Abstract Pangolins (Pholidota: Manidae) are frequently hunted as a source of bushmeat in Ghana. However, no information exists with regards to the level of trade of pangolins outside of major bushmeat market surveys in Ghana. The aim of this study was to determine the level of trade among other stakeholders in the bushmeat commodity chain for pangolins in Ghana. Data were collected from 153 stakeholders using semi-structured interviews and direct observation between September 2013 and January 2014. A total of 341 pangolins were recorded to have been traded in this study period. The white-bellied pangolin (Phataginus tricuspis) represented 82 % and the black-bellied pangolin (Phataginus tetradactyla) 18 % of the observed pangolins traded by the stakeholders. Chopbar operators accounted for the highest retailer sales to consumers. The number of pangolins traded was negatively correlated to the distance between settlements and protected forest regions. The levels of pangolin trade were previously underestimated in Ghana as the pangolin bushmeat commodity chain does not form the supply chain to the major bushmeat markets where most surveys were undertaken. The Wildlife Conservation Act of 1971 (LI 685) that prohibits the hunting of pangolins can be regarded as ineffective and not serving as a deterrent to poaching.

京都大学 / 0048 / 新制・課程博士 / 博士(地域研究) / 甲第20734号 / 地博第225号 / 新制||地||83(附属図書館) / 京都大学大学院アジア・アフリカ地域研究研究科アフリカ地域研究専攻 / (主査)教授 木村 大治, 准教授 安岡 宏和, 助教 佐藤 宏樹, 教授 市川 光雄 / 学位規則第4条第1項該当 / Doctor of Area Studies / Kyoto University / DGAM

Duikers are a species rich subfamily of threatened African antelope whose recent origin poses a challenge to the molecular identification of taxa and estimation of their phylogeny. I test the ability of DNA barcodes to identify all taxa within this group. I then use mitochondrial and nuclear genes to estimate a multi-locus species tree and to date divergence times. DNA barcodes are unable to distinguish many sister taxa, calling into question the utility of barcodes for the regulation of duiker trade or in identification of field-collected feces. The multi-locus phylogeny provides support for the relationships among major duiker lineages and placement of two problematic taxa, but challenges the validity of the savanna genus and identifies hybridization between taxa. This study reveals that most duikers diverged during the Pleistocene, meriting further inquiry into the role that Pleistocene glacial cycling played in the diversification and population structuring of duikers.

This thesis explores how indigenous communities in the neotropics affect the biodiversity of the forests in which they live; and assesses how the culture, preferences and perceptions of communities can influence the outcome of this relationship. This is first investigated via a case study that compares primate populations between a protected area in the Ecuadorian Amazon and a territory in its adjacent buffer zone that is owned by an indigenous Kichwa community. I then use an ethnoprimatological approach to investigate the attitudes of this community to primates, namely looking at (a) whether primates are seen as a distinct group, (b) the relative importance of primates as sources of bushmeat and pets and (c) the perceived value of primates in terms of their value as a resource or their ecological role. I show that diurnal primates are seen as a cohesive group, but that tree-dwelling non-primates including sloths, kinkajous and tamanduas are also frequently classified as 'monkeys'. The community's perceptions of the value of primates are more closely associated with their potential as bushmeat and pets, whereas few respondents view their importance in terms of their role in the forest ecosystem. I compare our findings to those in studies of other indigenous groups and discuss how they could contribute to more effective conservation planning. Next, I assess how hunting preferences for mammals and birds vary across communities over the whole of central America, Amazonia and the Guianan shield. I show that primates, cetartiodactyls and rodents are the mammalian cornerstones of prey provision for hunters in neotropical communities, whereas Galliformes, Tinamiformes, Psittaciformes, Gruiformes, Piciformes are the most commonly hunted bird orders. The location of a community alone is a significant but weak predictor of the structure of its hunting profile in terms of order preferences. In addition, I found no relationship between a community's age and size and the average biomass of birds or mammals hunted, or the number of mammal species that are targeted. I discuss whether the age and size of communities are robust indicators of past and current hunting pressure, as well as the suitability of cross-sectional data for monitoring large-scale hunting patterns.

