saxatilis sensu stricto and another species (possibly L. victoriae), and a "capensis" group with L. capensis s. str. and another, yet to be described species. Applying a molecular clock for cytochrome b, the historical dates for the separation of the South African hares from European outgroup species and the split between the two South African species groups were calculated as 4.84 and 3.45 million years ago, respectively. The divergence dates between the sister species was 1.09-1.45 million years ago. Following the biological species concept, the two major clades represent two species: L. saxatilis sensu lata and L. capensis s. I. , that are both subdivided into two geographically separated phylogroups, one in the southern parts of the country and one in the northern. These intraspecific lineages meet the criteria of evolutionarily significant units and should be considered separately in conservation actions. The evolutionary history of scrub and Cape hares in South Africa has been influenced mainly by contiguous range expansions and sudden population size expansions during the Pleistocene climate changes. / Thesis (PhD (Zoology))--University of Pretoria, 2002. / Zoology and Entomology / unrestricted

The aim of this project was to study the population genetics of Echinostoma trivolvis, a parasitic trematode that uses multiple hosts in its lifecycle and has a significant impact on amphibian populations. Microsatellite markers were to be identified and isolated because of their highly variable nature and reported ease of use with PCR. Parasite DNA was extracted from planorbid snails from several locations within California including: Point Reyes National Seashore, Lake Tahoe, and the San Francisco Bay Area. In addition, parasite samples were obtained from Manitoba, Canada. Several microsatellites were identified and 29 PCR primers sets were designed, six of which were capable of amplifying consistently. Sequencing other published molecular markers, COl, NDl, and ITS, unveiled intriguing phylogenetic relationships and potential cryptic species. The echinostome population in central California, as a result of this project, may be much more diverse than has long been reported in the literature.

Thesis (M.S.)--State University of New York at Binghamton, Department of Biological Studies, 2009. / Includes bibliographical references.

The Benguela Current is a cold eastern boundary current located on the south-western coast of the African continent. The establishment of its present day features approximately two million years ago has triggered allopatric events which have driven genetic and/or phenotypic differentiation in many of the warm-temperate organisms that previously had continuous distributions along the south and west coast of southern Africa. However, since many of these species have responded differently, despite similar isolation times, research in this region provides a unique opportunity to increase our understanding of evolutionary processes. The common octopus (Octopus vulgaris, Cuvier 1797) is a coastal, sedentary species, inhabiting coral reefs or rocky environments at depths of up to a 100m. It is considered to be one of the most extensively studied cephalopod species due to its worldwide distribution. However, very little research has been conducted on O. vulgaris in southern Africa. In order to gain a holistic understanding of the effects of the Benguela Current on population connectivity, genetic and phenotypic diversity, and evolutionary history of O. vulgaris, a comparative genetic and morphological study was conducted across the Benguela region. A total of 168 specimens of O. vulgaris were collected from four different regions across the Benguela system. A small tissue sample was preserved in ethanol for molecular analysis, and the specimen was frozen whole for morphometric analysis in the laboratory. Octopus vulgaris genetic population structure and evolutionary history was investigated using a 580bp fragment of the mitochondrial cytochrome b (cytb) gene for 76 individuals located within the Benguela region, yielding 10 different haplotypes. AMOVA and pairwise FST analyses revealed significant genetic differentiation suggesting a northern-southern Benguela divergence. Estimates of time since most recent common ancestor, based on biogeographical calibrators and coalescent analyses, indicated that isolation between the Angolan and South African population occurred between ~231 Ka and 1 Ma. Mismatch distribution analyses revealed a past population expansion within the South African O. vulgaris roughly 129.31 Ka, whilst Bayesian skyline plots were indicative of gradual demographic growth within the Angolan population in the last ~100 Ka. Observed O. vulgaris population structure and demographic history was likely the result of historical climate-induced change within the system. Reconstruction of phylogenetic relationships within the Octopus genus, using cytb and COI suggest that O. vulgaris is not a monophyletic group and a major systematic revision is required. Furthermore, unidentified individuals from South Africa were found to group with species from Indo-West Pacific Oceans and were therefore considered to have been translocated through ballast water from Asia. While the molecular analysis indicated a significant northern-southern Benguela structure results from the principle component analysis (PCA) and discriminate function analysis (DFA) were unable to distinguish between O. vulgaris from different sampling localities throughout the Benguela Current region based on soft-parts, hard-parts and meristic characters. The lack of phenotypic variation, despite significant genetic divergence, highlights the importance of multi-method approaches in gaining a holistic understanding of the taxonomy and biogeography of species.

