Patterns of genetic connectivity can help answer key questions about the evolutionary ecology of fishes. This knowledge is particularly useful when considering the management and conservation of species that are impacted by fisheries. Population connectivity in ocean habitats is heavily influenced by environmental and oceanographic factors. These factors can lead to strong genetic differences within populations, causing fragmentation into smaller subpopulations. The Red Sea exhibits pronounced oceanographic gradients in temperature, chlorophyll, and salinity, which have been assessed in various species’ populations and which have been found to have potential impacts on gene flow. The Red Sea also features strong cyclonic and anticyclonic eddies that may facilitate, or possibly inhibit, the transport of larvae throughout the Red Sea, potentially influencing gene flow themselves. The ability of oceanographic factors like eddies to structure wild fisheries populations in this region has yet to be fully determined. To address this, the genetic composition of two of the most highly fished species, (Plectropomus areolatus and Plectropomus pessuliferus marisrubri), in the Red Sea were evaluated utilizing genetic markers (polymorphic microsatellite loci). Samples from three geographically separate regions along the Saudi Arabian Red Sea coastline, as well as from Sudan, were analyzed to address latitudinal and cross-sea connectivity. I was able to determine that little genetic differentiation exists within Plectropomus species across all regions of the Red Sea, indicating high gene flow for these species throughout. These findings highlight the ability of currents and eddies to transport larvae along and across the Red Sea. The results from this study also indicate that a single population of P. areolatus and a single population of P. pessuliferus marisrubri occurs in the Red Sea. The high degree of genetic flow suggests that each species should be managed as individual units. This study presents a plausible avenue for buffering the effects of overfishing currently occurring in Saudi Arabia; Saudi Arabian fish subpopulations may be reseeded by the Sudanese subpopulations.

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

Doctor of Philosophy / A number of types of molecular polymorphisms can be used for studying genetic relationship and evolutionary history. Microsatellites are hypervariable and can be very useful tools to determine population structure, distinguish sibling species, as well as verifying parental relationships and pedigrees. However, while microsatellite polymorphisms are useful for solving relationships between populations within a species, relations among species or genera will probably be obscured due to a high degree of homoplasy —identity arising from evolutionary convergence not by descent. For long range evolutionary history, such as phylogeny from old world monkey to human, mtDNA markers may be better candidates. The aim of this thesis is to assess molecular polymorphisms of different types and their optimal use in different situations. Two widely separated taxa were used for testing –the green monkey Chlorocebus sabaeus, and the sibling dipteran flies Bactrocera tryoni and B. neohumeralis, known collectively as the Queensland fruit fly. In the present study a complete 16,550 bp mtDNA sequence of the green monkey Chlorocebus sabaeus is reported for the fist time and has been annotated (Chapter 2). Knowledge of the mtDNA genome contributes not only to identification of large scale single nucleotide polymorphisms (SNPs) (Chapter 4) or other mtDNA polymorphisms development, but also to primate phylogenetic and evolutionary study (Chapter 3). Microsatellites used for the green monkey