Les zoonoses constituent plus des deux tiers des pathologies virales qui concernent l’homme. Le développement et la démocratisation des outils de métagénomique en font de bons outils d’inventaire et de surveillance de virus potentiellement émergents.Dans un premier temps j’ai développé et validé un protocole expérimental de purification des viromes à ARN qui permettait le maintien de l’infectivité des particules virales. Ce protocole a ensuite été appliqué pour caractériser les communautés virales d’arthropodes hématophages et de prélèvements de faune sauvage. J’ai par la suite réalisé l’inventaire des communautés virales de viande de singe fumée illégalement importée en France et confisquée par les douanes, qui a révélé la présence de nombreux bactériophages, dont certains pourraient infecter des bactéries potentiellement pathogènes pour l’homme.Enfin j’ai caractérisé les communautés virales de culicoïdes collectés au Sénégal, ce qui a permis de mettre en évidence la présence de nombreux virus géants à ADN infectant les amibes. Le séquençage des viromes à ARN a quant à lui révélé la présence d'un certain nombre d'arbovirus qui pourraient constituer un risque d’émergence pour la santé humaine. Du fait de nombreux facteurs intrinsèques et extérieurs à l’agent infectieux, la prédiction des futures émergences de virus zoonotiques est très compliquée voire utopique, mais elle reste un challenge crucial et d’actualité. La stratégie de réalisation d’inventaires des communautés virales présentes dans les différents acteurs des cycles de transmission zoonotique est un premier pas indispensable dans la connaissance des risques potentiels d’émergence en population humaine. / Zoonoses are responsible of more than two thirds of human viral infections. The development of high-throughput sequencing tools and their application in metagenomics allow inventorying the viral communities of various reservoirs in order to detect the emergence of viruses before their infection to humans. In this context, I characterized the viral communities of simian bushmeat illegally imported into France and of Culicoides biting midges, recognized vectors of several viruses of human and veterinary medicine importance. I have first developed a protocol for the purification of RNA viromes which allowed maintaining the infectivity of viral particles. This protocol was subsequently applied to characterize viral communities of bloodsucking arthropods and wildlife samples. In a second part I realized the inventory of viral communities of smoked simian bushmeat illegally imported into France and confiscated by the French customs. This study revealed the presence of a wide diversity of bacteriophages, in which some of them could infect bacteria potentially pathogenic for humans.Finally I characterized the viral communities of Culicoides biting midges collected in Senegal, which revealed the presence of sequences related to several giant DNA viruses infecting amoeba. Sequencing of the RNA virome revealed the presence of several arboviruses that could constitute a risk of emergence of zoonoses for humans.The prediction of future emerging zoonotic viruses is very difficult, if not impossible. However the characterization of viral communities present in the different actors of zoonotic transmission cycle is a first step to evaluate potential risks of transmission to humans.

