The species–area relationship (SAR) has been applied to predict species richness declines as area is converted to human-dominated land covers.In many areas of the world, however, many species persist in human-dominated areas, including threatened species. Because SARs are decelerating nonlinear, small extents of natural habitat can be converted to human use with little expected loss of associated species, but with the addition of more species that are associated with human land uses. Decelerating SARs suggest that, as area is converted to human-dominated forms, more species will be added to the rare habitat than are lost from the common one. This should lead to a peaked relationship between richness and natural area. I found that the effect of natural area on avian richness across Ontario was consistent with the sum of SARs for natural habitat species and human-dominated habitat species, suggesting that almost half the natural area can be converted to human-dominated forms before richness declines. However, I found that this spatial relationship did not remain consistent through time: bird richness increased when natural cover was removed (up to 4%), irrespective of its original extent. The inclusion of metapopulation processes in predictive models of species presence improves predictions of diversity change through time dramatically. Variability in site occupancy was common among bird species evaluated in this study, likely resulting from local extinction-colonization dynamics. Likelihood of species presence declined when few neighbouring sites were previously occupied by the species. Site occupancy was also less likely when little suitable habitat was present. Consistent with expectations that larger habitats are easier targets for colonists, habitat area was more important for more isolated sites. Accounting for the effect of metapopulation dynamics on site occupancy predicted change in richness better than land cover change and increased the strength of the regional richness–natural area relationship to levels observed for continental richness–environment relationships suggesting that these metapopulation processes “scale up” to modify regional species richness patterns making them more difficult to predict. It is the existence of absences in otherwise suitable habitat within species’ ranges that appears to weaken regional richness–environment relationships.

The species–area relationship (SAR) has been applied to predict species richness declines as area is converted to human-dominated land covers.In many areas of the world, however, many species persist in human-dominated areas, including threatened species. Because SARs are decelerating nonlinear, small extents of natural habitat can be converted to human use with little expected loss of associated species, but with the addition of more species that are associated with human land uses. Decelerating SARs suggest that, as area is converted to human-dominated forms, more species will be added to the rare habitat than are lost from the common one. This should lead to a peaked relationship between richness and natural area. I found that the effect of natural area on avian richness across Ontario was consistent with the sum of SARs for natural habitat species and human-dominated habitat species, suggesting that almost half the natural area can be converted to human-dominated forms before richness declines. However, I found that this spatial relationship did not remain consistent through time: bird richness increased when natural cover was removed (up to 4%), irrespective of its original extent. The inclusion of metapopulation processes in predictive models of species presence improves predictions of diversity change through time dramatically. Variability in site occupancy was common among bird species evaluated in this study, likely resulting from local extinction-colonization dynamics. Likelihood of species presence declined when few neighbouring sites were previously occupied by the species. Site occupancy was also less likely when little suitable habitat was present. Consistent with expectations that larger habitats are easier targets for colonists, habitat area was more important for more isolated sites. Accounting for the effect of metapopulation dynamics on site occupancy predicted change in richness better than land cover change and increased the strength of the regional richness–natural area relationship to levels observed for continental richness–environment relationships suggesting that these metapopulation processes “scale up” to modify regional species richness patterns making them more difficult to predict. It is the existence of absences in otherwise suitable habitat within species’ ranges that appears to weaken regional richness–environment relationships.

