The Guiana Shield is a sub-region of Amazonia, one of the richest areas on earth in terms of species number. It is also one of the most pristine areas and is still largely unexplored. Species number, distribution, boundaries and their evolutionary histories remain at least unclear but most of the time largely unknown. This is the case for most Anurans, a group which is recognized as threatened globally and is disappearing even from pristine tropical forests. Given the pace of forest destruction and the growing concerns about climate change it is urgently necessary to obtain a better estimate of regional biodiversity in Amazonian frogs as well as a better understanding of the origin and distribution of Anuran diversity. Furthermore, given their sensitivity to climatic conditions, amphibians are a good model to investigate the influence of paleoclimatic events on Neotropical diversification which was supposedly the driving force on biotic evolution during Pleistocene in the Guiana Shield. I first test species boundaries in two species Scinax ruber and Rhinella margaritifera. These species are widely distributed, abundant and largely recognized as species complexes. I used an original species delineation method based on the combined use of mitochondrial and nuclear DNA in phylogenetic and phylogeographic analyses. Phylogenetic analyses demonstrated the polyphyly of Scinax ruber and Rhinella margaritifera. These species consist of multiple lineages that may all merit species status. Conflicting signals of mitochondrial and nuclear markers indicated the possibility of ongoing hybridization processes. Phylogeographic analyses added further information in support of the specific status of these lineages. Our results highlight the utility of combining phylogenetic and phylogeographic methods, as well as the use of both mitochondrial and nuclear markers within one study. This approach helped to better understand the evolutionary history of taxonomically complex groups of species. The assessment of the geographic distribution of genetic diversity in tropical amphibian communities can lead to conclusions that differ strongly from prior analyses based on the occurrence of currently recognized species alone. Such studies, therefore, hold the potential to contribute to a more objective assessment of amphibian conservation priorities in tropical areas. Subsequently, I tested if these first results on cryptic species are generalisable, questioning what would potentially be a minimum estimate of the number of cryptic frog species in Amazonia and the Guiana Shield, using mtDNA with multiple complementary approaches. I also combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs. In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contra to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher genetic distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species. Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates of around 170 to 460 frog taxa unrecognized in Amazonia-Guianas. As a consequence the global amphibian decline detected especially in the Neotropics may be worse than realised. The Rhinella margaritifera complex is characterisized by the presence of many cryptic species throughout its wide distribution, ranging from Panama to Bolivia and almost entire Amazonia. French Guiana has long been thought to harbor two species of this group, though molecular data analysed in previous chapters indicated as many as five lineages. I tested whether morphological measurements are correlated or not with genetic data using discriminant analysis and if diagnostic characteristics among the previously determined lineages can be used to describe these new species. This is a novel integrative method which can lead to a facilitation of the description of cryptic species that have been detected by phylogenetic and/or phylogeographic studies. These analyses, combined with published data of other Rhinella species, indicated that two of these lineages represent previously unnamed species. Two of the remaining are allocable to R. margaritifera while the status of the fifth is still unclear because so far it is morphologically indistinguishable from R. castaneotica. Determining if codistributed species responded to climate change in an independent or concerted manner is a basic objective of comparative phylogeography. Species boundaries, histories, ecologies and their geographical ranges are still to be explored in the Guiana Shield. According to the refugia hypothesis this region was supposed to host a forest refugium during climatic oscillations of the Pleistocene but the causes and timing for this have been criticized. We investigated patterns of genetic structure within 18 frog species in the eastern Guiana Shield to explore species boundaries and their evolutionary history. We used mtDNA and nuclear DNA and complementary methods to compare the genetic diversity spatially and temporally. With one exception all the species studied diversified repeatedly within the eastern Guiana Shield during the last 4 million years. Instead of one Pleistocene forest refugium the Guiana Shield has probably hosted multiple refugia during late Pliocene and Pleistocene. Most of these Pleistocene refugia were probably situated on the coast of French Guiana, Amapà, Suriname and Guyana. This diversification likely resulted from forest fragmentation. Many species deserve taxonomic revisions and their ranges to be reconsidered. The local endemism of the Anuran fauna of the Guiana Shield is likely to be much higher and some areas consequently deserve more conservation efforts. Specifically I questioned whether major intraspecific diversification started before the Pleistocene and occurred within the Guiana Shield or ex situ. According to ecological characteristics of the species involved I will test different diversification hypotheses. The consequences on the diversity and the endemism of the Guiana Shield will be explored. My results demonstrate that we have been grossly underestimating local biological diversity in the Guiana Shield but also in Amazonia in general. The order of magnitude for potential species richness means that the eastern Guiana Shield hosts one of the richest frog fauna on earth. In most of the species studied high levels of mtDNA differentiation between populations call for a reassessment of the taxonomic status of what is being recognised as single species. Most species display deep divergence between eastern Guiana Shield populations and Amazonian ones. This emphasizes that the local endemism in the Guiana Shield of these zones is higher than previously recognized and must be prioritised elements taken into account in conservation planning. Nevertheless, a few other species appear widely distributed showing that widespread species do exist. This underlines the fact that some species have efficient dispersal abilities and that the frog fauna of the eastern Guiana Shield is a mixture of old Guianan endemic lineages that diversified in situ mostly during late Pliocene and Pleistocene and more recently exchanged lineages with the rest of Amazonia. Recognizing this strong historical component is necessary and timely for local conservation as these zones are likely to be irremediably modified in the near future.