Snappers of the genus Lutjanus are small to large predatory fishes occurring in inshore circumtropical and subtropical waters throughout the world. These fishes support fisheries across their distribution range. Within the Western Indian Ocean (WIO), previous studies on Lutjanus kasmira revealed limited spatial genetic differentiation, whereas Lutjanus fulviflamma showed high genetic connectivity. The phylogenetic relationships among WIO snappers are unknown. Previous studies in the Indo-Pacific (IP) did not include any WIO representatives. This study examined (1) the phylogeographic patterns in Lutjanus bohar, L. fulviflamma and L. lutjanus to understand the origins and factors influencing the distribution of diversity in the region, (2) how the physical environment, biological, and ecological factors influence genetic diversity, (3) the placement of WIO snappers in context to those from the IP, as well as the placement of taxa not included previously, (4) extent of differentiation among conspecifics from the two regions, and (5) the relationship of the Caesionidae to the Lutjanidae. Samples were sourced from across the WIO and from peripheral localities, where possible. DNA sequence data were generated from two mitochondrial gene regions (cyt-b and NADH-2) and a nuclear gene region (S7 intron 1). Data were analysed under a phylogeographic framework to examine genetic structure, diversity and differentiation among identified regions for each of the three species. Other sequence data were generated from two mitochondrial gene regions (COII and 16S rDNA) to examine the phylogenetic placement of WIO snappers in context of the IP snappers and the relationship of the Caesionidae to the Lutjanidae. Lutjanus bohar and L. fulviflamma displayed high genetic diversity, but lower diversities were observed for L. lutjanus. Genetic differentiation was observed between Mozambique and Maldives in L. bohar. Lutjanus fulviflamma was differentiated in South Africa, Mozambique, Mauritius and Thailand, while differentiation was observed between Kenya and Tanzania in Lutjanus lutjanus. Overall, low genetic differentiation and high connectivity were observed for each of the three species. This differentiation may result from intrinsic features of the species and extrinsic features of the environment, whereas the connectivity is mainly influenced by the pelagic larval duration. These patterns of differentiation are in accordance with a proposed vicariant biogeographic hypothesis for the origins of regional faunas of the IP. Phylogenies were similar to those published, with additional taxa not altering the previous groupings found. Conspecifics from the two regions clustered together, with varying degrees of differentiation among the WIO and IP, depending on the species. Members of the Caesionidae were nested within Lutjanidae, suggesting that morphological characters separating the two families are taxonomically insignificant. This affirms previous notions that the Caesionidae should be a subfamily within the Lutjanidae. This is the first multi-gene study, examining differentiation in multiple species of snapper over a wide geographic area in the WIO, and the results of this study could have potential implications for fisheries management and conservation.

Thesis (M.S.)--State University of New York at Binghamton, Department of Biological Sciences, 2009. / Includes bibliographical references.

Orientador: Fosca Pedini Pereira Leite / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-14T00:36:25Z (GMT). No. of bitstreams: 1 Pavani_Lilian_M.pdf: 1390022 bytes, checksum: 43df8a085a06d86b5eadaf092c0fbf14 (MD5) Previous issue date: 2009 / Resumo: Na região do Canal de São Sebastião, onde opera o maior terminal petrolífero do Brasil, há extensos bancos de algas pardas do gênero Sargassum e anfípodes associados, mas também existem hidrocarbonetos alifáticos e aromáticos de petróleo na água e no sedimento. Sabese que os anfípodes são eficientes bioindicadores de qualidade ambiental, assim como as algas são importantes bioacumuladores. Avaliou-se a presença de hidrocarbonetos em Sargassum e buscou-se relacionar suas concentrações com distâncias crescentes a partir do terminal, tanto ao norte quanto ao sul da Ilha de São Sebastião. Essas concentrações e distâncias também foram utilizadas para verificar a estruturação das comunidades de anfípodes do fital de Sargassum. Essa avaliação foi feita para anfípodes, abordando-se a composição de grupos tróficos e de espécies. Não foi constatada relação entre as distâncias e concentrações de hidrocarbonetos presentes nas algas e na estruturação das comunidades de anfípodes em nenhuma das abordagens. No entanto, notou-se correspondência entre elas, o que indica que a identificação em famílias para o estabelecimento de grupos tróficos pode ser eficiente numa avaliação ambiental mais rápida. Também se obteve importante informação em relação à fauna de anfípodes do litoral do Estado de São Paulo, uma vez que ainda não havia estudos na Ilha de São Sebastião e a fauna de ilhas do estado ainda é pouco conhecida / Abstract: In the São Sebastião Channel region, where operates the greatest Brazilian petroliferous terminal, there are extensive banks of the brown seaweed Sargassum with many associated amphipods, but also polyciclic aromatic hydrocarbons and aliphatic hydrocarbons, which are present both in sedment and water. The amphipods are known to be efficient bioindicators of environmental quality, as well as the seaweed are important bioacumulators. The presence of hydrocarbons in Sargassum and its relationship with increasing distances from the terminal, both north and south of the São Sebastião Island, was evaluated. These concentrations and distances were also used to verify the structure of amphipod communities associated to Sargassum . This evaluation was made for amphipods identified in trofic groups and in species. There was no significant relationship between distances from the terminal and concentrations of hydrocarbons in the seaweed or the estructure of the amphipod communities. However, correspondence between the aproachs (trofic groups and species) was noticed, which indicates that the identification in families for the establishment of trofic groups can be efficient in a faster ambient evaluation. Also, important information related to amphipods of the São Paulo State coast was achieved, as far as the fauna of São Sebastião Island was first studied and the islands fauna of the State are still little known / Mestrado / Ecologia / Mestre em Ecologia

