This thesis examines the European phylogeography of the meadow grasshopper Chorthippus paralleJus. This common species has a very large range covering Europe, southern Scandinavia, Turkey and Russia, with two recognized subspecies. These are c.p.erythropus in Spain and c.p.paraJ1eJus in other regions. This species has been studied using mtDNA RFLPs and sequence data. The greatest levels of genetic subdivision were found to occur between southern Spain, southern Italy and the Balkans. No subdivision was detected between Balkan populations and those in central and northern Europe. These data were interpreted as indications that at least three refugia existed in Europe during the last glaciation. The historical locations of these refugia can be inferred to have been in southern Spain, southern Italy and the Balkans. Furthermore, postglacial expansion from the Balkan refugium is indicated as the origin of central and northern European populations of C.paralleJus. A phylogeny of common European Chorthippus species, and closely related genera, is presented from analysis of mtDNA sequence data. This analysis indicates that, although there are many similarities to the traditional morphological taxonomic arrangement, several revisions need to be considered and investigated further. These include the position of the monospecific genus Stauroderus outside of the Chorthippus clade and the division of these Chorthippus species into 3 subgenera. Finally, the evolutionary patterns of the cytochrome oxidase subunit I (COl) gene, which was used for the Chorthippus studies, are investigated for insects in general. The patterns of amino acid variability indicate regions of very different substitutional rates within this gene. These regions are discussed in terms of the known and assumed functional constraints on gene function. The variety of evolutionary rates in adjacent regions are considered further with regard to their utility in different levels of phylogenetic study, and conserved insect primers for the exploitation of these regions are presented.

The Atlantic sailfish (Istiophorus platypterus) is considered over-fished in U.S. waters. Furthermore, preliminary analyses of abundance indicate that a decline in biomass has occurred. While seminal studies have provided useful baseline data about intra- and inter-oceanic variation within sailfish, such studies may have underestimated the amount of genetic variability as a result of small sample sizes and the poor resolution of restriction fragment length polymorphism data. We used 263 base pairs from the hypervariable mitochondrial control region and fragment polymorphisms from five microsatellite loci to assess the contemporary population structure between eastern (n = 30) and western (n = 192) Atlantic sailfish stocks. We failed to reject the hypothesis of panmixia in Atlantic sailfish; however, higher levels of genetic variation were observed within the eastern Atlantic sailfish, and the nature of this difference needs to be investigated further. Having found no evidence of transatlantic differentiation, we pooled the Atlantic samples (n = 222) and compared them to a sample from the eastern Pacific (n = 22) and rejected the null hypothesis, concluding that sailfish from separate ocean basins do not share a common gene pool. We also found evidence of a recent sudden expansion of Clade I (the ubiquitous clade found in both Atlantic and Pacific Oceans) sailfish into the Atlantic that appears to have occurred between 164000 and 351000 years ago, coinciding with interglacial periods during the Pleistocene. This study also presents the first evidence of a recent sudden expansion of sailfish into the eastern Pacific, roughly 85400 to 173000 years ago, following a period when cooling in the eastern Pacific would have restricted the sailfish range to the warmer waters of the western Indo-Pacific. We emphasize that sailfish from this region of the Pacific are phenotypically distinct from those in the rest of the species' range and encourage further studies in order to determine if the eastern Pacific sailfish population should be managed as a separate stock.

