https://www.um.edu.mt/library/oar/handle/123456789/21577 2026-04-15T04:06:02Z https://www.um.edu.mt/library/oar/handle/123456789/121359 Title: Global phylogeography and Mediterranean genetic structure of the endangered dusky grouper, Epinephelus marginatus (Teleostei: Serranidae), based on mitochondrial and microsatellite genetic markers Abstract: The aim of this research is to describe the evolutionary relationship, demographic history and connectivity patterns of the endangered marine fish Epinephelus marginatus (Lowe, 1834) on a local, regional and global scale for the purpose of aiding in conservation management strategies. Assessment was based on an integrative approach to molecular population genetics using comparative phylogeography and coalescent based methodologies which has allowed for resolution of evolutionary processes, diversification of lineages, and phylogenetic species delimitation. The basis of molecular analyses were conducted using subsets from 377 E. marginatus samples collected from 17 localities and three continents throughout their global distribution in the Atlantic Ocean, SW Indian Ocean and Mediterranean Sea. Local and regional assessment pertaining to the central Mediterranean Maltese Fisheries Management Zone was based on 14 microsatellite genetic markers and describes a population decreasing in size (θH = 2.2), which has gone through a significant size reduction in the past (M = 0.41) and consequently shows signs of moderate inbreeding (FIS = 0.10, ρ < 0.001) with an estimated effective population size (Ne) of 130. Spatially explicit Bayesian genetic cluster analysis detected two geographically distinct subpopulations within the Fisheries Management Zone and resolved that they are regionally connected to a larger network within the Sicily Channel. Evaluation of global phylogeography was based on a 398 base pair catenated alignment of high density intraspecific variation spanning part of the tRNA proline gene and d-loop from the mitochondrial control region. Spatial Bayesian inference identified five explicit biogeographic populations throughout their global range in the Azores, Brazil, Senegal, South Africa and Mediterranean Sea. Molecular clock convergence analysis founded on within lineage mutation rate divergence surmised that E. marginatus has been present in the Azores since the Calabrian Age during the Pleistocene Epoch, however establishment of the remaining global populations began more recently during the Middle Pleistocene with colonisation of the nouveau Mediterranean lineage occurring around 150,000 years ago. Analysis conducted using a Bayesian model of random coalescence estimated that the global population of E. marginatus’ has grown roughly 25% over the last 100,000 years, mostly owing to expansion in west Africa, with a modern effective population size estimate (Nef) of around 4.4 million. Global AMOVA (ΦST = 0.44647, ρ < 0.001) and an exact test of population differentiation (ρ < 0.001) detected great and significant bifurcation between global populations. These findings are likely a reflection of strong biogeographic barriers to gene flow detected by Monmonier’s algorithm (bootstrap 92-100) leading to vicariance of global lineages. The high haplotype (h = 0.51-0.99) and low nucleotide (π = 0.019-0.037) diversity found is consistent with the hypothesis of itinerant peripatetic pelagic larval dispersal as the main mode of global spatial expansion. A haplotype network constructed with the TCS algorithm also revealed several substitutions between lineages suggesting once established each region has remained historically independent. Long-term estimates of asymmetrical immigration between global populations predicted using the Metropolis-Hastings sampler method of random coalescence were found to be low (ɣ̅ji = 1.73 individuals gen-1), reinforcing the notion of independent lineage trajectory following long-distance founder events. Whilst E. marginatus’ appear to display morphological cohesiveness throughout their global distribution, intraspecific genetic partitioning of lineages can be seen reflected in significant pairwise ΦST (0.31–0.69, ρ < 0.001) and Nei’s DXY (3.5–16.3, ρ < 0.001), where objective use of Nei’s D (DXY > 0.15), ΦST (ΦST > 0.25) and the Poisson Tree Process (bootstrap > 95) collectively identified the Azorean population as a separate phylogenetic unit. Mantel tests revealed genetic isolation by distance was not a fundamental factor influencing global population vicariance or lineage divergence. The process of vicariance leading to allopatric speciation is often gradual, where lineage divergence is representative of cryptic speciation on a continuum. In conclusion, evidence presented suggests that five Evolutionarily Significant Units should be assigned to each of the biogeographically discrete global populations and that assessment of species status and conservation management should be undertaken at a local level due to habitat fragmentation and population substructuring. Description: PH.D. 2017-01-01T00:00:00Z