Description: Three species of Mycosphaerella, namely M. eumusae, M. fijiensis, and M. musicola are involved in the Sigatoka disease complex of bananas. Besides these three primary pathogens, several additional species of Mycosphaerella or their anamorphs have been described from Musa. However, very little is known about these taxa, and for the majority of these species no culture or DNA is available for study. In the present study, we collected a global set of Mycosphaerella strains from banana, and compared them by means of morphology and a multi-gene nucleotide sequence data set. The phylogeny inferred from the ITS region and the combined data set containing partial gene sequences of the actin gene, the small subunit mitochondrial ribosomal DNA and the histone H3 gene revealed a rich diversity of Mycosphaerella species on Musa. Integration of morphological and molecular data sets confirmed more than 20 species of Mycosphaerella (incl. anamorphs) to occur on banana. This study reconfirmed the previously described presence of Cercospora apii, M. citri and M. thailandica, and also identified Mycosphaerella communis, M. lateralis and Passalora loranthi on this host. Moreover, eight new species identified from Musa are described, namely Dissoconium musae, Mycosphaerella mozambica, Pseudocercospora assamensis, P. indonesiana, P. longispora, Stenella musae, S. musicola, and S. queenslandica.

Description: Tropical coastal benthic communities will change in species composition and relative dominance due to global (e.g., increasing water temperature) and local (e.g., increasing terrestrial influence due to land-based activity) stressors. This study aimed to gain insight into possible trajectories of coastal benthic assemblages in Raja Ampat, Indonesia, by studying coral reefs at varying distances from human activities and marine lakes with high turbidity in three temperature categories (〈31 °C, 31–32 °C, and 〉32 °C). The benthic community diversity and relative coverage of major benthic groups were quantified via replicate photo transects. The composition of benthic assemblages varied significantly among the reef and marine lake habitats. The marine lakes 〈31 °C contained hard coral, crustose coralline algae (CCA), and turf algae with coverages similar to those found in the coral reefs (17.4–18.8% hard coral, 3.5–26.3% CCA, and 15–15.5% turf algae, respectively), while the higher temperature marine lakes (31–32 °C and 〉32 °C) did not harbor hard coral or CCA. Benthic composition in the reefs was significantly influenced by geographic distance among sites but not by human activity or depth. Benthic composition in the marine lakes appeared to be structured by temperature, salinity, and degree of connection to the adjacent sea. Our results suggest that beyond a certain temperature (〉31 °C), benthic communities shift away from coral dominance, but new outcomes of assemblages can be highly distinct, with a possible varied dominance of macroalgae, benthic cyanobacterial mats, or filter feeders such as bivalves and tubeworms. This study illustrates the possible use of marine lake model systems to gain insight into shifts in the benthic community structure of tropical coastal ecosystems if hard corals are no longer dominant.

Description: The evolution of the Pontocaspian lakes and seas (Caspian Sea, Black Sea, Aral Sea) is characterised by major changes in water levels, which developed into a pulsating system of connected and isolated basins. During the late Quaternary (Late Pleistocene and Holocene), these basins have hosted a unique endemic biodiversity that experienced species turnover events. There are indications that the Pontocaspian species diversity is now in demise because of anthropogenic modifications of the ecosystem, such as habitat alteration, poaching, pollution and invasive species. Little data is available on faunal changes and resilience of Pontocaspian species to help discerning the effect of natural drivers and anthropogenic drivers on the endemic fauna, which is of direct relevance for conservation strategies. \nThis thesis aims to characterize species richness and abundance of fossil faunas to establish a baseline for comparison with the changing biodiversity of today. Mollusc species are used as the study group as they easily fossilize and are abundant in the geological record. They inform us about the composition of communities and how they change, and enable us to reconstruct environments (\xe2\x80\x98habitats\xe2\x80\x99). This is necessary in order to compare biodiversity through different time intervals and establish whether comparable habitats existed as those of today. A baseline of Pontocaspian mollusc faunas was achieved by analysing snapshots from the Caspian Sea basin and the Black Sea basin. Caspian mollusc assemblages are analysed from late Pleistocene (corresponding to the late Khazarian, Hyrcanian, early Khvalynian and late Khvalynian regional stages) and pre-20th century Holocene (Novocaspian) assemblages. Black Sea assemblages from the late Neoeuxinian and late Holocene are described. They are both compared with modern day assemblages. \nThis study shows clear indications of a Pontocaspian mollusc diversity crisis. Overall, in the 20th\xe2\x80\x9321st century, Pontocaspian molluscs have experienced a severe decline in species richness and abundance: a strong turnover towards invasive species in the Caspian basin, a strong habitat decline in parts of the Black Sea basin and a total obliteration in the Aral basin. The late Quaternary mollusc fauna snapshots demonstrate that endemic species dominated the Caspian communities with minor contributions of native species until the late Holocene. The Pontocaspian mollusc species richness in the Caspian Sea basin is higher than in the Pontocaspian habitats of the Black Sea basin, or the Aral Sea basin. Throughout the Late Quaternary, the strong natural fluctuations of Caspian Sea level affected shallow water bivalve species of the genus Didacna, but barely changed the overall composition of the mollusc faunas. Late Quaternary mollusc fauna snapshots of the Black Sea basin show very little change in the Pontocaspian species community since humans impacted the habitats. However, the Black Sea Pontocaspian mollusc communities are currently under severe threat of habitat deterioration and destruction. \nThis research indicates that the Caspian Sea could act as a source for Pontocaspian biota, hence conservation efforts are imperative there. The deeper parts (〉50 m water depth) possibly present a (partial) refuge, and urgent research is required to assess these habitats and their faunas. Future research should focus on improving the taxonomic framework to elucidate the identity of some Pontocaspian cryptic and sister species. We need more distribution and ecological data of current Pontocaspian species and more detailed biodiversity time series coupled with detailed environmental proxies to assess the nature of the Pontocaspian biodiversity crisis more comprehensively and plan conservation actions accordingly.