Indiana University-Purdue University Indianapolis (IUPUI) / DNA double strand break (DSB) is one of the most threatening of all types of DNA damages as it leads to a complete breakage of the chromosome. The cell has evolved several mechanisms to repair DSBs, one of which is break-induced replication (BIR). BIR repair of DSBs occurs through invasion of one end of the broken chromosome into a homologous template followed by processive replication of DNA from the donor molecule. BIR is a key cellular process and is implicated in the restart of collapsed replication forks and several chromosomal instabilities. Recently, our lab demonstrated that the fidelity of DNA synthesis associated with BIR in yeast Saccharomyces Cerevisiae is extremely low. The level of frameshift mutations associated with BIR is 1000-fold higher as compared to normal DNA replication. This work demonstrates that BIR stimulates base substitution mutations, which comprise 90% of all point mutations, making them 400-1400 times more frequent than during S-phase DNA replication. We show that DNA Polymerase δ proofreading corrects many of the base substitutions in BIR. Further, we demonstrate that Pif1, a 5’-3’ DNA helicase, is responsible for making BIR efficient and also highly mutagenic. Pif1p is responsible for the majority of BIR mutagenesis not only close to the DSB site, where BIR is less stable but also at chromosomal regions far away from the DSB break site, where BIR is fast, processive and stable. This work further reveals that, at positions close to the DSB, BIR mutagenesis in the absence of Pif1 depends on Rev3, the catalytic subunit of translesion DNA Polymerase ζ. We observe that mutations promoted by Pol ζ are often complex and propose that they are generated by a Pol ζ- led template switching mechanism. These complex mutations were also found to be frequently associated with gross chromosomal rearrangements. Finally we demonstrate that BIR is carried out by unusual conservative mode of DNA synthesis. Based on this study, we speculate that the unusual mode of DNA synthesis associated with BIR leads to various kinds of genomic instability including mutations and chromosomal rearrangements.

Indiana University-Purdue University Indianapolis (IUPUI) / Alzheimer's disease (AD) is the most common form of dementia defined by loss in memory and cognitive abilities severe enough to interfere significantly with daily life activities. Amnestic mild cognitive impairment (MCI) is a clinical condition in which an individual has memory deficits not normal for the individual's age, but not severe enough to interfere significantly with daily functioning. Every year, approximately 10-15% of individuals with MCI will progress to dementia. Currently, there is no treatment to slow or halt AD progression, but research studies are being conducted to identify causes that can lead to its earlier diagnosis and treatment. Genetic variation plays a key role in the development of AD, but not all genetic factors associated with the disease have been identified. Copy number variants (CNVs), a form of genetic variation, are DNA regions that have added genetic material (duplications) or loss of genetic material (deletions). The regions may overlap one or more genes possibly affecting their function. CNVs have been shown to play a role in certain diseases. At the start of this work, only one published study had examined CNVs in late-onset AD and none had examined MCI. In order to determine the possible involvement of CNVs in AD and MCI susceptibility, genome-wide CNV analyses were performed in participants from three cohorts: the ADNI cohort, the NIA-LOAD/NCRAD Family Study cohort, and a unique cohort of clinically characterized and neuropathologically verified individuals. Only participants with DNA samples extracted from blood/brain tissue were included in the analyses. CNV calls were generated using genome-wide array data available on these samples. After detailed quality review, case (AD and/or MCI)/control association analyses including candidate gene and genome-wide approaches were performed. Although no excess CNV burden was observed in cases compared to controls in the three cohorts, gene-based association analyses identified a number of genes including the AD candidate genes CHRFAM7A, RELN and DOPEY2. Thus, the present work highlights the possible role of CNVs in AD and MCI susceptibility warranting further investigation. Future work will include replication of the findings in independent samples and confirmation by molecular validation experiments.