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Japan is one of the world’s 34 biodiversity hotspots, according to Conservation International (CI). The methods used by various organisations to define priorities differ, however, and all have weaknesses when trying to identify hotspots at finer resolutions. The goal of this thesis is to investigate how biodiversity hotspots in Japan could be revealed and mapped in order to encapsulate conservation elements of biodiversity in practical ways and at various scales. Bioquality is a term that emphasises the concentration within a community of elements of biodiversity with high conservation value. It evaluates the global rarity and taxonomic distinctiveness of plant species or infra-specific taxa using four Star categories. At a plant community level, the Genetic Heat Index (GHI), which is a standardised global range size rarity score, is calculated using weighted Star statuses of species in the community. Bioquality hotspots are assessed here for the first time for the flora and vegetation in Japan – and for temperate Asia – by categorising the Japanese flora into Stars and by applying GHI to survey data and literature-based sources. Keys to Stars are developed for the Japanese flora, with adjustments for variability in species geographic range size information and for taxonomic relatedness. A Flora of Japan (FOJ) database was compiled as a BRAHMS database, containing 8,262 accepted names (30,656 taxon names in total, including synonyms) in 258 families – the first full database of Japanese vascular plants. A total of 7,145 taxa are assigned Stars; from the rarest to the widespread class, there are 884 Black, 756 Gold, 833 Blue, and 4,672 Green Star taxa, confirming that Japan as a whole contains a high proportion of globally rare taxa (23% taxa in Black or Gold). A protocol for calibrating the weight of Stars based on species geographic range is developed based on fine-resolution distribution maps within Japan and coarse–resolution Taxonomic Database Working Group (TDWG) code information. The protocol optimises calculation for temperate regions. The first ever bioquality hotspot maps of Japan are produced using two independent data sources on species distribution at national level: 1) 50 botanical prefectures using 4,830 species from the FOJ database; 2) 1,418 Horikawa ‘geoquadrats’ (0.1° latitude by 0.15° longitude grid) maps covering 829 species. The Ryukyu Islands and Ogasawara Islands are identified as bioquality hotspots, and high mountain ranges in mainland Japan are predicted to contain areas potentially high in GHI; the spatial patterns of GHI are generally concordant between maps of different resolutions. These findings highlight that bioquality assessment can be applied meaningfully at various spatial resolutions. Using field sampling data and existing literature, three study sites are further investigated on a local level: 1) the satochi-satoyama landscape, the current national priority area for biodiversity conservation; 2) various vegetation types of Okinawa-jima Island, the Ryukyu Islands; and 3) the Utaki sacred groves within the predicted hotspot of the Ryukyu Islands. The Ryukyu Islands are confirmed to contain bioquality hotspots within many individual sites, while there was generally low GHI across the satochi-satoyama landscape. The field study outcomes, together with a gap analysis of the existing coverage of protected areas, highlight three important points that are directly relevant to national biodiversity conservation planning: 1) the Ryukyu Islands urgently need newly designated protected areas; 2) the satochi-satoyama landscape conservation should redirect its focus on cultural benefits to the public; 3) the existing protected areas, particularly on mountain areas, need re-evaluation in terms of upgrading their status in light of the bioquality assessment.

Few studies of tropical fish communities compare fish distributions across the full range of near-shore tropical marine habitats. As a result, our understanding of tropical marine fish communities is often biased towards habitats preferred by researchers. The distribution and habitat preferences of all 136 fish species occurring at 106 stations in three bays off Tortola in the British Virgin Islands were assessed. At a species level, habitat type was often the key factor influencing fish distribution. Of the 44 species occurring at more than 10 stations, 3 were sand specialists, 5 were strongly associated with mangroves, 7 were dependent on seagrass and algal beds and 14 were found only on the forereef. Eleven species were widely distributed both on the forereef and in bays, and 9 of them showed clear evidence of ontogenetic partitioning. The juveniles all preferred bay habitat types and moved onto the forereef as they approached sexual maturity. At a community level, five distinct fish assemblages were found. The assemblage types were classified according to their distribution: 1) forereef, 2) reef flat, 3) non-mangrove associated seagrass, 4) mangrove associated seagrass and 5) eutrophic areas. Forereef stations were the most species-rich with 24 species per station while eutrophic stations had the most depauperate communities with only 4 species per station. Variation in fish species richness at each station was largely explained by a simple habitat complexity index. It accounted for 70% of the variation in fish species richness and 21% of the variation in fish abundance. Rugosity and variety of growth forms were the most important predictors of species richness, but the height of the habitat architecture was the most useful predictor of fish abundance. Artificial reefs were constructed to test the effects of each habitat complexity variable experimentally. Increasing rugosity, variety of growth forms and percentage hard substrate increased the observed number of species but increasing the variety of hole-sizes, and height had no effect. The only complexity variable that had a significant effect on fish abundance was percentage hard substrate. In addition to the static substrate structure, long-spined sea urchins Diadema antillarum affected fish distribution because small fish shelter from predators in their spines. The urchins increase species richness and abundance in low complexity seagrass beds, but on artificial reefs, where shelter was not a limiting factor, the effect was less pronounced. Organic pollution is another factor that negatively affects the fish community by reducing fish species richness and abundance. Poor water quality often alters the natural habitat, confounding observations, but fish species richness was reduced in polluted areas even when artificial reefs were used as habitat controls. The applications of these findings to the management and conservation of fish in the British Virgin Islands are discussed.

A survey of arthropods associated with exotic multipurpose trees and food crops used in agroforestry and indigenous tree species (Tamarindus indicus) grown in the wild was conducted in 1990 and 1991. The exotic multipurpose tree species (MPTs) used were: Gliricidia septum, Leucaena leucocephala and Cassia siamea growing in an alley cropping system and the food crops were Vigna unguiculata, Zea mays, and Cajanus cajan. The consequences of growing taxonomically related plant species in agroforestry systems were considered. Insecticidal knockdown technique was used to sample arthropods from the foliage. 92 species of arthropods belonging to 48 Families were found to be associated with tree species and the crops. Of these, 27 species were on MPTs, 3 species on crops, 12 species on the chosen wild tree, 13 species were shared amongst MPTs and crops while 14 species were shared between MPTs and the wild tree. A further 19 species were shared between all the groups of plant species (MPTs, crops and the wild tree) with 4 species being shared between the wild and the crop. The effect of tree pruning on arthropod communities on trees was also investigated and the results showed that pruned trees supported a richer arthropod fauna than unpruned trees. Through simulated defoliation, the impact of insect defoliators on four MPTs was also investigated. There was a considerable reduction in overall growth rate, height and diameter increment depending on the level of defoliation. Several stress factors often predispose plants to insect attack. Pruning, as a stressing agent was investigated in relation to infestation of Cassia siamea by the stem borer Xyleutes capensis. Out of the 200 pruned trees surveyed, 90 % showed the signs of borer attack, compared with only 31.5 % of unpruned trees. The role MPTs can play in aggravating infestation of stored pulses by a bruchid beetle, Callosobruchus chinensis was investigated by comparing its survival on seeds of three MPTs and Cajanus cajan. Whereas the bruchid was able to oviposit on both the MPT and crop seeds, no larval emergence was observed in any of the MPTs showing that the MPTs may not support reproduction and development of C. chinensis in the field.