Description: Much remains to be discovered about the biodiversity of coral reefs in Malaysia, making this area a priority for coral reef research. This thesis aims to provide insights into the patterns of reef coral species richness and the degree of reef connectivity across Malaysia. For the species richness study, the scleractinian coral families Fungiidae, Agariciidae and Euphylliidae were selected as model taxa. Species of these families have a wide geographical distribution in the Indo-Pacific, and they can be found in a large range of reef habitats, from shallow coastal reefs to deep offshore environments. The connectivity of reefs were inferred by examining the genetic population structures of three reef invertebrate species, the mushroom coral Heliofungia actiniformis, the blue seastar Linckia laevigata, and the boring giant clam Tridacna crocea. Data on coral species and specimens of reef invertebrates were collected from reef areas along a geographical range from east to west Malaysia. Reef coral species richness patterns were revealed and indicated common and rare species, as well as potential endemics. Factors to explain the population structure and connectivity patterns across Malaysia are discussed. The findings in this thesis may be relevant for conservation and management of coral reef areas in Malaysia.

Description: During large-scale surveys for soilborne Phytophthora species in forests and semi-natural stands and nurseries in Europe during the last decade, homothallic Phytophthora isolates with paragynous antheridia, semipapillate persistent sporangia and a growth optimum around 25 \xc2\xb0C which did not form catenulate hyphal swellings, were recovered from 39 host species in 16 families. Based on their morphological and physiological characters and the similarity of their ITS DNA sequences with P. citricola as designated on GenBank, these isolates were routinely identified as P. citricola. In this study DNA sequence data from the internal transcribed spacer regions (ITS1 and ITS2) and 5.8S gene of the rRNA operon, the mitochondrial cox1 and \xce\xb2-tubulin genes were used in combination with morphological and physiological characteristics to characterise these isolates and compare them to the ex-type and the authentic type isolates of P. citricola, and two other taxa of the P. citricola complex, P. citricola I and the recently described P. multivora. Due to their unique combination of morphological, physiological and molecular characters these semipapillate homothallic isolates are described here as a new species, P. plurivora sp. nov.

Description: In vertebrates, the relative proportion of the number of trunk and caudal vertebrae is an important determinant of body shape. While among amphibians frogs and toads show low variation in vertebrae numbers, in salamanders the numbers of trunk and caudal vertebrae vary widely, giving rise to phenotypes in the range from short-bodied and long-tailed to long-bodied and short-tailed. We analysed vertebral numbers in the family Salamandridae in a phylogenetic context and calculated the relationship between vertebral changes and changes in climate and other environmental parameters. A significant association was found between morphological change with precipitation and temperature. However, annual precipitation affected the two main groups of salamandrid salamanders differently, with trunk elongation in the terrestrial \xe2\x80\x98true salamanders\xe2\x80\x99 and tail elongation in the more aquatic \xe2\x80\x98newts\xe2\x80\x99. A - male biased - sexual dimorphism was only observed in Lissotriton vulgaris vulgaris in the number of trunk vertebrae and in Ommatotriton ophryticus and Lissotriton species for the number of caudal vertebrae. Our data indicated that the number of trunk and caudal vertebrae are highly evolvable traits with frequent evolutionary reversals. In some groups (e.g. Cynops, Lyciasalamandra, Neurergus and the Laotriton-Pachytriton-Paramesotriton clade) the number of trunk vertebrae is stable, while in many groups it is subject to change (e.g. Tylototriton). This latter, species-rich genus appears to be an excellent group to further test effects of the environment on body shape.

