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

Chameleons are an understudied taxon facing many threats, including collection for the international pet trade and habitat loss and fragmentation. A recent field study reports a highly female-biased sex ratio in the Eastern Arc Endemic Usambara three horned chameleon, Trioceros deremensis, a large, sexually dimorphic species. This species is collected for the pet trade, and local collectors report males bring a higher price because only this sex has horns. Thus, sex ratios may vary due to differential rates of survival or harvesting. Alternatively, they may simply appear to be skewed if differences in habitat use biases detection of the sexes. Another threat facing chameleons is that of habitat loss and fragmentation. Despite enormous amounts of research, the factors of fragmentation that different species respond to is still under debate. Understanding these responses is important for current mitigation efforts as well as predicting how species will respond to future habitat alteration and climate change. My study suggests that differences in survival and detection may explain much of the observed seasonal sex skew in adult T. deremensis. Within fragmented habitat chameleons consistently responded more to edge effects and vegetative characteristics associated with fragmentation than to area or isolation effects. This may bode poorly for chameleon populations in the coming decades as climate change further alters vegetative communities and exacerbates edge effects.

Thesis (PhD)--Stellenbosch University, 2010. / ENGLISH ABSTRACT: Biological invasions are a growing threat to biodiversity, trade and agriculture in South Africa. Though alien reptiles and amphibians (herpetofauna) are not currently a major issue, escalating problems worldwide and increased trade in South Africa suggest a possible increase in future problems. In this thesis I explore practical measures for risk assessment implementable under national legislation. I began by documenting record-keeping and legislative differences between provinces in South Africa. This revealed some serious deficiencies, complicating attempts to compile accurate inventories and discern import trends. International trade data, however, revealed an exponential increase in the number of imports to South Africa over the last 30 years. Characterising the abundance of species in this trade is important as species introduced in large numbers pose a higher establishment risk. In South Africa, I found a tendency for venomous and expensive species to be traded in low numbers, whereas species that are easy to breed and handle, or that are colourful or patterned are traded in higher numbers. Unlike South Africa, California and Florida have had a large number of well-documented herpetofaunal introductions. These introductions were used to verify the role of several key predictors in species establishment. I first evaluated the role of each variable separately. I examined different approaches for bioclimatic modelling, the predictive power of different sources of distribution data, and methods of assigning a climate-match score. I also present the first test of Darwin’s naturalization hypothesis for land vertebrates using two new phylogenies inferred for native and introduced reptiles in California and Florida. I then used boosted regression trees (BRT) to infer the relative contribution of each factor to species establishment success. Results from the BRTs were incorporated into a user-friendly spreadsheet model for use by assessors inexperienced in complex modelling techniques. Introduction effort was found to be the strongest contributor to establishment success. Furthermore, species with short juvenile periods were more likely to establish than species that started breeding later, as were species with more distant relatives in regional biotas. Average climate match and life form were also important. Of the herpetofaunal groups, frogs and lizards were most likely to establish, while snakes and turtles established at much lower rates, though analysis of all recorded herpetofaunal introductions shows slightly different patterns. Predictions made by the BRT model to independent data were relatively poor, though this is unlikely to be unique