paternity and pedigree studies were developed by cross-amplification using human primers (Chapter 5). For studies of population structure and species discrimination in Queensland fruit fly (Chapter 7), microsatellites were isolated from a genomic library of Bactrocera tryoni (Chapter 6) The total length of 16550 bp of complete mtDNA of the green monkey C. sabaeus, which has been sequenced and annotated here, adds a new node to the primate phylogenetic tree, and creates great opportunity for SNP marker development. The heteroplasmic region was cloned and five different sequences from a single individual were obtained; the implication of this are discussed. The phylogenetic tree reconstructed using the complete mtDNA sequence of C. sabaeus and other primates was used to solve controversial taxonomic status of C. sabaeus. Phylogenies of primate evolution using different genes from mtDNA are discussed. Primate evolutionary trees using different substitution types are compared and the phylogenetic trees constructed using transversions for the complete mtDNA were found close to preconceived expectations than those with transversions + transitions. The sequence of C. sabaeus 12SrRNA reported here agrees with the one published by ven der Kuyl et al. (1996), but additional SNPs were identified. SNPs for other regions of mtDNA were explored using dHPLC. Twenty two PCR segments for 96 individuals were tested by dHPLC. Fifty five SNPs were found and 10 haplogroups were established. Microsatellite markers were used to construct a genealogy for a colony of green monkeys (C. sabaeus) in the UCLA Vervet Monkey Research Colony. Sixteen microsatellites cross-amplified from human primers were used to conduct paternity analysis and pedigree construction. Seventy-eight out of 417 offspring were assigned paternity successfully. The low success rate is attributed to a certain proportion of mismatches between mothers and offspring; the fact that not all candidate fathers were sampled, the limitations of microsatellite polymorphisms; and weakness of the exclusion method for paternity assessment. Due to the low success rate, the pedigree is split into a few small ones. In a complicated pedigree composed of 75 animals and up to four generations with multiple links a power male mated with 8 females and contributed 10 offspring to the pedigree. Close inbreeding was avoided. Population structure within two species of Queensland fruit fly Bactrocera tryoni and Bactrocera neohumeralis (Tephritidae: Diptera) is examined using microsatellite polymorphisms. Queensland fruit flies B. tryoni and B. neohumeralis are sympatric sibling species that have similar morphological and ecological features. They even share polymorphism at the molecular level. Mating time difference is the main mechanism by which they maintain separate species. In the present study, 22 polymorphic and scorable microsatellites were isolated from B. tryoni and tested in the two species sampled from sympatric distribution areas. Pairwise genetic distance analysis showed explicit differentiation in allele frequencies between the two species, but very weak differences between conspecific populations. Gene flow is higher within B. tryoni than within B. neohumeralis, and gene exchange between the two species exists. An averaging linkage clustering tree constructed by UPGMA showed two major clusters distinguishing the two species, and it appears that population structure is highly correlated with geographic distance. The relationship between molecular markers, evolution, and selection are discussed using comparative studies within two large taxa: primate and insect. The degree of conservation and polymorphism in microsatellites varies between taxa, over evolutionary time.