https://www.um.edu.mt/library/oar/handle/123456789/36062 Title: Presence of microplastics in upper infralittoral soft sediment habitat and influence on infaunal assemblages Abstract: The purpose of this research was to establish the presence of microplastics in upper infralittoral soft sediment habitat and influence on infaunal assemblages. Ten beaches were selected from Malta, Comino and Gozo and samples were collected at 0m, 3m and 7m depth using traditional SCUBA techniques. Samples were then analyzed for percentage organic carbon, mean grain size, levels of microplastic and biotic studies. The present results indicate a relationship between mean sediment grain size and percentage organic carbon in sediment, both of which appear to affect macrofauna found in sediments. Sediment grain size appears to have an overriding effect on other variables. On the other hand, the present results do not indicate a relationship between levels of microplastics in sediment and biological attributes of the macrofaunal assemblages associated with soft sediment habitat. Microplastics sizes ranged from 0.5mm to 5mm whilst the majority of the microplastics identified were filamentous with a variety of colours. Lowest levels were found at 7m depth Mellieha Bay with no microplastics collected whereas highest levels were found at 0m depth Mellieha Bay and St George’s Bay at 7.5 items per 50g. These values are considerably higher than those recorded in the Maltese Islands in previous studies as well as higher than most global studies suggesting a substantial problem in the Maltese Islands. Sizes ranged from 0.5mm to 5mm whilst the majority of the microplastics identified were filamentous with a variety of colours. Findings of this study are useful as they represent a first indication of levels of microplastics in shallow waters infralittoral coastal waters around the Maltese Islands, however future studies should be aimed at a design that considers extensive sampling effort over smaller spatial scales. Description: M.SC.BIOLOGY 2017-01-01T00:00:00Z https://www.um.edu.mt/library/oar/handle/123456789/22055 Title: Multiscale analysis of the species diversity of Maltese shrubland Abstract: The aim of this study was to determine whether the species diversity and composition of a plant community depend on the scale at which the study is carried out, and to determine the effect of certain site characteristics and the presence of dominant species on species diversity at different spatial scales. The study was carried out using a hierarchically nested sampling design at four spatial scales (125m x 125m, 25m x 25m, 5m x 5m, and 1m x 1m) in six shrubland sites in the Maltese islands. The design was balanced across scales meaning that the change in scale from a smaller unit to a larger one was consistently incremental. Each sampling plot comprised five subplots of the next lower scale. Amalgamated abundance data for all perennial plant species was collected from the study plots between October 2015 and August 2016. Seven site characteristics (Aspect, Slope, Elevation, Rock type, Exposure, Soil pH, and Soil electrical conductivity) were measured for each site, but only the three that contributed most to the variation between sites (Elevation, Exposure, and Slope) were included in the analyses. The data was analysed using multivariate techniques (RDA, DCA, CCA, and PCA) and the vegetation distribution patterns were related to the site characteristics. The plant communities in each of the six sites had their own distinctive ‘vegetation signature’ that was recognizable at all scales, although less clearly at the 1m x 1m spatial scale. The observed species richness, estimated species richness (Chao-1 index), and N2 diversity all increased as the spatial scale increased in all six sites, while evenness decreased. Moreover, the observed and estimated species richness of a community at smaller scales was highly correlated with that at larger scales. The three site characteristics together explained 61.9% of the variability in community composition across the six sites at the largest spatial scale. When the abundance of Thymbra capitata was added as an explanatory factor, the explained variation rose to 86%. The abundance of Thymbra capitata explained more of the variation in community composition at the largest scale compared to the smallest. This effect of Thymbra capitata was unexpected, as previous studies had suggested that the effect of woody shrubs was greater at smaller scales. At all four spatial scales, higher species richness and diversity were associated with lower abundance of Thymbra capitata and vice versa. The results of this study showed that a multiscale approach towards species diversity would provide more relevant information than that obtained from a single scale. The results also showed that assessment of community composition should be carried out using study areas of at least 25m x 25m because at this scale, the vegetation ‘signatures’ of each community are still very distinct from each other. Description: M.SC.BIOLOGY 2017-01-01T00:00:00Z