to this study and can be partially explained by missing data. Though numerous uncertainties remain in this field, many can be lessened by applying case by case rules rather than generalising across all herpetofaunal groups. The purpose for import and potential trade volume of a species will influence the threat it poses. Considering this in conjunction with a species’ environmental tolerances and previous success of species with similar life histories, should provide a reasonable and defendable estimate of establishment risk. Finally, a brief summary of the potential impacts of introduced alien herpetofauna is provided in the thesis. / AFRIKAANSE OPSOMMING: Indringer spesies hou ‘n al groter bedreiging in vir die biodiversiteit, handel en landbou van Suid- Afrika. Alhoewel uitheemse reptiele en amfibieërs (herpetofauna) tans nie ‘n groot bedreiging in Suid-Afrika is nie, dui groeiende probleme wêreldwyd asook 'n toename in plaaslike handel op moontlike toekomstige probleme. In hierdie tesis, ondersoek ek praktiese metodes vir risikobepaling wat onder nasionale wetgewing toegepas kan word. Ek begin deur die verskille in stoor van rekords en wetgewing tussen provinsies te dokumenteer. Hierdie proses het ernstige tekortkominge uitgewys, wat pogings om akkurate inventarisse saam te stel en invoertendense te bepaal, bemoeilik. Internasionale handelsdata het egter getoon dat daar ‘n eksponensiële toename in die hoeveelheid invoere na Suid-Afrika oor die laaste 30 jaar was. Die hoeveelheid spesies in hierdie handel is belangrik omdat spesies wat in groot hoeveelhede ingevoer word, ‘n hoër vestigingsrisiko het. In Suid-Afrika is ‘n tendens gevind vir handel in giftige en duur spesies teen lae hoeveelhede, terwyl spesies wat maklik teel, maklik hanteer kan word en kleurvol is of mooi patrone het, in groter hoeveelhede mee handel gedryf word. Kalifornië and Florida, in teenstelling met Suid-Afrika, het ‘n hoë aantal goed-gedokumenteerde gevalle van herpetofauna wat in die natuur vrygestel is. Hierdie introduksies was gebruik om die rol van verskeie belangrike faktore in die vestiging van populasies te bepaal. Eerstens het ek die rol van elke faktor apart ondersoek. Ek het verskillende benaderinge vir bioklimatiese model-bou ondersoek, die akuraatheid van verskillende bronne van distribusiedata getoets en drie metodes om ‘n “climate match score” te bereken, voorgestel. Ek bied ook die eerste toets van Darwin se naturalisasie-hipotese vir landwerveldiere aan, deur gebruik te maak van twee nuwe filogenieë wat ek gebou het vir inheemse en ingevoerde reptiele in Kalifornië en Florida. Ek het verder gebruik gemaak van “boosted regression trees” (BRT) om die relatiewe bydrae van elke faktor tot die vestigings-potensiaal van spesies te bepaal. Resultate van hierdie BRTs was ingekorporeerd in ‘n gebruikersvriendelike ontledingstaat wat deur bestuurders, onervare in komplekse modelboutegnieke, gebruik kan word. Invoer-hoeveelheid was die faktor wat die sterktste bygedra het tot suksesvolle vestiging. Verder is spesies met kort jeugperiodes en dié met verlangse familie in streeks-biotas, meer geskik om suksesvol te vestig. Gemiddelde klimaatooreenstemming en lewensvorm was ook belangrik. Paddas en akkedisse was die mees waarskynlikste van die herpetofauna groepe om populasies te vestig, terwyl slange en skilpaaie teen laer tempo’s populasies gevestig het, alhoewel analise van alle gedokumenteerde gevalle van herpetofauna-invoerings wêreldwyd effens verskillende tendense toon. Voorspellings wat deur die BRT-model vir onafhangklike data gemaak is was redelik swak, alhoewel hierdie resultaat onwaarskynlik nie uniek aan die studie is nie, en word gedeeltelik verduidelik deur die gebrek aan data. Alhoewel talle onsekerhede steeds bestaan, kan dié verminder word deur geval-tot-geval reëls toe te pas eerder as om vir herpetofauna as ‘n groep te veralgemeen. Die doel van invoer en potensiële handel-volumes van ‘n spesie, sal die bedreiging wat die spesie toon, bepaal. Hierdie faktore moet saam met omgewingstoleransie en voorafgaande sukses van spesies met soortgelyke lewenswyses oorweeg word, om ‘n aanvaarbare en verdedigbare beraming van vestigingsrisiko te gee. Laastens, word ‘n kort opsomming van die effekte wat uitheemse herpetofauna mag hê, verskaf.