Minnows of the genus Dionda (Cyprinidae, Teleostei) inhabit spring-fed streams in the southwestern United States and Mexico. Five nominal species of Dionda (D. argentosa, D. diaboli, D. episcopa, D. nigrotaeniata and D. serena) are found in streams and rivers in central and west Texas. Because Dionda require clean, flowing water, they serve as aquatic indicator species of biological impacts of drought and human water use. Consequently, the ecological and conservation status of species of Dionda are important relative to monitoring habitat deterioration. This study used genetic data from geographic samples of the five nominal species of Dionda in Texas waters to document the conservation-genetics status of populations in each species. Fish were collected in cooperation with the Texas Parks and Wildlife Department and the U.S. Fish and Wildlife Service. Data from 585 base pairs of the mitochondrially encoded, protein coding ND-5 gene and from 21 to 33 nuclear-encoded microsatellites were used to assess genetic variation, population structure, historical demography, and genetic effective size of samples of each of the five species. The sample from Independence Creek, initially assumed to be D. episcopa because of its location, was found to be D. argentosa. Results of genetic assays indicate that each geographic sample in each species should be treated as a separate population and managed in a way that preserves the natural diversity found within each species. Genetic data revealed that all of the populations evaluated may be compromised genetically and should be monitored further.

The goal of this study was to examine the impact of Africanization on the genetic structure of the Welder Wildlife Refuge feral honey bee population by scoring mtDNA and microsatellite polymorphisms. Adult honey bee workers, collected between 1991 and 2001, were screened for mtDNA using the cytochrome b/BglII, ls rRNA/EcoRI, and COI/HinfI PCR-based assays. The procedure allowed identification of four mitotypes: eastern European, western European, A. m. lamarckii, and A. m. scutellata. The relative frequencies of the four mitotypes changed radically during the 11-year period. Prior to immigration of Africanized honey bees, the resident population was essentially of eastern European maternal ancestry. The first colony of A. m. scutellata mitotype was detected in 1993. Between 1995 and 1996 there was a mitotype turnover in the population from predominantly eastern European to predominantly A. m. scutellata. From 1997 onward, most colonies (69 %) were of A. m. scutellata mitotype. The temporal change in mtDNA was paralleled by nuclear DNA. The 12 microsatellite loci analyzed indicated (1) the mechanism of Africanization of the Welder population involved both maternal and paternal bi-directional gene flow (hybridization) between European and Africanized honey bees; and (2) the resident panmitic European population was replaced by panmitic asymmetrical admixtures of A. m. scutellata and European genes. The steepest increase in the proportion of introgressed A. m. scutellata nuclear alleles occurred between 1994 and 1997. The post-Africanization gene pool was composed of a diverse array of recombinant classes with a substantial European genetic contribution (mean proportion of European-derived alleles was 37 % as given by mR estimator or 25 % as given by mY estimator, for 1998-2001). If European genes continue to be retained at moderate frequencies, then the Africanized population is best viewed as a "hybrid swarm" instead of "pure African". The most radical change in the genetic structure of the Welder Wildlife Refuge feral honey bee population (observed between 1995 and 1997) coincided with arrival of the parasitic Varroa mite. We suggest that Varroa likely hastened the demise of European honey bees and had a major role in restructuring the Welder Wildlife Refuge feral honey bee population.

Massive declines in the latter half of the 20th century left black rhinoceros populations perilously close to extinction with only approximately 3600 individuals remaining, in contrast to estimated census numbers of over 100,000 individuals in 1900. While Diceros bicornis bicornis is the second most abundant subspecies of black rhino, behind D. b. minor, relatively few genetic studies have focused on this taxon. I used polymorphic DNA microsatellite markers to describe population structure in this subspecies. Using these genetic markers, the goals of this study were: i) to characterize the genetic variability of D.b. bicornis individuals (n = 170) found in Etosha National Park, Namibia, using seven DNA microsatellite markers, ii) to determine if there is population structure within Etosha National Park, using both traditional Wright’s F-statistics and a Bayesian model that requires no a priori population assignment, iii) to determine relatedness amongst founding and newly introduced black rhinoceroses held in private game farms throughout Namibia, using moment estimators of relatedness; and iv) to determine parentage of game farm rhinos with partial or no pedigree data available, using likelihood-based methods. I found that: i) the levels of genetic diversity in D.b. bicornis from Etosha National Park are consistent with previously published studies using microsatellite markers, and are relatively high; ii) the population structure within Etosha National Park is ambiguous using traditional F-statistics, but can be subdivided into three diagnosable clusters (western, central and eastern) using a Bayesian approach; iii) a relatively high degree of relatedness exists among founding members of game farm rhinos; and iv) assignments of parentage had greater success when there were fewer candidate parents and support the notion that black rhinoceroses are polygynous. / Thesis (Master, Biology) -- Queen's University, 2009-06-01 10:18:14.064

Mulloway are a large native inshore marine fish that are currently being evaluated by NSW Fisheries for their potential in aquaculture. The current study developed and applied molecular genetic markers to assess the geographical scale at which future hatcheries should be developed for the species. In addition, it evaluated the impact that current breeding practices in NSW have had on genetic diversity in culture cohorts. The study showed that wild Australian populations of this species constitute a single management unit (genetic stock), but that current hatchery practices employed in NSW are eroding natural genetic diversity. Thus a single hatchery could provide cultures stock to the whole Australian industry without compromising wild populations but that hatchery management practices will need to be modified in the future, to minimise levels of inbreeding.