A wide range of ecological communities ranging from polar terrestrial to tropical marine environments are affectedby global climate change. Over the last century, atmospheric temperature has increased by an average of 0. 60 C andis expected to rise by 1.1- 6.40C over the next 100 years. This rising temperature has increased the intensity andfrequency of weather extremes due to which a large number of species are facing risk of extinction. Studies haveshown that species existing on lower latitude are more sensitive to temperature variability compared to speciesexisting on higher latitude but temperature is increasing rapidly in higher latitude compare to lower latitude. Thisuneven distribution of temperature sensitive species and warming rate has highlighted the need for combined studiesof temperature variability and sensitiveness of species to predict how the ecosystems will respond to increasinglyvariable climate. Using a generalized Rosenzweig-MacArthur model, I explored how temperature variability andsensitivity of species will affect the extinction risks of species and how the connectance and species-richness ofecological communities will govern this response. This study showed that the risk of extinction of species mostlydepends on their sensitivity to temperature deviation from the optimum value and level of temperature variability.Among these two, sensitivity of species to temperature deviation was most prominent factor affecting extinction risk.In this study, connectance did not show any effect on mean extinction risk and time taken by a certain proportion ofspecies to reach pre-defined extinction thresholds. But, species-richness showed some effect on mean extinction riskof species. It was found that risk of extinction of species in species-rich communities was higher compared tospecies-poor communities. Species-rich communities also took shorter time before they lost 1/6 of the species. Thepresent study also suggests a possible tipping point due to increasing temperature variability in near future. In furtherstudies, different sensitivity of species at different trophic levels and the possible evolution of sensitivity of speciesshould also be consider while predicting how ecological communities will respond to changing climate in the longrun.

The goal of this dissertation is to further our understanding of how spatially heterogeneous landscapes may impact the formation of range boundaries that then aggregate to form large-scale biodiversity patterns. These patterns have been analyzed from many different perspectives by ecologists, evolutionary biologist, and physiologists using a variety of different theoretical, statistical, and mechanistic models. For some species, there is an obvious abrupt change in the environment causing a range boundary. Other environments change gradually, and it is unclear why species fail to adapt and expand their range. The first chapter develops a novel theoretical model of how the establishment of new mutations allows for adaptation to an environmental gradient, when there is no genetic variation for the trait that limits the range. Shallow environmental gradients favor mutations that arise nearer to the range margin, have smaller phenotypic effects, and allow for proportionately larger expansions than steep gradients. Mutations that allow for range expansion tend to have large phenotypic effects causing substantial range expansions. Spatial and temporal variation in climatic and environmental variables is important for understanding species response to climate change. The second chapter uses a mechanistic model to simulate switchgrass (Panicum virgatum L.) productivity across the central and eastern U.S. for current and future climate conditions. Florida and the Gulf Coast of Texas and Louisiana have the highest predicted current and future yields. Regions where future temperature and precipitation are anticipated to increase, larger future yields are expected. Large-scale geographic patterns of biodiversity are documented for many taxa. The mechanisms allowing for the coexistence of more of species in certain regions are poorly understood. The third chapter employs a newly developed wavelet lifting technique to extract scale-dependent patterns from irregularly spaced two-dimensional ecological data and analyzes the relationship between breeding avian richness and four energy variables. Evapotranspiration, temperature, and precipitation are significant predictors of richness at intermediate-to-large scales. Net primary production is the only significant predictor across small-to-large scales, and explains the most variation in richness (~40%) at an intermediate scale. Changes in the species-energy relationship with scale, may indicate a shift in the mechanism governing species richness. / text

Either tropical niche divergence or tropical niche conservatism could drive the latitudinal diversity gradient. Greater niche divergence in the tropics could accelerate reproductive isolation leading to more rapid species formation. Alternatively, latitudinal asymmetry in niche conservatism, whereby tropical species are more conserved than high latitude species, could promote more dispersal in to than out of the tropics, leading to greater tropical richness. Here I test whether rates of climatic niche evolution vary across the latitudinal gradient for 164 closely related pairs of species. Using the evolutionary ages at which sister species diverge, and the niche divergence between them, I applied Brownian motion models to test whether rates of climatic niche evolution varied with latitude. My results indicate that climatic niche conservatism is strongest in the tropics. This suggests that the latitudinal diversity gradient is driven by the inability of tropical to adapt to temperate climates and colonize non-tropical latitudes.

Either tropical niche divergence or tropical niche conservatism could drive the latitudinal diversity gradient. Greater niche divergence in the tropics could accelerate reproductive isolation leading to more rapid species formation. Alternatively, latitudinal asymmetry in niche conservatism, whereby tropical species are more conserved than high latitude species, could promote more dispersal in to than out of the tropics, leading to greater tropical richness. Here I test whether rates of climatic niche evolution vary across the latitudinal gradient for 164 closely related pairs of species. Using the evolutionary ages at which sister species diverge, and the niche divergence between them, I applied Brownian motion models to test whether rates of climatic niche evolution varied with latitude. My results indicate that climatic niche conservatism is strongest in the tropics. This suggests that the latitudinal diversity gradient is driven by the inability of tropical to adapt to temperate climates and colonize non-tropical latitudes.