Cryptic species complexes are common in many marine groups. Recent phylogeographic studies in the megadiverse Gulf of California basin have found high levels of cryptic allopatric genetic differentiation in supralittoral isopods. Long standing isolation among populations of these isopods appears to stem from biological characteristics that severely limit their dispersal potential, such as direct development (i.e., lacking a larval stage), as well as a strong association to specific intertidal patchy habitats. Studies of other intertidal isopods have the potential to reveal high levels of cryptic allopatric genetic differentiation. This study examined phylogeographic patterns of intertidal isopods of the genus Excirolana distributed in the Gulf of California. Adults of these isopods are distributed at the highest tidal levels, and phylogeographic studies of Excirolana in Panama and Chile have shown restricted gene flow among populations separated by relatively short distances. Excirolana samples were collected across the Gulf of California, as well as from the Atlantic and Pacific coasts of South and Central America, and from several Caribbean islands; encompassing most of the geographic range for the Excirolana species reported in the Gulf of California. Sequences of DNA fragments from four mitochondrial genes were obtained, and phylogenetic analyses with Maximum Likelihood and Bayesian methods were conducted. Diagnostic morphological characteristics were examined to determine whether individuals corresponded with any of the three species reported in the Gulf of California: E. braziliensis; E. mayana; and E. chamensis. Isopods with morphological characteristics of E. braziliensis and E. mayana were found. In general, relatively low genetic diversity was observed within localities. Phylogenetic analyses indicate that samples with the morphology of E. braziliensis formed a well-supported clade, whereas individuals with the E. mayana morphology formed another well-supported clade. Highly divergent lineages were observed within each of these clades, suggesting they represent cryptic species complexes. In the Gulf of California, several regional clades and subclades of Excirolana exhibit similar distributions to those of several clades within the supralittoral isopods Ligia and Tylos. This study allows a better understanding on the phylogenetic relationships, phylogeographic patterns, and diversity of Excirolana in the Gulf of California, and the Americas in general.

Thesis (M.S.)--Auburn University, 2007. / Abstract. Includes bibliographic references.

Chronic copper toxicity was found to result in growth hormesis in both C. hvalina and E. pilosa. Tolerance levels of the bryozoans to copper contamination were found to be high in comparison with those of other marine organisms. Generally, both genotype and copper dosage affected growth and sexual functions, but genotype had no affect on organism response to copper. Nonetheless, large differences in responses were detected between the two E. pilosa populations examined. Variation in tentacle number of C. hyalina colonies was found to be very limited and dietary regime was not observed to have a marked influence upon this trait. In contrast, colonies of E. pilosa were found to produce more tentacles per lophophore in optimal dietary conditions. Significant differences were detected between two E. pilosa populations in astogeny, sexual maturity and tentacle number. Laboratory experiments designed to identify the cue for induction of extended (long) medium proximal spines in E. pilosa colonies were unsuccessful. Differences in spine growth were again identified between the two E. pilosa populations from contrasting sites. Reciprocal transplantation demonstrated that `long' spine formation was triggered in colonies previously possessing only `short' spines and vice versa. Flume observations of particle path trajectories imply that spine formation may result in near-colony flow conditions which are more favourable to feeding in high flow velocities. Demographic analysis using the RAPD technique for both C. hyalina and E. pilosa indicate population structuring corresponding to their contrasting modes of larval dispersal. Populations of C. hyalina appear to exhibit considerable genetic differentiation over distancesa s small as 100 m, whereasE . pilosa is characterisedb y high levels of genetic heterogeneity over much larger spatial scales. E. pilosa population differentiation is observed at a site some 80 Km distance, which may be a consequenceo f hydrographic features. Evidence from analysis of mtDNA (COI) and observations on reproductive isolation and morphological differentiation indicate high levels of cryptic speciation amongst globally distributed populations of C. hyalina. It is suggested that the Chilean C. hyalina population is sufficiently different from all other populations examined to be considered a separate species.

