The distribution and abundance of many coral reef organisms are affected by their predator’s distribution and abundance. Loss of predators may cause a shift in species compositions that will cascade down to other ecological processes on the reef. One example of a shift like this is the growing sea urchin populations inhabiting the coral reefs of East Africa. Areas with high fishing pressure often have large populations of sea urchins. The large populations of sea urchins have a negative impact on the reef ecology both by their grazing and bio-erosion as well as on fish growth and the recovery of fish populations. Previous population genetic studies conducted on Diadema setsosum, using mtDNA and allozymes, found genetic structuring between populations on a large geographical and evolutionary scale. The aim of this study was to examine the genetic population structure of the sea urchin Diadema setosum, at four sites around Zanzibar. We used the amplified fragment length polymorphism (AFLP) technique, a fast and effective method with high resolution. The long term objective is to understand the migration pattern and colonization of D. setosum to facilitate possible management actions. We found a significant genetic structuring of D. setosum hence the populations can not be considered panmictic. The reason behind this structure does not seem to be based on the geography nor size. One possible explanation might be that the structure lies on a larger geographical scale than we have studied, further studies around the Western Indian Ocean may reveal this. Another explanation may be that the structuring is due to differences in spawning time between the different phenotypes and an analysis of gonad maturations may give information about this. To find the reasons behind the observed genetic structure is of great importance for management of the sea urchins and therefore the management of whole reef ecosystems.

In this study, mtDNA was used to examine the phylogenetic and molecular relationships of the freshwater shrimp family Atyidae. The phylogeographical variations of two landlocked Caridina pseudodenticulata and Neocaridina denticulata were also discussed. Four genera and 32 species of the Atyidae were identified and divided into 6 groups. In addition to 14 previously recorded species, eight of them are new records, while another 10 species remain unconfirmed. The combination of morphological and molecular characteristics can effectively differentiate species within the family Atyidae. Analysis of demographic parameters indicates a recent population expansion of C. pseudodenticulata, but not for N. denticulata. The result of Bayesian skyline plot analysis implies that the expansion of C. pseudodenticulata began about 70,000 years ago, followed by a very recent rapid expansion approximately 4,000-6,000 years ago. Four major geographical regions of N. denticulata can be identified, including: (1) Southern Taiwan group; (2) Hualian group; (3) Northern Taiwan group; and (4) Ilan group. The study on the phylogenetic relationship of Atyidae in Taiwan could provide valuable information for future study of speciation and geological variation in tropical island.

The pecan nut casebearer, Acrobasis nuxvorella Neunzig (Lepidoptera: Pyralidae) is the most damaging insect pest of pecan, Carya illinoinensis (Wang) K. Koch (Fagales: Juglandaceae). Two sex pheromones have been identified for this species and are currently being used to assist pecan growers in the timing of insecticide applications. The discovery that there are two pheromone types produced by A. nuxvorella has led to complications in the implementation of pheromone monitoring programs. One pheromone (referred to as standard) is attractive to moths in the southern US, but not in Mexico. The other pheromone (referred to as Mexican) is attractive to moths in the southern US and in Mexico. Because most male lepidopterans respond only to a specific pheromone, it was suspected that there were two pheromone strains of A. nuxvorella, one exclusively present in the northern distribution of A. nuxvorella (US strain) and the other widely distributed from Sonora, Chihuahua, and Durango in Northern Mexico to Texas, Georgia, and Oklahoma in the US (Mexican strain). In order to confirm the existence of the two alleged pheromone strains, AFLP markers were obtained and analyzed, male response to pheromones was observed and phenological differences were assessed. Additionally, the relative abundance of each of the two pherotypes was evaluated and the population structure of this pest across its geographic distribution was determined. Results of genetic analysis show that the genetic differentiation between these insects is not explained by pheromone type. This information is further supported by a pheromone assay in which a large proportion of US collected A. nuxvorella males and Mexican collected A. nuxvorella males chose both pheromones when tested multiple times. Furthermore, no phenological differences were detected between the two pherotypes in the US, although significantly more male A. nuxvorella in the US are attracted to field-deployed pheromone traps baited with the standard pheromone than the Mexican pheromone. Finally, population genetic analyses indicate a high degree of genetic structure in A. nuxvorella across its geographic distribution, with the genetically distinct populations occurring in areas where A. nuxvorella is not native, but has been introduced.