The impact of invasive predators on native prey may depend on the availability and distribution of invader-free refugia across landscapes, if predators create demographic ‘sink’ populations in invaded patches, giving rise to source-sink dynamics in prey populations. Propagule pressure of immigrants dispersing from refugia (or sources) may consequently drive persistence in sink habitat, affecting predator-prey co-existence across the landscape. I studied whether introduced brown (Salmo trutta) and rainbow trout (Oncorhynchus mykiss) create source-sink structuring in two native galaxiid fish species (Galaxias vulgaris and G. paucispondylus) in the rivers of the central South Island, New Zealand, and whether such dynamics affected the distributions of either species across river networks or “riverscapes”. Young-of-the-year (YOY) G. vulgaris recruitment was rare in trout-invaded streams and consistently high in trout-free streams. Thus, trout-free reaches appeared to act as sources in a river network, while the majority of the trout-invaded riverscape was a demographic sink (i.e., no local recruitment occurred). Surveys of YOY G. paucispondylus did not reveal trout-induced source-sink dynamics, although mesocosm predation experiments suggested both species were highly vulnerable to predation by large trout. Galaxias paucispondylus recruitment was highest in intermittently flowing streams that were marginal habitats for trout, suggesting indirect interactions between trout and habitat affect G. paucispondylus distribution. Network configuration of trout-free source populations affected the distribution of G. vulgaris, as galaxiids were excluded from small streams with high bed stability that were far from sources. The interaction between propagule pressure and habitat gradients in mediating effects of trout on G. vulgaris distributions indicates habitat characteristics affect predator-prey interactions in a spatially explicit manner. Furthermore, the outcome of predator-prey interactions should be able to be modelled using habitat data alone if habitat consistently mediates predator impacts. I developed a GIS-based spatial model to predict where trout would exclude G. vulgaris in river networks, based on stream size and distance to galaxiid source populations. The model was tested in three different riverscapes using fish occurrence patterns obtained from electrofishing surveys, and successfully predicted G. vulgaris exclusion by trout. This further demonstrates the importance of habitat configuration in driving interspecific interactions at the landscape scale. These findings suggest removing trout from small, stable tributaries to create new demographic sources could improve overall persistence of G. vulgaris across trout-invaded riverscapes. The galaxiid exclusion model should also be used to detect undiscovered trout-free source populations, and to aid in selecting streams for restoration of galaxiid populations through trout eradication.

The threatened Florida manatee (Trichechus manatus latirostris) migrates seasonally to warm-water refugia throughout the state of Florida due to metabolic requirements from low thermal conductance. Broward County’s two power plant refugia, Port Everglades (PEP) and Lauderdale (LPP), are known heavily-utilized aggregation sites for the Atlantic sub-population. Broward County collected relative abundance counts via aerial surveys from 2004–2013 siting 31,418 manatees during 169 surveys within 18 defined waterway zones. Counts during manatee wintering seasons were significantly different from January 2005-March 2008 and November 2008-March 2013, likely related to flight path and frequency standardization. Mean percentage of adults (90.12%) to calves (9.88%) demonstrates a higher usage by cow-calf pairs than other aggregation sites. Counts of manatees traveling south to Miami-Dade County comprised only 0.83% of all aerial counts, contrary to the theory of the extensive usage of Biscayne Bay foraging grounds. The LPP zone had 57.21% of all manatees with Port Everglades Inlet zone accounting for 23.88% and the South Fork New River zone with 5.95%. This study provided a baseline for pre-construction distributions prior to Port Everglades plant reenergization. With PEP construction now finished and LPP planned for reenergization in the next 10 years, monitoring data studies be compared to these baseline data to better assess the impact of the disruption of Broward County’s main refugia sources.

