Species distribution models

Species distribution models are a group of methods often used to estimate consequences of global change, to assess ecological status and for other ecological applications. The main idea behind species distribution models is that the geographical distributions of species can, to a large part, be explained by environmental factors and that species distributions therefore can be predicted in time or space. For robust and reliable applications, models need to be based on sound ecological principles, predictions need to be as accurate as possible, and model uncertainties need to be understood. Two approaches are available for modelling entire species communities: (1) each species can be modelled individually and independently of other species or (2) community information can be incorporated into the models. The first study in this thesis compares these two modelling approaches for predicting phytoplankton assemblages in lakes. The results showed that predictive accuracy was higher when species were modelled individually. The results also showed that phytoplankton can be used for model-based assessment of ecological status. This finding is important because phytoplankton is required for assessing the ecological status of European water bodies according to the European Water Framework Directive. Dispersal barriers in the landscape or limited dispersal ability of species might be a reason for species being absent from suitable habitats, and these factors might therefore affect model accuracy. The second study in this thesis examines the influence of dispersal and the spatial configuration of ecosystems on prediction accuracy of benthic invertebrate and phytoplankton distribution and assemblage composition. The results showed only a minor influence of spatial configuration and no effect of flight ability of invertebrates on model accuracy. However, the models used may partly account for dispersal constraints, since dispersal-related factors, such as lake surface area, are included as predictor variables. The result also showed that composition of littoral invertebrate assemblages was easier to predict at sites located in well-connected lake systems, possibly because the relatively unstable littoral zone necessitates a need for species to re-colonize disturbed habitats from source populations

Small-mammal assemblage response to deforestation and afforestation in central China

International audienceDeforestation is a major environmental issue driving the loss of animal and plant species. Afforestation has recently been promoted to conserve and restore Chinese forest ecosystems. We investigated the distribution of small-mammal assemblages in an area where forest and associated deforestation habitats dominate and in an agricultural area where afforestation is ongoing in the Loess Plateau of southern Ningxia Autonomous Region, P.R. China. Multiple trapping was used. Assemblages were defined based on the multinomial probability distribution and information theory. Species turnover between assemblages of deforested and afforested habitats was high, although no clear effect on species richness was observed. The two assemblages described along the deforestation gradient displayed higher diversity, whereas diversity was lower in assemblages identified in afforested habitats where Cricetulus longicaudatus, known agricultural pest in various areas of China, clearly dominated. The threatened Sorex cylindricauda and Eozapus setchuanus were recorded along the deforestation gradient but not in plantations. Therefore, habitats present along a deforestation succession in this part of Ningxia sustain a high diversity of small mammals and include species of conservation concern. At the present stage of its process (maximum 15 years), afforestation in southern Ningxia favours the dominance of an agricultural pest

Toward a Census of Bacteria in Soil

For more than a century, microbiologists have sought to determine the species richness of bacteria in soil, but the extreme complexity and unknown structure of soil microbial communities have obscured the answer. We developed a statistical model that makes the problem of estimating richness statistically accessible by evaluating the characteristics of samples drawn from simulated communities with parametric community distributions. We identified simulated communities with rank-abundance distributions that followed a truncated lognormal distribution whose samples resembled the structure of 16S rRNA gene sequence collections made using Alaskan and Minnesotan soils. The simulated communities constructed based on the distribution of 16S rRNA gene sequences sampled from the Alaskan and Minnesotan soils had a richness of 5,000 and 2,000 operational taxonomic units (OTUs), respectively, where an OTU represents a collection of sequences not more than 3% distant from each other. To sample each of these OTUs in the Alaskan 16S rRNA gene library at least twice, 480,000 sequences would be required; however, to estimate the richness of the simulated communities using nonparametric richness estimators would require only 18,000 sequences. Quantifying the richness of complex environments such as soil is an important step in building an ecological framework. We have shown that generating sufficient sequence data to do so requires less sequencing effort than completely sequencing a bacterial genome

Competition model explains trends of long‐term fertilization in plant communities

