This thesis concerns the cortical connectivity in Primates. The efficacy of Diffusion weighted MRI (dMRI) is examined. White matter (“WM”) systems subjacent to cortex (“superficial WM” ) are found to be a limiting factor to dMRI tractography. Superficial WM systems are examined with dMRI itself, and with analysis of histological data from the scanned brains. dMRI data was acquired ex-vivo at exceptional spatial and angular resolution (250μm in Rhesus, 150μm in Marmoset). The superficial WM was found to be complex, and with current dMRI methods, an effective barrier to tracking to and from around 50% of cortex in Rhesus. The quality of our data allowed Gray matter seeding, so that penetration both into and out of cortex was examined. We summarize the history of cortical connectivity and current work in tractography. We present an account of the formation and properties of the superficial WM. We compare tracking behaviors to tracer results, and develop a series of scalar maps on cortical surface models to summarize tracking behaviors. We attempt to explain these maps by examining the underlying tracking behavior and the brain tissue itself, revealing the intricate nature of the superficial WM. Chapter 4 contains a separate but related project in which a histologically accurate high resolution 3D and surface atlas of the Rhesus cortex is constructed with unprecedented accuracy. A method to rapidly and accurately non-linearly transform the atlas to a scan of another animal is developed, thus labelling its cortex. accuracy is by comparison to histology of the scanned animals.

Understanding the impacts of landscape fragmentation, degradation and hunting on arboreal species of conservation concern, such as the critically endangered brownheaded spider monkey (Ateles fusciceps fusciceps), remains a major challenge in conservation biology. Current research on the population status of this primate and the area it inhabits in the Ecuadorian Choco is urgently needed to aid in the design of specific and effective conservation strategies. I surveyed the population of A. f. fusciceps in the unprotected forest cooperative Tesoro Escondido in the buffer zone of the Cotacachi Cayapas Ecological Reserve during the year 2012-2013. Using the line transect method I estimated a population density of 15.79 individuals/km2. I found an average subgroup size of 3.42 individuals and a female biased population. Identifying key food resources for critically endangered species is vital in their conservation, particularly if these resources are also targeted by anthropogenic activities such as logging. The province where A. f. fusciceps is found is also heavily dependent on commercial logging with no information available on its impacts on key feeding resources for this primate. I characterised the oristic composition of the habitat of A. f. fusciceps and estimated the availability of fruit resources for the annual cycle of 2012-2013 in sixteen 0.1 hectare vegetation plots. I determined feeding preferences for A. f. fusciceps using behavioural observations applying the Chesson ε index to identify key feeding tree species. I reviewed regional logging permits to identify species targeted for extraction by the timber industry and calculated extraction volumes in primary forest for key feeding tree species to identify potential conflict between logging and primate diet. I identified 65 fruiting tree species from 34 families that formed the diet of A. f. fusciceps . The Chesson ε index identified twelve species as preferred species with further phenological observations identifying seven species as staple foods and two palms as potential foods consumed in times of fruit scarcity. Additionally, I found that the lipid rich fruits of Brosimum utile make this an important resource for this primate throughout the year. Furthermore, of 65 feeding tree species identified for A. f. fusciceps , 35 species are also targeted as sources of timber. Five key feeding species would be depleted under current sustainable management extraction protocols while two other species would be significantly impacted in terms of local abundance. Hunting pressure on A. f. fusciceps has been reported as one of the main causes of its population decline. However, no current research on the extent of this activity or its causes was available. I carried out semi-structured interviews in nine indigenous Chachi villages, as well as two Colono towns, to evaluate the occurrence of hunting activity and to identify drivers, attitudes and behaviour of hunters. In total I interviewed 62 people, 41 Chachis and 21 Colonos. From the Chachi interviewees 93% identified themselves as hunters, with subsistence hunting the main driver for this activity and central to their culture, especially for men. Colonos identified less with this activity (only 38%), and with more varied reasons, such as commerce and conflict. Only Chachis accepted the hunting of spider monkeys, with the main reason given as their taste. Keeping spider monkeys as pets was also a regular activity prior to tougher law enforcement by the Ministry of Environment (MAE). Information on medicinal uses from spider monkeys was also gathered, as well as information of other species hunted in the area. Even though Ecuadorian law recognises the right of indigenous peoples to hunt within their territories, it also forbids hunting critically endangered species. From the interviews it is evident that information and understanding of this law has not been successfully transmitted. Determining the effects of fragmentation, hunting and habitat degradation on populations viability of this primate is crucial before investing heavily in local sustainable livelihoods and conservation initiatives. A range of fragmentation metrics are available to study habitat fragmentation, yet their relationship to survival of populations of conservation concern remains to be quantified. I applied an agent-based model (ABM), calibrated on field-collected datasets on forest fruit dynamics, behaviour and feeding ecology of A. f. fusciceps, to first identify an optimised fragmentation statistic to be used to screen satellite imagery and identify remaining priority conservation areas in unprotected, fragmented forests in NW Ecuador. I then used the ABM to further explore the combined impacts of fragmentation, hunting and logging. Mean Patch Area was the best fragmentation metric predictor of population numbers, I identified a MPA of 174.9 hectares as the cut-off point for the survival of brown-headed spider monkeys given the lowest combinations of logging activity and hunting pressure and I used it to identify priority conservation areas in NW Ecuador. Implementing conservation strategies in areas where people and nature interact is a challenging task. I designed a step by step framework for the conservation of critically endangered species. Based on my experience with Ateles fusciceps fusciceps as a case study, I present the design, assessment and implementation of different community-based strategies.