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The biological diversity of the planet is at great risk as a direct result of an ever-expanding human population and its associated activities. Landscape transformation to accommodate such activities leads to habitat loss and habitat fragmentation, often creating patches of relatively undisturbed habitat within a matrix of transformed areas that are often too small too support most species previously occupying the area and as a result loses its ecological integrity. A century ago the escarpment region of Mpumalanga consisted of large open plains covered with montane grassland dissected by montane forests and riparian vegetation alongside mountain streams. Today the grasslands and forests have almost disappeared from the area, the remaining patches mostly small fragments within a matrix of exotic tree plantations which have also dried up many of the rivers and streams in the area. The natural grassland areas persisting in the region are unique in habitat characteristics and floral species composition. It is also high in plant species richness, diversity and endemicity. The high degree of isolation experienced by these floral communities poses serious threats to both the floral and faunal species that currently exits within these isolated ‘islands’, many of which are endemic to the area and at great risk of extinction. These risks call for serious collaboration between the land owners (mostly forestry companies) and conservationists to assure the practical and necessary preservation and management of this unique and crucially valuable natural resource. This study aims to provide the first step into understanding the ecological principles associated with habitat fragmentation related specifically to the mountain grassland fragments within the afforestation matrix of the escarpment region of Mpumalanga, and to create a platform for the process of collaboration between land owners and conservation agencies to assess and manage these grassland patches. The aims of Chapter 2 included: 1 To determine if any marked human-induced disturbance to the plant communities in the grassland fragments has occurred. I do this in three ways: a) To compare the plant community composition of eighteen fragments with those of six control plots outside of the plantations where no marked disturbance to the grassland can be observed. b) To determine whether the plant assemblages in the fragments can be assigned to any of the natural and intact plant communities that Matthews (1993) described from a large-scale survey of undisturbed mountain areas. c) To determine the presence of any known intruder plant species within the fragments. 2 To assign conservation priorities to the remaining grassland fragments. The results obtained from the TWINSPAN analysis revealed six alliances of plant communities grouped hierarchically into four orders and two major classes of montane grassland. The DECORANA supported these results, indicating clear differences between communities 1.1 (Eriosema salignum – Loudetia simplex grassland of the wetter North region), 1.2 (Lobelia erinus – Panicum natalense grassland of the Transitional region), 2.1 (Parinari capensis – Eragrostis racemosa grassland) and 2.2 (Helichrysum rugulosum – Eragrostis racemosa grassland). Different plant communities revealed different combinations of geological characteristics, slope, aspect and elevation. The sample plots of isolated grassland fragments and those of large unfragmented areas compare well with each other - the species richness of experimental and control plots do not differ significantly. Also, the species composition of plots from the Wetter North, Transitional and Drier South regions show more variation than is evident between experimental and control plots. There was also good qualitative comparisons (quantitative comparisons were not possible as a results of sampling and analytic discrepancies) between the sample plots used in this study and the plant communities described by Graham Deall and Wayne Matthews. Some evidence of exotic invader plants was found within the sample plots, notably Pteridium aquilinum. Fortunately such species were localized in their distribution and restricted to community 1.1.2.2. The aims of Chapter 3 included the following: 1. To compare the faunal biodiversity in grassland fragments within afforested areas to that of control plots in large, relatively undisturbed grassland areas. 2. To determine to which degree the Coleoptera, Orthoptera, Lepidoptera and bird communities reflect recognized plant communities, and are restricted to specific plant communities. 3. To compare the habitat specificity (degree of stenotopy) of the different taxonomic groups and trophic levels of animals. 4. To make recommendations for the conservation of the Afromontane grassland fauna in the remaining grassland fragments in afforested areas. The sampling of 15602 beetles, grasshoppers and crickets were collected, with an average of 3900 per sampling period, revealed unique combinations of animal species linked to the different plant communities mentioned above. Significant differences were evident from the one-way analyses of similarity (ANOSIM) used to compare the faunal community structures of sample plots of the Wetter North, Transitional and Dryer South regions. The faunal community structures of the experimental and control plots of the Wetter North and Transitional regions did not differ significantly. The indexes of habitat specificity (fractions of species constricted to certain plant communities) indicated that the plants and butterflies were more habitat-specific than the Coleoptera, Orthoptera and Birds. The carnivorous insects showed a surprisingly high level of habitat specificity compared to the relatively low level of the phytophagous insects. This surprising trend was also evident in various insect families – Acrididae, Scarabaeidae and Nymphalidae had relatively high levels of habitat specificity compared to that of the Curculionidae and the Chrysomelidae. Chapter 4 has the following aims: 1. To quantify the effect of several environmental characteristics (slope, rainfall, geology, etc) on the faunal community structure of the grassland fragments. 