Doctor of Philosophy / A number of types of molecular polymorphisms can be used for studying genetic relationship and evolutionary history. Microsatellites are hypervariable and can be very useful tools to determine population structure, distinguish sibling species, as well as verifying parental relationships and pedigrees. However, while microsatellite polymorphisms are useful for solving relationships between populations within a species, relations among species or genera will probably be obscured due to a high degree of homoplasy —identity arising from evolutionary convergence not by descent. For long range evolutionary history, such as phylogeny from old world monkey to human, mtDNA markers may be better candidates. The aim of this thesis is to assess molecular polymorphisms of different types and their optimal use in different situations. Two widely separated taxa were used for testing –the green monkey Chlorocebus sabaeus, and the sibling dipteran flies Bactrocera tryoni and B. neohumeralis, known collectively as the Queensland fruit fly. In the present study a complete 16,550 bp mtDNA sequence of the green monkey Chlorocebus sabaeus is reported for the fist time and has been annotated (Chapter 2). Knowledge of the mtDNA genome contributes not only to identification of large scale single nucleotide polymorphisms (SNPs) (Chapter 4) or other mtDNA polymorphisms development, but also to primate phylogenetic and evolutionary study (Chapter 3). Microsatellites used for the green monkey paternity and pedigree studies were developed by cross-amplification using human primers (Chapter 5). For studies of population structure and species discrimination in Queensland fruit fly (Chapter 7), microsatellites were isolated from a genomic library of Bactrocera tryoni (Chapter 6) The total length of 16550 bp of complete mtDNA of the green monkey C. sabaeus, which has been sequenced and annotated here, adds a new node to the primate phylogenetic tree, and creates great opportunity for SNP marker development. The heteroplasmic region was cloned and five different sequences from a single individual were obtained; the implication of this are discussed. The phylogenetic tree reconstructed using the complete mtDNA sequence of C. sabaeus and other primates was used to solve controversial taxonomic status of C. sabaeus. Phylogenies of primate evolution using different genes from mtDNA are discussed. Primate evolutionary trees using different substitution types are compared and the phylogenetic trees constructed using transversions for the complete mtDNA were found close to preconceived expectations than those with transversions + transitions. The sequence of C. sabaeus 12SrRNA reported here agrees with the one published by ven der Kuyl et al. (1996), but additional SNPs were identified. SNPs for other regions of mtDNA were explored using dHPLC. Twenty two PCR segments for 96 individuals were tested by dHPLC. Fifty five SNPs were found and 10 haplogroups were established. Microsatellite markers were used to construct a genealogy for a colony of green monkeys (C. sabaeus) in the UCLA Vervet Monkey Research Colony. Sixteen microsatellites cross-amplified from human primers were used to conduct paternity analysis and pedigree construction. Seventy-eight out of 417 offspring were assigned paternity successfully. The low success rate is attributed to a certain proportion of mismatches between mothers and offspring; the fact that not all candidate fathers were sampled, the limitations of microsatellite polymorphisms; and weakness of the exclusion method for paternity assessment. Due to the low success rate, the pedigree is split into a few small ones. In a complicated pedigree composed of 75 animals and up to four generations with multiple links a power male mated with 8 females and contributed 10 offspring to the pedigree. Close inbreeding was avoided. Population structure within two species of Queensland fruit fly Bactrocera tryoni and Bactrocera neohumeralis (Tephritidae: Diptera) is examined using microsatellite polymorphisms. Queensland fruit flies B. tryoni and B. neohumeralis are sympatric sibling species that have similar morphological and ecological features. They even share polymorphism at the molecular level. Mating time difference is the main mechanism by which they maintain separate species. In the present study, 22 polymorphic and scorable microsatellites were isolated from B. tryoni and tested in the two species sampled from sympatric distribution areas. Pairwise genetic distance analysis showed explicit differentiation in allele frequencies between the two species, but very weak differences between conspecific populations. Gene flow is higher within B. tryoni than within B. neohumeralis, and gene exchange between the two species exists. An averaging linkage clustering tree constructed by UPGMA showed two major clusters distinguishing the two species, and it appears that population structure is highly correlated with geographic distance. The relationship between molecular markers, evolution, and selection are discussed using comparative studies within two large taxa: primate and insect. The degree of conservation and polymorphism in microsatellites varies between taxa, over evolutionary time.

Thesis (M.Sc.)--University of Western Australia, 2006.

Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (leaves [98]-108).