Over 40 years ago, Kempton (Biometrics, 35, 1979, 307) reported significant modification to plant community structure following a long-term fertilization experiment. Many researchers have investigated this phenomenon in the years since. Collectively, these studies have shown consistent shifts in rank abundance relationships among species in communities following fertilization. The previous studies indicated that fertilization affects community structure through several critical processes, including trait-based functional response, reordering of species in rank abundance diagram (RAD), and niche dimensionality, although some questions have remained. How does the species reordering driven by the plant responses cause characteristic trends in temporal changes of RAD? Why are those trends ubiquitous in various systems? To answer those questions, we theoretically investigated the effects of fertilization on community structure based on a colonization model (or Levins model) with competition–fecundity trade-offs, which can result in the coexistence of multiple species under competition. The model represents characteristic RAD, which can be an adequate tool to study community composition. Our theoretical model comprehensively represents observed trends in rank abundance relationships following long-term fertilization and suggests that competitive interactions among species are a critical factor in structuring species diversity in plant communities

Inherited microbial symbionts increase herbivore abundances and alter arthropod diversity on a native grass

Some microbial symbionts of plants are maternally inherited and thus functionally increase genetic and phenotypic variation within plant populations. This variation, coupled with that of the host plant and environment, may alter abundances, diversity, and trophic structure of associated plant and animal communities. Fungal endophytes in the genus Neotyphodium are vertically transmitted, asexual microbial symbionts of grasses that remain asymptomatic and rely upon their hosts for resources and transmission via seeds, often providing benefits to their hosts, including protection against herbivores. Endophyte infections may influence associated arthropod communities in agronomic grasses, but the long-term effects of endophytes and variation in host genotype and resource availability on arthropod communities in native grass populations are unknown. We conducted a long-term field experiment with four maternal genotypes of an infected (E+) native grass (Festuca arizonica) from whence the endophyte was experimentally removed (E-) and water availability was controlled, to test the effects of infection, plant genotype, and resources on abundances, biomass, diversity (richness and evenness), and trophic structure of the arthropod community. Generally, E+ grasses harbored more arthropods, including more herbivores, predators, and detritivores, suggesting that the effects of endophytes cascaded upward through trophic levels in terms of abundances, at least in early ontogeny of the host. That E+ plants harbored more herbivorous insects than E- plants suggests that infection does not increase but instead decreases resistance to herbivores, contrary to prevailing concepts of endophytes as defensive mutualists. Infection did not alter overall species richness of the arthropod community or richness of herbivores but reduced natural enemy richness, especially that of parasites, and increased richness of detritivores. Reduced richness and shifts in evenness of natural enemies on E+ plants suggest that endophytes may disproportionately affect diversity at higher trophic levels and may partially explain increases in abundances of herbivorous insects on E+ plants. Biomass of predators, detritivores, and omnivores increased on plants with supplemented water, and arthropod and herbivore biomass varied by plant genotype. Symbiont-mediated phenotypic variation interacts with variation from plant genotype and environmental factors to alter arthropod abundances and diversity, and these effects shift with ontogeny of the host

A null model of community disassembly effects on vector-borne disease risk

Community structure is heterogeneous at a variety of spatial and temporal scales, and this variation has been shown to influence the risk of zoonotic diseases such as West Nile Virus and Lyme disease. Theoretical models and most empirical evidence suggest that the greatest influence of host diversity occurs when transmission is frequency-dependent (i.e., the rate of contact is constant). These theoretical models are generally based on ordinary differential equations and become intractable when considering more than a few species. This makes it particularly difficult to predict how we might expect the transmission of infectious diseases to change as community structure changes in space or in time. Here we develop a model in which we construct a network of interactions between hosts and vectors to quantify the change in risk under different scenarios of community disassembly. Decreased vector biodiversity always reduced mean risk, while a change in host community structure led to increased or decreased mean risk depending on the manner in which community disassembly altered mean competence of the “new” community. These trends in mean risk can be generalized across a multitude of natural systems because they do not depend on the distribution of host quality, though simulation suggests that variation around the mean can be very high. The primary value of model is that it can be used to establish upper and lower bounds on the expected change in disease risk with decreasing biodiversity

The Development Of A Data Driven Management Plan For The Tater Hill Plant Preserve