The anthropogenic use of natural resources has become a major cause of biodiversity loss and habitat degradation throughout the world. Deforestation - the conversion of forests to alternative land covers - has led to a decrease in local biodiversity directly through a decrease in habitat, and indirectly through habitat fragmentation. Likewise, defaunation – the loss of animals both directly through hunting and indirectly through deforestation – has led to the empty forest syndrome and subsequent deterioration of forest ecosystems. In many cases, areas where anthropogenic use of natural resources is high overlap with areas of high biodiversity value. Therefore, the present series of studies aims to better understand the impacts that different types of natural resources use and habitat degradation have on biodiversity. This dissertation details the results of five studies, which aimed to: 1) examine the effects of habitat degradation on plant-frugivore networks; 2), understand the live capture and extent of ownership of lemurs in Madagascar; 3) understand the micro- and macro-level drivers of wild meat consumption in Madagascar; 4) describe the capture, movement, and trade of wild meat in Madagascar; and 5) the impacts of habitat changes on the diets and vertical stratification of frugivorous bats. For the first study, our objectives were to understand the effects of habitat degradation on (1) community structure, (2) network structure, and (3) seed dispersal services. We focused on fruit-bearing trees and frugivores (two lemur and five bird species) across a three-point gradient of habitat degradation in a tropical dry forest in Madagascar. Our objectives were to understand the effects of habitat degradation on (1) community structure, (2) network structure, and (3) seed dispersal services. We focused on fruit-bearing trees and frugivores (two lemur and five bird species) across a three-point gradient of habitat degradation in a tropical dry forest in Madagascar. Data on fruit consumption by frugivores were collected over 592 hours of observations at 13 fruiting tree species. We found that as habitat became more degraded: (1) the community structure of both frugivores and fruiting tree communities changed; (2) the mutualistic network structure became less complex and less connected; (3) the interaction strengths of pair-wise interactions changed and the asymmetries of these interactions shifted; and (4) seed dispersal decreased by 91% in the secondary forest, compared to the primary forest. In addition, we show that frugivores: (1) sometimes stopped eating fruit in the degraded forest, even when they had consumed it in other forests; and (2) appeared to avoid some fruiting tree species while showing preference for others. The mutualistic network studied in this paper appeared sensitive to anthropogenic disturbance and a novel measure of effectiveness helped quantify these changes. For the second study, our objectives were to provide the first quantitative estimates of the prevalence, spatial extent, correlates and timing of lemur ownership, procurement methods, within-country movements, and numbers and duration of ownership. Using semi-structured interviews of 1,093 households and 61 transporters, across 17 study sites, we found that lemur ownership was widespread and affected a variety of taxa. We estimate that 28,253 lemurs have been affected since 2010. Most lemurs were caught by owners and kept for either short (≤1 week) or long (≥3 years) periods. The live capture of lemurs in Madagascar is not highly organized but may threaten several endangered species. For the third study, we investigated the role of wild meat in food security in Madagascar, a country where wild meat consumption is poorly understood in urban areas and at regional scales. Using semi-structured interviews (n = 1339 heads-of-households, 21 towns), we aimed to: 1) quantify the amount and purpose of; 2) understand the drivers behind; and, 3) examine recent changes in wild meat consumption in Madagascar. Few respondents preferred wild meat (8 ± 3%) but most had eaten it at least once (78 ± 7%), and consumption occurred across ethnic groups, in urban and rural settings. More food insecure areas reported higher rates of recent consumption of wild meat. However, consumption was best explained by individual preferences and taboos. Few respondents (<1 ± <1%) had increased rates of consumption during their lifetimes, and wild meat prices showed no change from 2005-2013. Most consumption involved wild pigs and small-bodied animals, though these animal groups and lemurs were consumed less in recent years. Given these data, wild meat is unlikely to enhance food security for most Malagasy people in urban and well-connected rural areas. For the fourth study, and to improve understanding of the wild meat trade in Madagascar, our objectives were to: (1) quantify the volume of consumption, transport, and sale for different animal groups, compared to domestic meat; (2) describe the methods of capture and hunting for different animal groups; (3) analyze the patterns of movement of wild meat from the capture location to the final consumer, compared to domestic meat; and (4) examine how the prices of wild meat change depending on the venue through which the consumer purchases it. Data was collected in May-August 2013 using semi-structured interviews of consumers (n = 1343 households, 21 towns), meatsellers (n = 520 restaurants, open-air markets stalls, and supermarkets, 9 towns), and drivers of inter-city transit vehicles (n = 61, 5 towns). We found that: (1) a wide range of hunting methods were used, though their prevalence of use differed by animal group; (2) wild meat traveled distances of up to 166 km to reach consumers, though some animal groups were hunted locally (<10 km) in rural areas; (3) most wild meat was procured from free sources (hunting and receiving meat as a gift), though urban respondents who consumed bats and wild pigs were more likely to purchase those meats; and (4) wild meat was consumed at lower rates than domestic meat, though urban respondents consumed twice as much wild meat as rural respondents. We conclude that urban and rural respondents differ in how they interact with the wild meat commodity chain. We also believe that the consumption and trade of wild meat in Madagascar is likely more formalized that previously thought. Finally, for our fifth study, we used stable isotope analysis to examine how foraging by three fruit bat species in Madagascar, Pteropus rufus, Eidolon dupreanum, and Rousettus madagascariensis, are impacted by habitat change across a large spatial scale. Our results indicated that the three species had broadly overlapping diets. Differences in diet were nonetheless detectable and consistent between P. rufus and E. dupreanum, and these diets shifted when they co-occurred, suggesting resource partitioning across habitats and vertical strata within the canopy to avoid competition. Changes in diet were also correlated with a decrease in forest cover, though at a larger spatial scale in P. rufus than in E. dupreanum. These results suggest fruit bat species exhibit differing foraging strategies in response to habitat change. They also highlight the key threats that fruit bats face from habitat change, and clarify the spatial scales at which conservation efforts should be implemented to mitigate threats for these bat species in Madagascar. / Biology