Florida manatees (Trichechus manatus latirostris) seek out warmer waters during winter months when ambient water temperatures drop below 20 degrees Celsius. Over time, manatees have discovered artificial warm water sites from power plant discharges in addition to natural sites such as springs and passive thermal refugia (PTRs). The Florida Power and Light (FPL) Port Everglades power plant in Broward County is one such artificial warm water refuge used by manatees. This plant was shutdown on July 16, 2013, and is expected to remain off line for at least three years during demolition and construction of a new facility. The purpose of this study was to determine changes in habitat usage and other responses to the disruption of a warm water refugia (the closure of a power plant) on Florida manatees within the greater Port Everglades region. From November 15, 2013 to March 31, 2014, manatees were counted at the site via shore line and aerial surveys. Environmental data were collected to determine variables correlated to manatee presence and absense. Two manatees were radio-tagged using remote sensing devices in an effort to identify alternative warm water refugia and feeding areas. Data were collected from state and local organizations and photo-identified manatees were used to analyze for trends in cold stress syndrome (CSS) lesions and watercraft scarring. Results confirmed that manatee presence was positively correlated with heater outlet temperature. Differences did not exist between the results of survey methods between the FPL Port Everglades (PE) and Fort Lauderdale (FL) power plant sites, however, differrences in the aerial survey counts showed an increased presence at the FL site during the colder month of January 2014. Data from tagging identified one manatee that preferred the FL site while another preferred PE, presumably due to more convenient access to feeding grounds in Biscayne Bay. Data from mortality events indicated a low number of CSS and watercraft deaths in Broward County as compared to other parts of the state of Florida. Further monitoring of the study area for the remainder of the shutdown period is recommended, as are improvements in survey design, expansion to include additional environmental data from FL, continued mortality statistic analysis and locating possible PTRs.

No description available.

No description available.

No description available.

The concept of biodiversity – the phenotypic and genotypic variation among organisms – is central to conservation biology. There is growing recognition that biodiversity does not exist in isolation, but rather is intrinsically and evolutionarily linked to cultural diversity and indigenous knowledge systems. In Canada, caribou (Rangifer tarandus) occupy a central place in the livelihoods and identities of indigenous people and display substantial variation across their distribution. However, quantifying caribou intraspecific variation has proven challenging. Interdisciplinary approaches are necessary to produce effective species characterizations and conservation strategies that acknowledge the interdependent relationships between people and nature in complex social-ecological systems. In this dissertation I use multiple disciplinary traditions to develop comprehensive and united representations of caribou variation through an exploration of population genetics, phylogenetics, traditional knowledge, language, and visual approaches in the Sahtú region of the Northwest Territories, Canada. First, I examine caribou variation through analysis of population genetics and the relationships Dene and Métis people establish with animals within bioculturally diverse systems. Next, I focus on how the Pleistocene glacial-interglacial cycles have shaped the current patterns of caribou phylogeographic lineage diversification. Finally, I explore how art can be used to facilitate cross-cultural collaboration and externalize the unique heterogeneity of biocultural diversity. The results demonstrate a broad scale understanding of the distribution, spatial organization, and the degree of differentiation of caribou populations in the region. I found evidence for caribou population differentiation that corresponds to the caribou types recognized by Dene people: tǫdzı “boreal woodland caribou,” ɂekwę́ “barren-ground caribou,” and shúhta ɂepę́ “mountain caribou.” Phylogenetic results reveal that in their northern margin the boreal ecotype of woodland caribou evolved independently from the northern Beringian lineage in contrast with southern boreal caribou which belong to the sub-Laurentide refugia lineage. In addition, I demonstrate how art can be used improve communication, participation, and knowledge production among interdisciplinary research collaborations and across language and knowledge systems. A collaborative process of research that facilitates łeghágots'enetę “learning together” has the potential to produce sustainable conservation solutions, develop efficient and effective wildlife management policies, and ensure caribou remain an important part of the landscape. / February 2017