2. To quantify the effects of degree of isolation on species richness, species diversity and assemblage structure of plants, insects and birds in grassland remnants. 3. To test for the effects of edges on the extant insect biodiversity in the grassland fragments inside plantations. 4. To quantify the effects of fragment size on species richness, species diversity and assemblage structure of plants, insects and birds. 5. To rank the grassland fragments in an order of conservation importance using factors such as biodiversity and uniqueness of the floral community. No clear relationship between fragment size and area sampled and species richness and/or – diversity was evident from the results. Indeed, the smallest area sampled had the fourth highest species richness and the largest area sampled had the fourth lowest species richness and species diversity. Regressions results did not show any significant effects of the geographical area sampled on the biodiversity estimates of the fragments. Therefore I assume that the estimates arrived at for the area sampled within each fragment is representative of that of the complete fragment. The Detrended correspondence analysis (DCA - using square root transformed abundance data) used, indicated the need to perform a gradient analysis using a redundancy analysis (RDA). The permutation test resulting from this analysis revealed a non-significant value for the first canonical axis, but a significant value for the first four canonical axes together. The ten species contributing the most to above-mentioned result include two Scarabs (Scarabaeidae – Aphodius sp 1 and Melolonthinae sp 2), two weevils (Curculionidae – Eudraces sp 1 and Curculionidae sp 42), one leaf beetle (Chrysomelidae – Asbecesta near capensis), one darkling beetle (Tenebrionidae – Lagria sp 1), one longhorn beetle (Cerambycidae – Anubis scalaris), one jewel beetle (Buprestidae – Buprestidae sp 1), one ladybird (Coccinellidae – Coccinellidae sp 4) and one Dor beetle (Bolboceratidae – Mimobolbus maculicollis). Of these ten beetles only three are not restricted to the Drier South Region (Anubis scalaris – Wetter North and Drier South, Lagria sp 1 – throughout and Eudraces sp 1 – throughout). The associated stepwise multivariate regression showed distance to the nearest grassland to be the only environmental characteristic to significantly influence the faunal community structure of the fragments. Slope was the environmental characteristic with the smallest effect. In contrast with the results from redundancy analysis, the analysis of similarity (ANOSIM) and t-tests did not reveal significant differences in the faunal community structure of fragments closer to – and further than one kilometre from the nearest grassland neighbour. This trend was the most evident for fragments of the Transitional region and the least obvious for the fragments of the study area as a whole. The SIMPER analysis showed that of the ten species contributing most to the dissimilarity between insect communities of fragments closer/further than one kilometre from the nearest grassland neighbour, eight were also in the group of ten species characterizing the faunal communities of either/both groups (contributing towards similarity). The insect communities found at 10, 20 and 50 metres from the edge of the grassland fragments did not differ significantly, nor did an ANOSIM performed separately for each of the three major plant communities reveal any significant edge-related differences. The ANOVA results for the individual species revealed only one (of 57 - in the Transitional region) having a distribution that differs significantly with respect to distance from the habitat edge:Eremnus sp. 2 was only found at 10 metres from the edge of the fragment, close to the plantations. Of all the groups, only bird diversity, bird richness and general faunal diversity showed significant relationships with fragment size. There was a non-significant trend for insects to biodiversity to be reduced in very small fragments. Most of the botanical data exhibited no significant relationship with fragment size. The species composition of control sites were not found to be significantly different from that of experimental fragments for all the faunal groups pooled together or for the fragments of the Transitional Region and the Wetter North Region. Using the four separate scores for birds, butterflies, beetles and grasshoppers, each fragment was assigned a total conservation score. The twenty-four fragments were then ranked in order of conservation importance. Fragments of the Wetter North had an average score of 65.3, fragments of The Transitional Region 66.6 and fragments of the Drier South 52.3. The results relating to this study has lead to the following conclusions: o It is concluded that afforestation and habitat fragmentation have not significantly impacted on the flora of the montane grassland of the study area since many of the grassland fragments surrounded by plantations are still easily identifiable as natural communities, described by Matthews and Deall in broader-scale surveys in the past. Also, no obvious invader – or disturbed plant communities are discernible even though some of them have been isolated for as long as 40 years. o The plant communities of conservation importance described by Matthews coincide with the important communities recognized in this study. Rare and endangered plant species, as well as species endemic to the region, are more often than not found on the scarce Black Reef quartzite of the