The carnivores of Madagascar are likely the least studied of the world's carnivores, thus little is known about threats to their persistence. I provide the first long-term assessment of Madagascar's rainforest carnivore community, including: 1) how multiple forms of habitat degradation (i.e., fragmentation, exotic carnivores, human encroachment, and hunting) affect native and exotic carnivore occupancy; 2) how native and exotic carnivore temporal activity overlap and how body size and niche explain these patterns; 3) how native and exotic carnivores spatially co-occur across the landscape and which variables explain these relationships; and 4) how native and exotic carnivores and humans co-occur with lemurs across Madagascar's largest protected landscape: the Masoala-Makira landscape. From 2008 to 2013 I photographically sampled carnivores and conducted line-transect surveys of lemurs at seven study sites with varying degrees of degradation and human encroachment, including repeat surveys of two sites. As degradation increased, exotic carnivores showed increases in activity and occupancy while endemic carnivore, small mammal, and lemur occupancy and/or activity decreased. Wild/feral cats (Felis sp.) and dogs (Canis familiaris) had higher occupancy (0.37 ± SE 0.08 and 0.61 ± SE 0.07, respectively) than half of the endemic carnivore species across the landscape. Additionally, exotic carnivores had both direct and indirect negative effects on native carnivore occupancy. For example, spotted fanaloka (Fossa fossana) occupancy (0.70 ± SE 0.07) was negatively impacted by both wild/feral cat (beta = -2.65) and Indian civets (beta = -1.20). My results revealed intense pressure from hunting (ex. n = 31 fosa Cryptoprocta ferox consumed per year from 2005-2011 across four villages), including evidence that hunters target intact forest where native carnivore and lemur occupancy and/or activity are highest. I found evidence of high temporal overlap between native and exotic carnivores (ex. temporal overlap between brown-tail vontsira Salanoia concolor and dogs is 0.88), including fosa (Cryptoprocta ferox) avoiding dogs and humans across all seasons. However, I found no evidence of body size or correlates of ecological niche explaining temporal overlap among carnivores. Estimates of spatial co-occurrence among native and exotic carnivores in rainforest habitat revealed strong evidence that native and exotic carnivores occur together less often than expected and that exotic carnivores may be replacing native carnivores in forests close to human settlements. For example, falanouc show a strong increase in occupancy when dogs are absent (0.69 ± SE 0.11) compared to when they are present (0.23 ± SE 0.05). Finally, the two-species interaction occupancy models for carnivores and lemurs, revealed a higher number of interactions among species across contiguous forest where carnivore and lemur occupancy were highest. These various anthropogenic pressures and their effects on carnivore and lemur populations, particularly increases in exotic carnivores and hunting, have wide-ranging, global implications and demand effective management plans to target the influx of exotic carnivores and unsustainable hunting affecting carnivore and primate populations across Madagascar and worldwide. / Ph. D.