Black grouse (Tetrao tetrix) is a bird species with a lek mating system found in the Palearctic boreal taiga. It is assumed that it has a continuous distribution along Scandinavia and Siberia, whereas in Central Europe it has declined during the last decades. The primary objective of this thesis was to obtain a deeper understanding of the history, systematic classification and the genetic structure of black grouse on different geographical scales using microsatellites and control region mtDNA sequences (CR). I determined how much the mating system, habitat fragmentation and historical population processes have influenced the partitioning of genetic diversity in this species. Phylogeographical results are consistent with a demographic population expansion, and the patterns of postglacial dispersal suggest that a glacial refugium was located somewhere in central Asia, and from there black grouse spread out to Europe following the retreat of glacial ice sheets. I suggest that the two European black grouse subspecies, T. t. Tetrix and T. t. britannicus correspond to only one subspecies: T. t. tetrix, and that this lineage has diverged from T.t. viridanus, a subspecies found in Kazakhstan. The British population is significantly divergent from the remaining Eurasian samples for microsatellites but it is not for mtDNA. Therefore, they should regard as a separate Management Unit and not as a subspecies. Furthermore, British black grouse occur in three independent genetic units, corresponding to Wales, northern England/southern Scotland and northern Scotland. There was also genetic structure within Sweden. Habitat fragmentation is the main cause of population genetic structure in southern Swedish black grouse. In contrast, low levels of genetic differentiation and high connectivity were found in northern Sweden due to female-biased dispersal. On a finer geographical scale, I found genetic differences between leks due to a mixture of related and unrelated individuals within leks. However, mean relatedness values hardly differed from zero. Some leks were similar to one another and I interpret this as a result of variation in local reproductive success and philopatry. These factors would cause genetic structuring but this by itself would not reveal that kin selection is operating within black grouse leks.

Genetically modified (GM) white and yellow maize, Zea mays, has been commercially released and cultivated in South Africa since 1997/1998. The traits expressed are insect resistance and herbicide tolerance conferred by the bacteria Bacillus thuringiensis (Bt) Cry genes and Agrobacterium 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase gene, respectively. The Cry genes have been used widely to control lepidopteran insect pests but insect resistance to GM Bt crops has been a concern since the introduction of this technology. A management strategy includes refugia planting of 5% non-Bt plants, with no insecticide application, and 20%, where insecticide application is allowed. These refugia are designed to allow the survival of insect pests within restricted planted zones. However, in South Africa there are reports of Bt-resistant stem borer (Busseola fusca) (Fuller) (Lepidoptera: Noctuidae) and non-compliance with refuge planting. The aims of this study were two-fold: 1. To conduct a survey among KwaZulu-Natal (KZN) GM maize growers to ascertain information such as level of compliance with refuge planting and to determine which refugia were predominantly planted and reasons thereof; 2. To conduct a replicated field trial to determine yield, insect borer damage and economic benefit of the 5% unsprayed and 20% sprayed refuge options (including three configurations namely strip, perimeter and block and a 5 and 20% ‘refuge-in-a-bag’ option). The survey indicated that 28 out of 29 (96.6%) KZN Bt maize growers plant the 5% non-sprayed refuge with 27 (96.4%) of those respondents planting the strip configuration for the purpose of insect management (75%) and ease of planting (32.2%). The survey also showed that 7 (seven) i.e. 21.9% of KZN Bt maize growers observed borer damage and although growers are now fully compliant with refugia planting requirements, initially 7 respondents (24.1%) did not comply with or plant refugia correctly. Furthermore, 7 respondents reported insect borer damage in their maize with 4 of the 7 instances (57.1%) likely stemming from incorrectly planted refugia. vii No significant differences in yield or insect damage were observed between the 5 and 20% refugia for any of the planting configurations in the field trial. However due to costs involved with insecticide application and labour required for the operation in the 20% option, these treatments were less economically advantageous than the non-Bt control. The 20% block and strip configurations had a cost benefit ratio of ZAR 7.21 and ZAR 6.67 respectively, earned per R1 spent by the grower compared with ZAR 7.76 in the sprayed control. The cost-benefit comparison for the 5% block and strip configurations was ZAR 8.48 and ZAR 7.71, respectively compared with ZAR 9.44 in the unsprayed control. In addition, the 20% seed mixture limited borer damage to 4.95% when compared with 15.77% damage in the sprayed control (ANOVA, F pr = 0.124). The seed mixtures are not available commercially and the results from the survey indicated that some education and marketing by the seed companies would be advisable prior to their release to the farming community. In order to determine which of the refuge options between 5 and 20% would be more advantageous for growers overall, regardless of the planting configuration; data were grouped and analysed. There were no significant differences in either the yield or insect damage for the 5 and 20% refugia, but the cost-benefit calculations indicated that the 5% option was more cost effective – for the 5 and 20% refugia, ZAR 7.97 and ZAR 7.15 respectively, earned per ZAR 1 spent by the grower (ANOVA, F pr. = 0.03). This is because no insecticide was used in the 5% treatments. Mean ear damage comparisons between the 5 and 20% refugia showed that the 20% refuge in the perimeter configuration incurred the least damage (2.65% ear damage) compared with 5% perimeter (10.86% ear damage), although the reasons for this are not clear. While the results of the field trials showed no significant differences in insect damage and yield with regard to choice of refuge configuration, monitoring insect resistance management remains an integral part of Bt maize crops in South Africa, in order to delay further resistance development and to prolong the viability of Bt technology. / Agriculture and  Animal Health / M. Sc. (Agriculture)