This thesis examines the biogeography of world pinnipeds, a unique group of marine mammals that have adapted to marine foraging while maintaining terrestrial (land or ice) habitat links. Comparative analyses of species range sizes controlled for phylogenetic relationships using a multi-gene supertree with divergence dates estimated using fossil calibrations. Adaptations to aquatic mating and especially sea ice parturition have influenced range size distribution, and ranges are larger than those of terrestrially mating and/or pupping species. Small range size is endangering for many taxa, and most at risk pinnipeds are terrestrial species with small ranges. Ancestral state reconstructions suggest that pinnipeds had a long association with sea ice, an adaptation that would have allowed early seals to expand into novel habitats and increase their distribution. Range sizes exhibit a strong Rapoport effect (positive relationship between range size and latitude) at the global scale, even after controlling for phylogeny and body size allometry. A latitudinal gradient in species diversity cannot explain the Rapoport effect for global pinniped ranges, as diversity is highest at mid-latitudes in both hemispheres. These regions are characterized by marginal ice zones and variable climates, supporting a mix of pagophilic and temperate species. The climatic variability hypothesis also did not explain the Rapoport effect. Variability is bimodal, and annual sea surface temperature (SST) variability does explain diversity patterns. Range size has a significant negative relationship with annual mean SST, and the largest ranges are found in areas with low mean SST. Temperature responses are possibly related to thermoregulation, sea ice availability, and ecological relationships with other large marine predators. These results agree with other studies and suggest that ocean temperature, and not productivity, drives marine species richness patterns. Future research needs include studies of physiological tolerances, interactions with sharks as predators and competitors, and the role of climate and sea ice in speciation and evolution. A better understanding of distribution and diversity patterns, and the role of the environment in shaping these patterns, will improve conservation efforts, and studies on the role of SST and sea ice are particularly important given current warming trends and declines in ice extent.

It is generally assumed that when natural habitat is converted to human-dominated cover such area is “lost” to its native species. Extinctions will ensue. The literature generally assumes that species are extirpated as natural area is reduced, following the well-known species-area relationship (SAR). However, SARs have consistently over-estimated species losses resulting from conversion of natural habitat to human-dominated land covers. We hypothesize that the overestimation occurs because these area-based models assume that converted habitat is “lost”, eliminating all species. However, in the real world, conversion of natural land cover to human-dominated cover frequently produces new land covers, different from the original habitat, but not necessarily completely inhospitable to biodiversity. We evaluated the responses of total avian richness, forest bird richness and open habitat bird richness to remaining natural area within 991 quadrats, each 100 km2, across southern Ontario. Total bird species richness does not follow SAR predictions; rather, the number of bird species peaks at roughly 50% natural land cover. The richness of forest birds does follow the usual SAR power-law as a function of forested area. In contrast, richness of birds that prefer open-habitat does not increase monotonically with either natural- or human-dominated land cover. However, we can partition human-dominated land cover into an “available human-dominated” component and “lost” habitat. Richness of open-habitat species relates to the amount of available human-dominated cover. Distinguishing three habitat types (natural, available human-dominated, and lost) permits accurate predictions of species losses in response to natural habitat conversion.