The illegal bushmeat harvest has been identified as a reason for declining wildlife populations throughout much of Africa. For many years the trade was thought to exist primarily in Western Africa. The illegal use of bushmeat in Eastern Africa, including Kenya, went undocumented and unstudied. In 2004, the Born Free Foundation published a study which claimed illegal sale of wild game was substantial in butcheries throughout Nairobi, Kenya. In an effort to determine other markets of the commercial trade, the goal of this study was to analyze local restaurants in Voi, Kenya for illegal bushmeat sale. The town of Voi was selected due to recent published reports in the popular press, its proximity to Tsavo National Park, and its access to a major highway. Samples were collected and analyzed using mDNA sequencing analysis of the cytochrome B gene. None of the collected samples were identified as illegal game meat. The restaurants in Voi, Kenya were not a commercial outlet for illegal bushmeat trading in the local economy during the period of this study. The results from this study provide valuable baseline data which can be used in future research to help determine possible vectors of the bushmeat trade.

Une exposition aux viandes comporte un risque pour la santé, et les maladies transmises par ces viandes causent un fardeau important mondialement. En Afrique centrale, le gibier est une viande communément consommée en zone urbaine. L’absence d’information sur le niveau de consommation de gibier, ainsi que sur sa contamination, limite l’évaluation des risques sanitaires associés au gibier. Une étude transversale a visé la description du niveau de consommation des viandes parmi 205 ménages de Port-Gentil (Gabon), ainsi que certains déterminants de la consommation de ces viandes. Une seconde étude transversale a quantifié la contamination musculaire de gibier vendu à Port-Gentil par Salmonella, Campylobacter et Shigella. Sur une base de trois jours, 86% des ménages ont consommé de la volaille, 84% du poisson, 44% du bœuf, 25% du porc et 24% du gibier. La consommation de gibier fut plus fréquente le dimanche et parmi les ménages à revenu élevé. Le gibier fut principalement acquis en carcasse entière sans conservation particulière, mais toujours consommé bouilli. Des trois bactéries ciblées, seule Salmonella a été isolée parmi un de 128 échantillons de gibier. Ces études fournissent des informations utiles pour mieux comprendre les facteurs de risque pour la santé associés à la consommation de viandes au Gabon. Des études sur la contamination des viandes, notamment celles des carcasses de gibier, seront nécessaires pour mieux apprécier les risques spécifiques à chaque différente bactérie pathogène. / Meat poses some risks to human health and meat-borne diseases constitute a high burden worldwide. In central Africa, bushmeat is commonly consumed in the urban setting. A lack of information on bushmeat consumption and contamination limits the evaluation of risks to human health linked to bushmeat. A cross-sectional survey was conducted among 205 households of Port-Gentil (Gabon) to quantify relative consumption levels of different meat types and to explore certain determinants of meat consumption. A separate cross-sectional study aimed to determine the prevalence of Campylobacter, Salmonella and Shigella within bushmeat sold in markets of Port-Gentil. Based on a three-day recall period, 86% of household consumed poultry compared to 84% for fish, 44% for beef, 25% for pork and 24% for bushmeat. Bushmeat consumption was more important on Sundays and within high monthly income households. Most bushmeat was acquired as whole carcasses without formal meat conservation methods, but all bushmeat was boiled prior to consumption. One Salmonella was detected among one of 128 bushmeat samples, whereas no Campylobacter or Shigella were detected. This study provides useful information to help better understand risk factors associated with the consumption of bushmeat in Gabon. Further studies on bacterial contamination of meat, including bushmeat carcasses, are required to better understand potential health risks specific to different bacterial pathogens.

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