region, which is more evident to the Northern part of the study area. Communities 1.1 and 1.2.2 are therefore of particular conservation importance, not only as a result of their scare geological base, but also because of the high risk associated with the few grassland examples left of these communities. o The high levels of habitat specificity of many of the taxonomic and trophic faunal groups indicate that many of the invertebrate taxa are probably endemic to the region, and that the plant endemicity encountered in the Afromontane grasslands is reflected by a similar degree of animal endemicity. o The similarity in faunal assemblages and diversity between isolated fragments and large areas of grassland emphasizes the conservation importance of the fragments, even when smaller than 5 Ha in extent. o Appropriate management of the grassland fragments within the plantations is therefore important for the conservation of the plant and animal taxa encountered there. Experimental management involving grazing, mechanical cutting, grazing and burning is needed to decide on an efficient management regime, so that the grassland biodiversity can be conserved in a planned way. Such work will also allow empirical testing the efficiency of the indicator species suggested above. o Isolated grassland fragments in this study represent largely unaffected natural plant and insect communities, differing little from large unfragmented grasslands in the study area. o Fragments found within afforested areas therefore have a high conservation importance, since they represent ‘natural’ grassland areas and are often the only representative of a particular plant community left in the area. o No significant edge effects on the faunal communities 10, 20 and 50 metres from the fragments’ edges exist as a result of afforestation in the area. o Birds (and probably other vertebrates in these grasslands) are affected by fragment size, while invertebrates are much less affected and plants do not show any measurable effect of fragment size. o Fragments in the wetter northern part of the study area, characterized by high levels of plant endemicity, have a higher conservation importance as judged by faunal biodiversity. / Dissertation (MSc (Zoology and Entomology))--University of Pretoria, 2005. / Zoology and Entomology / unrestricted

Global climate change and habitat fragmentation represent two of the greatest threats to biodiversity and ecological processes worldwide. It is predicted that anthropogenic induced climate change could represent a key factor for extinctions in the near future, considering that the Earth is set to become warmer than at any period in the past 40 million years. Habitat fragmentation and isolation pose a number of challenges for the fauna inhabiting degraded areas, including lack of dispersal opportunities leading to inbreeding resulting in a loss of genetic diversity, reduced reproductive fitness; increases in vulnerability to predation, hunting, and disease, and an inability to deal with or respond to environmental changes and/or disease. Madagascar, the fourth largest island in the world, is home to unprecedented levels of endemism, including over 100 species of lemur. The island has undergone a range of historical and contemporary landscape transformations, both natural and anthropogenic. These landscape transformations combined with additional human-induced disturbances, such as the illegal pet and bushmeat trades, have had devastating effects on the island’s extant primate populations. Thus, Madagascar’s lemurs have been deemed the most endangered group of mammals and now represent the highest primate conservation priority in the world. The ring-tailed lemur (Lemur catta) is endemic to the southern regions of the island and occupies an array of habitats. L. catta is known for its remarkable behavioral and ecological flexibility, which contributes to its ability to exist in a mostly fragmented landscape. While this species represents one of the most well studied Malagasy strepsirhines, there has been a paucity of research regarding the population and conservation genetics of this endangered species. The goal of my dissertation was to examine the influence of habitat fragmentation and isolation on the genetic diversity and population structuring of this flagship species in three populations living in the central highlands of Madagascar: Anja Reserve, Sakaviro, and Tsaranoro Valley. Non-invasive fecal samples from 30 individual lemurs were collected from three fragmented forests and genotyped at six polymorphic microsatellite loci. Population genetic analyses were examined via GenAlEx software and revealed a moderate level genetic diversity. Genetic differentiation (FST) among the three fragmented populations ranged from 0.05-0.11. These data suggest that the L. catta populations within south-central Madagascar have not yet lost significant genetic variation. To examine past and recent demographic declines or genetic bottlenecks, I employed three approaches, including mode-shift and M-Ratio tests, as well as a test to detect heterozygosity excess using three mutation models: the two-phase model (TPM), step-wise mutation model (SMM), and the infinite allele model (IAM). Results were equivocal depending on the test that was applied; however, a mode-shift was detected for Anja, signifying this population underwent a historical bottleneck. M-ratio tests revealed that all three populations suffered historical bottlenecks. A population bottleneck was indicated via heterozygosity excess under the IAM for both the Anja and Sakaviro populations. To understand the impact of natural (e.g., mountains) and anthropogenic disturbances (e.g., roads, habitat fragmentation) on male reproductive strategies (dispersal) and population structuring, I utilized both GenAlEx and STRUCTURE software. Population assignment analyses suffered from a likely ‘lack of signal’. Therefore, individuals were unable to be reliably assigned to their population of origin. Genetic population structure was ambiguous. These data suggest that that these three fragmented populations are not genetically differentiated enough for proper population assignment, or perhaps the sample is not robust enough for population assignment analyses to produce unequivocal results. My research represents the first population genetic data for ring-tailed lemurs within the central highlands, and thus, serves as a baseline for future investigations into the genetic health of these populations. These data support the suggestion that these three fragments represent areas in which concerted conservation efforts are necessary if genetic diversity is to be maintained and future demographic declines are to be prevented. My results are informative for the local community conservation associations working within south-central Madagascar and can now be applied to determine areas of conservation priority and where forest corridors will be the most beneficial for maintaining gene flow. The loss and fragmentation of habitat continues across Madagascar, including the central highlands; thus, all remaining L. catta populations should be considered a high conservation priority. If we are to safeguard the long-term viability of this species, continued conservation and research initiatives will be crucial. / Graduate / 0327 / 0369 / lemurgirl.clarke@gmail.com

Sustainable Built Environments Senior Capstone Project / This study analyzes 15 years of wildlife tracking data across more than 40 transects in the Sky Islands surrounding landscape to investigate how human-wildlife encounters may respond to a decade of land development. The average detection of species per visit (ADPV), the quantification for human-wildlife encounters and indicator of species richness, was calculated for each transect across two sample periods 2001-2011 and 2011-2015. ArcMap was used to visualize the ADPV across sampling sites in the Sky Islands region. The p-value was then calculated to determine whether there was a significant difference between the ADPV of all species and of focal species before and after 2011. The results concluded there was no significant difference and the null hypothesis was accepted.

Habitat loss, habitat fragmentation and species invasions have been recognized as three of the leading threats to biodiversity. I examined the effects of habitat loss and fragmentation on native and invasive plants in central Texas. During the last century, the density and abundance of woody plants has been increasing in the savannas of eastern Edwards Plateau. This process, known as woody plant encroachment, not only reduces the amount of open herbaceous habitat but also fragments that habitat creating smaller and more isolated patches. In three studies, I investigated the consequences of this habitat loss and fragmentation for plants which do not occur under the cover of woody plants including native grasses and forbs and the invasive Eurasian bunchgrass, Bothriochloa ischaemum (King Ranch Bluestem). In the first study, I show that woody plant encroachment reduces native herbaceous species richness (the number of species in a given area). Using a collection of historical aerial photographs, I demonstrate that current native herbaceous species richness was most strongly related to recent habitat amount, but to the degree of habitat fragmentation at least 50 years ago. In a second study, I show that the presence of B. ischaemum was negatively related to the degree of fragmentation in the surrounding landscape. Finally, I found that B. ischaemum had higher rates of germination and growth in experimental plots where the species commonly lost with woody plant encroachment were removed than in unmanipulated control plots. Together, this work suggests that woody plant encroachment is directly slowing the spread of an invasive species while indirectly facilitating its establishment. / text

Drastic alterations to the North American Southwest’s hydrology have highly influenced resident fish communities. In New Mexico and Texas, the Pecos River has been severely altered as a result of water manipulation, isolating backwaters and various habitats that were once connected to the main river. Cyprinodon pecosensis (Pecos pupfish) has been highly impacted due to the effects of anthropogenic water manipulation, as well as species introductions. Cyprinodon pecosensis populations have become isolated and scattered, residing in sinkholes, remnant lakes, and static backwaters, thus creating numerous micropopulations. The purpose of this study was to assess the morphological variation in cranial features that occur in response to varied habitats, especially in terms of environmental factors and species co-occurrence. Landmark-based geometric morphometrics was used to assess shape variation across the aforementioned micropopulations comprising four general habitat types and 27 different localities, each with varied community structure and salinity. Results from this study suggest that head and mandible morphology vary temporally, with year to year variation, as well as among different localities. The head morphology of C. pecosensis was most heavily influenced by habitat type and localities within habitat types, but was largely canalized with the exception of localities classified as deep sinkholes. Year to year variation and localities among habitat types were the most influential factors associated with mandible morphology, but there was strong overlap among the convex hulls that defined regions of morphospace for habitat types. As C. pecosensis is a threatened species, this research has important implications for future conservation and management. Additionally, these results could further aid in the understanding of preserving species in fragmented landscapes.