This thesis examines the biogeography of world pinnipeds, a unique group of marine mammals that have adapted to marine foraging while maintaining terrestrial (land or ice) habitat links. Comparative analyses of species range sizes controlled for phylogenetic relationships using a multi-gene supertree with divergence dates estimated using fossil calibrations. Adaptations to aquatic mating and especially sea ice parturition have influenced range size distribution, and ranges are larger than those of terrestrially mating and/or pupping species. Small range size is endangering for many taxa, and most at risk pinnipeds are terrestrial species with small ranges. Ancestral state reconstructions suggest that pinnipeds had a long association with sea ice, an adaptation that would have allowed early seals to expand into novel habitats and increase their distribution. Range sizes exhibit a strong Rapoport effect (positive relationship between range size and latitude) at the global scale, even after controlling for phylogeny and body size allometry. A latitudinal gradient in species diversity cannot explain the Rapoport effect for global pinniped ranges, as diversity is highest at mid-latitudes in both hemispheres. These regions are characterized by marginal ice zones and variable climates, supporting a mix of pagophilic and temperate species. The climatic variability hypothesis also did not explain the Rapoport effect. Variability is bimodal, and annual sea surface temperature (SST) variability does explain diversity patterns. Range size has a significant negative relationship with annual mean SST, and the largest ranges are found in areas with low mean SST. Temperature responses are possibly related to thermoregulation, sea ice availability, and ecological relationships with other large marine predators. These results agree with other studies and suggest that ocean temperature, and not productivity, drives marine species richness patterns. Future research needs include studies of physiological tolerances, interactions with sharks as predators and competitors, and the role of climate and sea ice in speciation and evolution. A better understanding of distribution and diversity patterns, and the role of the environment in shaping these patterns, will improve conservation efforts, and studies on the role of SST and sea ice are particularly important given current warming trends and declines in ice extent.

The planet is experiencing a dramatic loss of species. The majority of species are unknown to science, and it is usually infeasible to conduct a census of a region to acquire a complete inventory of all life forms. Therefore, it is important to estimate and conduct statistical inference on the total number of species in a region based on samples obtained from field observations. Such estimates may suggest the number of species new to science and at potential risk of extinction. In this thesis, we develop novel methodology to conduct statistical inference, based on abundance-based data collected from multiple sampling locations, on the number of species within a taxonomic group residing in a region. The primary contribution of this work is the formulation of novel statistical methodology for analysis in this setting, where abundances of species are recorded at multiple sampling units across a region. This particular area has received relatively little attention in the literature. In the first chapter, the problem of estimating the number of species is formulated in a broad context, one that occurs in several seemingly unrelated fields of study. Estimators are commonly developed from statistical sampling models. Depending on the organisms or objects under study, different sampling techniques are used, and consequently, a variety of statistical models have been developed for this problem. A review of existing estimation methods, categorized by the associated sampling model, is presented in the second chapter. The third chapter develops a new negative binomial mixture model. The negative binomial model is employed to account for the common tendency of individuals of a particular species to occur in clusters. An exponential mixing distribution permits inference on the number of species that exist in the region, but were in fact absent from the sampling units. Adopting a classical approach for statistical inference, we develop the maximum likelihood estimator, and a corresponding profile-log-likelihood interval estimate of species richness. In addition, a Gaussian-based confidence interval based on large-sample theory is presented. The fourth chapter further extends the hierarchical model developed in Chapter 3 into a Bayesian framework. The motivation for the Bayesian paradigm is explained, and a hierarchical model based on random effects and discrete latent variables is presented. Computing the posterior distribution in this case is not straight-forward. A data augmentation technique that indirectly places priors on species richness is employed to compute the model using a Metropolis-Hastings algorithm. The fifth chapter examines the performance of our new methodology. Simulation studies are used to examine the mean-squared error of our proposed estimators. Comparisons to several commonly-used non-parametric estimators are made. Several conclusions emerge, and settings where our approaches can yield superior performance are clarified. In the sixth chapter, we present a case study. The methodology is applied to a real data set of oribatid mites (a taxonomic order of micro-arthropods) collected from multiple sites in a tropical rainforest in Panama. We adjust our statistical sampling models to account for the varying masses of material sampled from the sites. The resulting estimates of species richness for the oribatid mites are useful, and contribute to a wider investigation, currently underway, examining the species richness of all arthropods in the rainforest. Our approaches are the only existing methods that can make full use of the abundance-based data from multiple sampling units located in a single region. The seventh and final chapter concludes the thesis with a discussion of key considerations related to implementation and modeling assumptions, and describes potential avenues for further investigation. / Graduate