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Australian Acacia species are an important group of invaders and are known to form dense monospecific cultures in invaded habitats. Despite the ecological and economic importance of invasive acacias, little is known about their invasive biology both from an ecological and evolutionary perspective. Molecular genetic methods have increasingly become important in identifying source populations for invasive species and determining the population genetic structure of these populations. This thesis applied molecular tools to understand the invasion ecology of Acacia pycnantha and its rhizobial symbionts as a model system of Australian Acacia introductions. Specific objectives were to: reconstruct the molecular phylogeny of invasive and native populations of populations of Acacia pycnantha and identify the native provenance of A. pycnantha; identify microsatellite markers for Acacia pycnantha and other invasive Australian acacias based on transferring microsatellite markers developed for A. mangium, A. saligna, Paraserianthes lophantha and universal chloroplast microsatellites developed from tobacco; assess the introduction dynamics of Acacia pycnantha in South Africa and identify the source populations in the species’ native range ; and determine which nitrogen fixing symbionts nodulate A. pycnantha and determine whether A. pycnantha brought its symbionts along from its native range or acquired them in the invasive range. Nuclear and chloroplast DNA sequence data were used to reconstruct phylogeographic relationships between native and invasive A. pycnantha populations. The chloroplast phylogeny showed that Australian populations of A. pycnantha are geographically structured into two previously informally recognized lineages (representing wetland and dry land forms). Habitat fragmentation is probably the result of cycles of aridity and abundant rainfall during the Pleistocene0. The invasive population in Portugal was found to be the wetland form while South African populations were found to be predominantly wetland form although some dryland forms were identified. Thirty microsatellites out of the forty nine tested microsatellites successfully amplified across all species tested (A. implexa, A. longifolia, A. melanoxylon, A. pycnantha and A. podalyriifolia). High Transfer rates varied between 85% for microsatellites developed for A. mangium to 50% for those developed in A. saligna. Although transfer rates were high only twelve microsatellites (24%) out of the fifty tested were polymorphic while the chloroplast microsatellites showed no polymorphism. The low level of polymorphic loci calls for development of more microsatellites in this genus especially for species that have high commodity value. Nuclear microsatellites revealed three genetic groupings with substantial admixture in the native range (1. wetland Victoria and South Australia populations; 2. dryland Victoria and Flinders Range population; and 3. New South Wales). Admixture in the native range may have occurred as a result of reforestation exercises. Acacia pycnantha has been widely used in rea forestation projects in Australia because of its fast growth rate and ease of germination. Admixed populations were most - likely introduced to South Africa thus establishment of A. pycnantha may have been facilitated by already admixed propagules in the invasive range. Extensive admixture in the native range made it difficult to identify source populations of invasive A. pycnantha found in South Africa. The rhizobial symbionts of A. pycnantha were identified, showing that this species utilizes a wider suite of symbionts in its invasive range than its native range and there is support for both the co-introduction and host jumping hypotheses. This creates substantial opportunities for horizontal gene transfer between previously allopatric bacterial lineages, with as yet unknown consequences for plant and bacterial invasions.

New Zealand is a continental island surrounded by deep-ocean, with a complex system of currents and oceanographic anomalies that may serve to isolate populations of coastal marine organisms. In particular Cook Strait is a 26 km wide body of water separating the North and South Islands which is characterised by complex interactions of tides and converging water masses. Cook Strait is a geologically recent formation that may also impart an historical influence on the biogeographic distribution of coastal marine taxa. In order to investigate the phylogeographic structure of coastal marine taxa around New Zealand's coastline and to investigate the processes that may contribute toward this genetic structure, I analysed mitochondrial DNA genes from limpet species of the Cellana genus. Phylogenetic analyses of the ribosomal 12S and 16S DNA genes showed that C. ornata may approximate the founding lineage to New Zealand, but these genes were unable to resolve between contrasting biogeographic hypotheses about the origin of Cellana in New Zealand. Intraspecific analyses of the mitochondrial cytochrome b gene from populations throughout the biogeographic range of Cellana ornata, C. radians and C. flava showed concordant genetic discontinuity at Cook Strait. Further analyses suggest that allopatric fragmentation and restricted gene flow have caused significant genetic differentiation between populations of the North and South Island. Demographic expansion was also identified for C. radians. The influence of contemporary nearshore currents and sea surface temperature was assessed using the mitochondrial cytochrome b gene for C. radians and C. ornata. Low levels of genetic differentiation between populations corresponding to 'current-zones' suggests that contemporary oceanic processes may be contributing to the genetic pattern observed for these species. However, the shallow divergence between haplotypes and populations restricted thorough investigation of contemporary gene flow. Genealogical concordance across co-distributed marine taxa of New Zealand also lends support to the historic association of genetic and species discontinuities with recent geological changes, such as sea level fluctuations.

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