The destruction and fragmentation of natural habitat is the leading driver of the current extinction crisis. As a result, a research area has emerged focused on studying ecology in islands of natural habitat surrounded by a sea of anthropogenic land uses, so called ‘habitat islands’. However, this research has largely been undertaken on small-medium scales, generally in single systems. Furthermore, many habitat island studies have used previous results and theory derived in the context of oceanic island research. Thus, this thesis aims to examine a variety of macroecological and biogeographical patterns using a large number of purely habitat datasets sourced from both the literature and my own sampling, with the objective of teasing out any general statistical patterns. The various macroecological and biogeographical patterns can be grouped under four broad headings: 1) species–area relationships (SAR), 2) nestedness, 3) species abundance distributions (SADs), and 4) species incidence functions (function of area). Overall, it was found that there were few hard macroecological generalities that hold in all cases across habitat island systems. This is because most habitat island systems are highly disturbed environments, with a variety of confounding variables and undesirable species (e.g. species associated with human land uses) acting to modulate the patterns of interest. Nonetheless, some clear patterns did emerge. In particular, it was found that the power model was by the far the best general SAR model for habitat islands. The slope of the island species–area relationship (ISAR) was related to the matrix type surrounding archipelagos, such that habitat island ISARs were shallower than true island ISARs. Significant compositional and functional nestedness was rare in habitat island datasets, although island area was seemingly responsible for what nestedness was observed. Species abundance distribution models were found to provide useful information for conservation in fragmented landscape, but the presence of undesirable species substantially affected the shape of the SAD. Species incidence function curves were found to vary across space for a given species, but not in any systematic manner. In conclusion, this thesis finds that the application of standard island biogeography theory to habitat islands is too simplistic. It is hoped that the results of this thesis will act as a catalyst for a more macroecological approach to habitat island research, and a starting point for the development of an integrated theory of habitat islands.

Doctor of Philosophy / Department of Biology / Keith B. Gido / Habitat fragmentation and loss threaten global biodiversity, but organism responses to changing habitat availability are mediated by structural properties of their habitats. In particular, organisms inhabiting dendritic landscapes with hierarchically arranged branches of habitat tend to have limited access to some patches even in the absence of fragmentation. Consequently, organisms inhabiting dendritic landscapes such as streams respond strongly to fragmentation. Using a combination of meta-analysis, field observations, and ecological network modeling I show that stream fishes respond to fragmentation in predictable ways. First, I addressed how dams and stream dewatering have created a mosaic of large river fragments throughout the Great Plains. Using a geographic information system and literature accounts of population status (i.e., stable, declining, extirpated) for eight “pelagic-spawning” fishes, I found stream fragment length predicted population status (ANOVA, F2,21 = 30.14, P < 0.01) and explained 71% of reported extirpations. In a second study, I applied a new measure of habitat connectivity (the Dendritic Connectivity Index; DCI) to 12 stream networks in Kansas to test the DCI as a predictor of fish response to fragmentation by road crossings. Results indicated fish communities in stream segments isolated by road crossings had reduced species richness (alpha diversity) and greater dissimilarity (beta diversity) to segments that maintained connectivity with the network, and the DCI predicted patterns in community similarity among networks (n = 12; F1,10 = 19.05, r2 = 0.66, P < 0.01). Finally, I modeled fish distributions in theoretical riverscapes to test for mechanistic linkages between fragmentation and local extirpations. Results suggested the number of small fragments predicted declines in patch occupancy, and the magnitude of change in occupancy varied with dispersal ability (“high” dispersers responded more strongly than “low” dispersers). Taken together, these works show context-dependencies in fish responses to fragmentation, but a unifying theme is that small fragments contribute to attenuated biodiversity. Moreover, the predictable manner in which stream fish react to fragmentation will aid in biodiversity conservation by revealing potential responses to future scenarios regarding changes to habitat connectivity.