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: The current list of Chinese quarantine pests includes 130 fungal species. However, recent changes in the taxonomy of fungi following the one fungus = one name initiative and the implementation of DNA phylogeny in taxonomic revisions, resulted in many changes of these species names, necessitating an update of the current list. In addition, many quarantine fungi lack modern morphological descriptions and authentic DNA sequences, posing significant challenges for the development of diagnostic protocols. The aim of the present study was to review the taxonomy and names of the 33 Chinese quarantine fungi in Dothideomycetes, and provide reliable DNA barcodes to facilitate rapid identification. Of these, 23 names were updated according to the single name nomenclature system, including one new combination, namely Cophinforma tumefaciens comb. nov. (syn. Sphaeropsis tumefaciens). On the basis of phylogenetic analyses and morphological comparisons, a new genus Xenosphaeropsis is introduced to accommodate the monotypic species Xenosphaeropsis pyriputrescens comb. nov. (syn. Sphaeropsis pyriputrescens), the causal agent of a post-harvest disease of pears. Furthermore, four lectotypes (Ascochyta petroselini, Mycosphaerella ligulicola, Physalospora laricina, Sphaeria lingam), three epitypes (Ascochyta petroselini, Phoma lycopersici, Sphaeria lingam), and two neotypes (Ascochyta pinodella, Deuterophoma tracheiphila) are designated to stabilise the use of these names. A further four reference strains are introduced for Cophinforma tumefaciens, Helminthosporium solani, Mycocentro spora acerina, and Septoria linicola. In addition, to assist future studies on these important pathogens, we sequenced and assembled whole genomes for 17 species, including Alternaria triticina, Boeremia foveata, B. lycopersici, Cladosporium cucumerinum, Didymella glomerata, Didymella pinodella, Diplodia mutila, Helminthosporium solani, Mycocentrospora acerina, Neofusicoccum laricinum, Parastagonospora pseudonodorum, Plenodomus libanotidis, Plenodomus lingam, Plenodomus tracheiphilus, Septoria petroselini, Stagonosporopsis chrysanthemi, and Xenosphaeropsis pyriputrescens.

Description: Rosa (Rosaceae) is an important ornamental and medicinal plant genus worldwide, with several species being cultivated in China. Members of Sporocadaceae (pestalotioid fungi) are globally distributed and include endophytes, saprobes but also plant pathogens, infecting a broad range of host plants on which they can cause important plant diseases. Although several Sporocadaceae species were recorded to inhabit Rosa spp., the taxa occurring on Rosa remain largely unresolved. In this study, a total of 295 diseased samples were collected from branches, fruits, leaves and spines of eight Rosa species (R. chinensis, R. helenae, R. laevigata, R. multiflora, R. omeiensis, R. rugosa, R. spinosissima and R. xanthina) in Gansu, Henan, Hunan, Qinghai, Shaanxi Provinces and the Ningxia Autonomous Region of China. Subsequently 126 strains were obtained and identified based on comparisons of DNA sequence data. Based on these results 15 species residing in six genera of Sporocadaceae were delineated, including four known species (Pestalotiopsis chamaeropis, Pes. rhodomyrtus, Sporocadus sorbi and Spo. trimorphus) and 11 new species described here as Monochaetia rosarum, Neopestalotiopsis concentrica, N. subepidermalis, Pestalotiopsis tumida, Seimatosporium centrale, Seim. gracile, Seim. nonappendiculatum, Seim. parvum, Seiridium rosae, Sporocadus brevis, and Spo. spiniger. This study also represents the first report of Pes. chamaeropis, Pes. rhodomyrtus and Spo. sorbi on Rosa. The overall data revealed that Pestalotiopsis was the most prevalent genus, followed by Seimatosporium, while Pes. chamaeropis and Pes. rhodomyrtus were the two most prevalent species. Analysis of Sporocadaceae abundance on Rosa species and plant organs revealed that spines of R. chinensis had the highest species diversity.