Description: Botanical and zoological collections may serve as archives for historical ecological research on the effects of global change and human impact on coral reef biota. Museum collections may harbour old specimens of reef-dwelling species that have become locally extinct. Such collections also help to determine whether early records of invasive species can be obtained from times when they were not yet recognized as such. A case study (2006) involving Saba Bank, Caribbean Netherlands (former Netherlands Antilles), suggests that the coral reef fauna here may have become impoverished when compared with data obtained during an earlier expedition in 1972. However, the 1972 sampling may have been incomplete, as it was performed by professional divers who were not trained taxonomists, whereas the collecting in 2006 was done by experienced marine biologists who knew the taxa they were sampling. As Saba Bank has been under stress due to the anchoring of large vessels, and invasive species have been a potential threat as well, future studies are needed to obtain more insights into the changing reef biota of Saba Bank. Using this Saba Bank example, we want to address the importance of natural history collections as reservoirs of valuable data relevant to coral reef biodiversity studies in a time of global change. As such, these collections are still underexplored and underexploited.

Description: A new Phytophthora species, isolated from rhizosphere soil of declining or dead trees of Eucalyptus gomphocephala, E. marginata, Agonis flexuosa, and another 13 plant species, and from fine roots of E. marginata and collar lesions of Banksia attenuata in Western Australia, is described as Phytophthora multivora sp. nov. It is homothallic and produces semipapillate sporangia, smooth-walled oogonia containing thick-walled oospores, and paragynous antheridia. Although morphologically similar to P. citricola, phylogenetic analyses of the ITS and cox1 gene regions demonstrate that P. multivora is unique. Phytophthora multivora is pathogenic to bark and cambium of E. gomphocephala and E. marginata and is believed to be involved in the decline syndrome of both eucalypt species within the tuart woodland in south-west Western Australia.

Description: During surveys of dying vegetation in natural ecosystems and associated waterways in Australia many new taxa have been identified from Phytophthora ITS Clade 6. For representative isolates, the region spanning the internal transcribed spacer region of the ribosomal DNA, the nuclear gene encoding heat shock protein 90 and the mitochondrial cox1 gene were PCR amplified and sequenced. Based on phylogenetic analysis and morphological and physiological comparison, four species and one informally designated taxon have been described; Phytophthora gibbosa, P. gregata, P. litoralis, P. thermophila and P. taxon paludosa. Phytophthora gibbosa, P. gregata and P. taxon paludosa form a new cluster and share a common ancestor; they are homothallic and generally associated with dying vegetation in swampy or water-logged areas. Phytophthora thermophila and P. litoralis are sister species to each other and more distantly to P. gonapodyides. Both new species are common in waterways and cause scattered mortality within native vegetation. They are self-sterile and appear well adapted for survival in an aquatic environment and inundated soils, filling the niche occupied by P. gonapodyides and P. taxon salixsoil in the northern hemisphere. Currently the origin of these new taxa, their pathogenicity and their role in natural ecosystems are unknown. Following the precautionary principle, they should be regarded as a potential threat to native ecosystems and managed to minimise their further spread.

Description: Southern African coral communities form a continuum from the more typical, accretive reefs in the tropics of Mozambique to the marginal, southernmost African distribution of this fauna in KwaZulu- Natal. While the latter are limited in size, they are gaining increasing attention as they provide a model for the study of many of the stresses to which these valuable systems are globally being subjected. Soft coral cover, comprising relatively few species, exceeds that of scleractinians over much of the southern reefs, and the coral communities attain a high biodiversity at this latitude on the East African coast. A long-term monitoring programme has revealed small yet significant changes in community structure on the reefs in recent years, concurrent with consistent increases in mean and maximum temperature. Insignificant bleaching was encountered during the 1998 ENSO event, unlike elsewhere in East Africa, but quantifiable bleaching occurred during an extended period of warming in 2000. Outbreaks of crown-of-thorns starfish (COTS) have caused longer-term changes in isolated areas. A study of coral larval dispersal and recruitment has been initiated to establish the capacity of the reefs to recover from the latter form of disturbance. The marginal nature of the reefs is further manifested by corals that generate aseasonal and atypical natural products and have a reproductive pattern that conforms with the pattern found on marginal reefs in western Australia. Calcium deposition on the reefs is also low due to physico-chemical factors that are related to latitude. Published projections on the long-term effects of climate change indicate that more reefs will become marginal as a result of global warming. Current monitoring on the South African reefs is being expanded to investigate the extent to which they will elucidate the future of more typical reefs.