Sex-change (or sequential hermaphroditism) is a phenomenon whereby an organism functions first as one sex, and then as the other in the later stage of its life. Sex change is an adaptation that has evolved to allow certain organisms to increase fitness through resource allocation of male and female functions in a single lifespan. Since the timing of sex change in an organism is critical to its reproductive output, the size or age at sex change is expected to be plastic in response to different environmental conditions. Social and environmental conditions usually convey the cues about the relative advantages of functioning as one sex or the other. Identifying the factors that influence the timing at sex change is important to understand the evolution of sex change in the life history. In order to elucidate how to optimize fitness through sex allocation in response to different environment, I studied the timing at sex change of Coralliophila violacea in different approach, including the age of individual, the compositions of social groups and the difference between two types of coral hosts in this thesis. Firstly, I present a method to determine the age of this snail and its age at sex change. The growth striae on the operculum were studied and compared to the age estimated by the Gompertz growth function based on growth data obtained from mark-recapture experiments. There is a significant correlation between the number of striae on the operculum and the age estimated from the Gompertz growth function, and the relationship is 1:1. These results suggest that the number of striae on the operculum can be used as an age index, with each stria representing 1 year of age. The age of sex change of this snail, according to my estimates by both stria number and aperture-length inferences, occurs between 4 and 6 years old. Growth rates of the snails are negatively correlated to size. Furthermore, individuals undergoing sex-change grew faster than males and females. This snail, Coralliophila violacea, forms snail patches on the surface of the massive coral, Porites spp. Secondly, the social factors were analyzed for the timing of this sedentary snail. These factors include the sex ratio, number of male and females, and the size of females in the snail patches, all of which could be important information in determining the timing of sex change. In this study only the size of the largest female could be significantly correlated with the size at sex change in a snail patch. Finally, I survey the distribution, size and reproductive characteristics of the snail, Coralliophila violacea (Lamarck), which inhabits the surface of both the branching coral Porites nigrescens and the massive corals, P. lobata and P. lutea. Based on these results I examined the host effect on (1) population structure and (2) reproductive characteristics, including the size at sex change of symbionts. On branching hosts, most snails were solitary, whereas on massive hosts, most had formed multiple-snail patches. Significantly smaller snails as well as proportionally more females were found on branching than on massive hosts. Furthermore, the fecundity of the females on the branching hosts was significantly lower than that on the massive hosts. The size at sex change (male to female) of the snails was smaller on the branching hosts than on massive hosts. Patch composition differences can partly explain the smaller size at sex change for snails on branching hosts; however, there was also evidence that host morphology had a significant effect on the timing of sex change.

Abstract This study uses different morphometric methods to study morphological variation in the population of Engyprosopon grandisquama near the southwestern coast of Taiwan. In addition to the traditional multivariates method , geomorphmetric methods, including the Baselined method and General resistant fit method were used and the results were compared. Results from ocular-side and blind-side analysis are similar. Appearance among locations is different. Overall, each sample including all specimens from all stations can be classified into either two or three groups, depending on the employed method, as well as characters of blind and ocular sides being used. The groups are¡GYung-an, Tso-ying, and Kao-ping-hsi. The latter area appeared to be shifting between the other two groups. Bigger fish, estaminated by centroid-size, morphometric methods, appeared to stay in deeper water(60~80m), and their morphometric performance is different from those in shallow water. Analysis of variance from the General linear model showed significant regression relationships of centroid-size against distances of sampling site to different harbor estuary. The orders of their effectiveness of dosal-side are Tso-ying, Kaohsiung, Yung-an and Kao-ping-hsi respectively. Effectiveness based on blind-side characters are Tso-ying, Kaohsiung, Kao-ping-hsi and water depth. Generally speaking, most samples can be separated into three area-groups, which are¡G(1)Yung-an, (2)Tso-ying and (3)Kao-ping-hsi. Effect of water depth are better expressed by the blind-side characters, whereas effect of the area-sites are better expressed by the ocular-side characters.

The Klamath-Siskiyou Ecoregion of northern California and southern Oregon has extremely high biodiversity, but conservation centers on the protection of habitat for the northern spotted owl. A network of late successional reserves has been established without consideration of potential for protecting overall biodiversity, including genetic diversity. Mitochondrial DNA sequences are used to examine the population structure of Acrotrichis xanthocera (Coleoptera: Ptiliidae) sampled from five late successional reserves within the Klamath-Siskiyou Ecoregion and five comparison sites from northern California. Measures of gene flow, phylogenetic analysis, and nested clade analysis are employed to infer historical demographic and phylogeographic processes. Results show that A. xanthocera populations have undergone past range expansion, but gene flow is currently limited. Individual late successional reserves do not adequately protect the genetic variation in this species. Although further research is needed, these results are likely to be congruent for other edaphic arthropod species. Improvement of the late successional reserve system is warranted for maximum protection of the genetic diversity of soil arthropod populations.