The Tater Hill Plant Preserve was established to protect rare and state-endangered plant species and their habitats. The acquisition and management of plant habitats have successfully increased population growth and limit external negative anthropogenic effects. This study demonstrates the importance of assessing biotic threats to rare plant populations and determining future actions to promote conservation management decisions. Trail camera technology was used to determine vertebrate occurrence, species richness, species composition, daily activity levels, and vertebrate movement patterns within the Tater Hill Plant Preserve. In addition, a microsatellite assessment of the invasive species Centaurea maculosa, commonly known as Spotted Knapweed found allelic richness and heterozygosity indicative of a founders effect with multiple introduction to the Tater Hill Plant Preserve. Finally, geographic information systems was used to create range distribution maps that update current locality data and can support future land management decisions. This study is a multidisplinary method to understand how vertebrates and invasive species are using the Tater Hill Plant preserve, and contributes to the protection and growth of rare plant populations in the Tater Hill Plant Preserve. These methods can be used to advance conservation practices across plant preserves around the state

A Decade-Long Change in the Elevational Distribution of Non-Volant Small Mammals on Mount Meru, Tanzania

Understanding species distribution across elevational gradients is crucial for developing conservation strategies for montane biotic systems. A survey of small mammals was conducted on Mount Meru at six elevations, ranging between 1500 m and 3650 m. A total of 803 small mammal individuals, including 2 shrew species and 13 rodent species, were documented. Of these, Crocidura newmarki and Lophuromys verhageni were endemic on Mount Meru. Species richness was highest at mid-elevations, which is in line with the global pattern for small mammals. Prior to our study, the most complete data on small mammals on Mount Meru was collected in 2009. Our study provides an opportunity to show how small mammal elevational distribution has changed, over the last decade. We found six species (Arvicanthis niloticus, Mastomys natalensis, Lemniscomys striatus, Dasymys incomtus, Cricetomys ansorgei, and Montemys delectorum), which were not documented in 2009, but did not find Otomys tropicalis. Interestingly, the community composition at higher elevations in 2021 resembles that at lower elevations in 2009, suggesting that small mammal species have moved their range upward over time. Climate change could be a factor associated with the distributional shift found

Bottom-up Effects of Substrate on Two Adjacent Shrub Communities and the Distribution of a Rare and Endangered Plant Species, Astragalus jaegerianus Munz.

Edaphic habitats are botanically interesting because of differences in vegetation with neighboring sites and because they tend to harbor rare species. In the central Mojave Desert, there are granite colluvial substrates where creosote bush, the dominant shrub in the area, is sparser and generally smaller than in the neighboring creosote bush communities. It is on these sites that the Lane Mountain milkvetch, a rare and federally endangered species, is restricted. The milkvetch is a nitrogen-fixer and grows under and within the canopy of host shrubs. Our previous studies have demonstrated that the milkvetch has no preference for species of host shrub, except Larrea tridentata, which appears to be an unsuitable host plant for the milkvetch. In this study, we surveyed three transects within milkvetch habitats and three transects in adjacent creosote bush habitats in the year 2000 and again in 2010, a period coincident with long-term drought conditions in the Mojave Desert. Our results show that adjacent milkvetch and creosote bush shrub communities differ significantly in shrub height, shrub volume, and shrub density in the year 2000: the shrubs in milkvetch communities were more numerous but smaller compared to adjacent creosote bush scrub. Species richness also differed between communities in the year 2000: milkvetch communities contained 19 different shrub species and creosote bush communities had only 9 species. Surveys in 2010 show that the drought had significant negative effects on both shrub communities. Total shrub mortality (166 shrubs) was high compared to shrub recruitment (16 shrubs), and the majority of mortality and recruitment occurred in milkvetch communities (131 deaths and 16 recruits). Shrub densities decreased significantly in milkvetch communities in 2010, but were still considerably higher than in creosote bush communities. These results suggest that the restricted distribution of the Lane Mountain milkvetch may be the result of higher shrub densities in milkvetch shrub communities; increased shrub densities increases the proximity of suitable host shrubs, which in turn increase the probability of successful seed dispersal and establishment