Incorporating molecular genetic data into management decisions would provide fisheries managers with new tools to identify the magnitude of population structure, metapopulation dynamics, at risk populations, and possible genetic interactions between species, so that management strategies could be tailored to better support long-term viability of species and populations. Alewife (Alosa pseudoharengus) and Blueback Herring (Alosa aestivalis) are two closely related anadromous clupeid fishes native to the Atlantic coast of North America. Current management strategies for these two species, collectively known as river herring, take no account of stock structure or even the distinction between the two species. Using 12 neutral microsatellite loci, I examined at multiple spatial scales the patterns of population structure and genetic differentiation for river herring, with particular reference to comparisons of population structure in the U.S., where extensive stocking has occurred, and Canada, where there has been no stocking. Results suggested strong population structure within the Canadian portion of the range and weaker population structure in the U.S. portion. Highly significant genetic isolation by distance (IBD) for parts of the range unaffected by stocking provided evidence of natal homing and limited dispersal. The differing IBD results obtained in three Canadian regions may reflect differences in historical biogeographical factors and contemporary dispersal patterns among regions. Very weak differentiation and an absence of significant IBD for American stocked populations provided evidence that stocking has reduced genetic differentiation between populations in the U.S. portion of the range, except for two divergent stocked populations that appeared to have resisted homogenization. Evidence of recent population bottlenecks were identified in both U.S. and Canadian populations. The genetic structure of Blueback Herring populations appeared to be similar to that seen in Alewife. When sampled in the same river, Alewife and Blueback Herring were strongly differentiated, although hybrids of the two species were detected. Evidence of genetic impacts of stocking, regional variation in patterns of population structure and complex genetic interactions between the species suggest that current management strategies should be re-evaluated.

Natural hybrid zones provide opportunities to study a range of evolutionary phenomena from speciation to the genetic basis of fitness-related traits. Additionally, investing the structure of hybrid zones can provide valuable insight in the ecology and evolution of species. The present dissertation approaches the investigation of natural hybrid zones between Xiphophorus birchmanni and X. malinche from a population genetics perspective. The goal of the chapters herein are to investigate the genetic structure of these natural hybrid zones overall and the genetic structure of the populations within them in an effort to better understand the factors producing and maintaining spatial genetic patterns among this species pair and their hybrids. Using informative single nucleotide polymorphisms (SNPs) in one mitochondrial and three nuclear intron loci, I show that hybrid zones occur in replicated fashion in multiple stream reaches along a gradient from high to low elevation. Tests of FIS and linkage disequilibrium (LD) revealed significant genetic structure within a small subset of populations. Specifically, parentals and hybrids all three occur in some locations while other locations appear to be hybrid swarms. I then investigated a behavioral mechanism of reproductive isolation - social association, which might affect population structure. In clean water, individuals shoaled significantly more closely with conspecifics. Additionally, genotyping of females and their embryos revealed signatures of non-random mating in structured populations. Taken together, assortative social grouping, which may translate to assortative female mate choice, likely plays a role in maintaining population structure. Finally, I show that fluctuating asymmetry is significantly higher in unstructured than structure populations. This is a further indication that some form of non-random mating occurs in structured populations and has effects on male phenotypes.

Population structure and phylogenetic relationships were studied in coccidia parasitizing the rodent families Muridae and Arvicolidae, in 40 localities in 14 European countries. Sequences of mitochondrial gene for cytochrome c oxidase subunit I (COI) and nuclear 18S rRNA gene (SSU) were used for phylogenetic analyses and for reconstruction of evolutionary relationships among coccidian species.

Abstract Mitochondrial DNA sequences were used to study the phylogeny, population structure and colonisation history of Parus species. The phylogenetic relationships of seven European and three American species were examined by sequencing a part of the cytochrome b gene. Phylogenetically the closest species were the great tit (Parus major) and the blue tit (P. caeruleus). Subgenus Poecile was divided into two clades, one consisting of the Siberian tit (P. cinctus), the Carolina chickadee (P. carolinensis) and the Black-capped chickadee (P. atricapillus) and the other consisting of the marsh tit (P. palustris) and the willow tit (P. montanus). The coal tit (P. ater) and the crested tit (P. cristatus) did not group with any of the species studied. The population structure and the colonisation history of the willow tit, the great tit and the blue tit were examined by using control region sequences. The results suggest that the historical effective population size in the willow tit has been large and not contracted by the last ice age. Current gene flow must also be extensive as no population structuring was detected. No population structuring was evident either in the great tit and the populations showed distinctive signs of a recent population expansion. The patterns of genetic variation probably reflect a population bottleneck during the ice age, and a recolonisation of the European continent thereafter, presumably from a refugium situated in the Balkans. Two maternal lineages were found in the blue tit. The southern lineage was restricted to the Iberian peninsula whereas the northern lineage was detected from all the populations. The colonisation history has been similar to the one suggested for the great tit. The southern lineage, however, may have survived the ice age in a different refugium in the Iberian peninsula and was not as successful as the northern lineage in colonising available regions when the ice retreated. Both, the blue tit and the great tit have continued to expand their distribution northwards during this century and gene flow plays an important role in homogenising the populations.