Changes to traditional taxonomic methods to incorporate new technologies and methods have already improved the quality of species hypotheses, but more work can be done to improve the speed of new species documentation. The mitochondrial COI DNA barcode has been successfully used to identify species with high accuracy since the early 2000s, and has been used in conjunction with morphological examinations and other DNA markers to discover and delimit new species. This thesis explores the application of DNA barcodes as the primary data for delimitation and diagnosis of new species of ichneumonoids. The genera Zelomorpha and Hemichoma are revised and 18 new species from the Área de Conservación Guanacaste in Costa Rica are diagnosed based on COI barcodes. Two additional species are described based on morphology. An illustrated morphological key and morphological diagnoses for each species are also included.

The biological diversity of reef-fish in the Florida Keys National Marine Sanctuary (FKNMS) from 1999 – 2016 was evaluated in terms of abundance, biomass, species richness, evenness, Shannon diversity, Simpson diversity, and functional diversity, using observations collected by multiple agencies and institutions under the Reef Visual Census (RVC) program. To compare the different diversity indices species richness, Shannon diversity, Simpson diversity, and functional diversity were converted into effective number of species. I examined the seven indices by no-take marine zones, in seven benthic habitat strata, and across the three-distinct geographic subregions in the Florida Keys domain (Upper, Middle, and Lower Keys). The objective was to describe changes in reef fish community responses through time and space in the Florida Keys, and to determine whether patterns in reef fish diversity indices were attributable to levels of protection, benthic habitat strata, or geographic subregion. The goal was to develop a framework for reef fish biodiversity assessments that can inform management and policy in the FKNMS, and support updates to the periodic Condition Reports generated by the Sanctuary. Diversity indices (with the exception of evenness) were significantly higher in no-take marine zones compared to areas open to fishing. All indices were significantly different by strata type. High Relief Reef habitats had the highest abundance, biomass, richness, Simpson diversity, Shannon diversity, and functional diversity, but had moderate evenness values. The biodiversity metrics for the Upper Keys and Lower Keys were not significantly different, but both of these areas were significantly different from the Middle Keys for all indices except species richness, which did not vary by subregion. Generalized additive models revealed that the principal driver across indices was habitat structure (strata and depth). Time (year), space (latitude, longitude), and no-take marine zones (0, unprotected and 1, protected) explained roughly similar proportions of deviance across all indices. Simpson diversity, Shannon diversity, and functional diversity showed similar trends in no-take marine zones, strata, and subregion through time. The Florida Keys is characterized as having relatively low functional diversity due to a few common traits shared by many individuals and many rare traits shared by a few individuals. This suggests that the Florida Keys reef fish are less vulnerable to functional loss due to high functional redundancy among species. However, functionally rare traits, those possessed by few individuals, are vulnerable to functional loss and will have a larger impact on ecosystem functioning than species that share similar traits. Low functional diversity also suggests lower adaptability to environmental perturbations. Given the minimal robustness of traits, the ecosystem is less likely to possess functions that can withstand disturbances. The impacts of two types of perturbations were examined in a qualitative manner: hurricanes and cold-temperature events. Disturbance by hurricanes in 2004 and 2005 and the extreme cold event of January 2010 had a high impact on reef fish community composition. Between 2004 and 2006, following two consecutive years of hurricanes, abundance of reef fish declined 31%, biomass declined 53%, species richness declined 18%, Simpson diversity declined 12%, Shannon diversity declined 14%, and functional diversity declined 8%. Following a year without hurricanes in 2007 abundance of reef fish increased 11%, biomass increased 13%, richness increased 14%, Simpson and Shannon diversity increased 10%, and functional diversity increased 6%. After the January 2010 extreme cold event, reef fish abundance and biomass also declined 17%, richness declined 10%, Simpson diversity and Shannon diversity declined 5% and 6%, and functional diversity declined 2%. All matrices increased the following year, where abundance increased 13%, biomass increased 31%, richness increased 13%, Simpson diversity increased 7%, Shannon diversity increased 10%, and functional diversity increased 8%. Based on my findings and literature review, to better preserve biodiversity and enhance ecosystem functioning, I recommend prioritizing conservation efforts in source habitats (e.g., High Relief Reefs) and habitats with varying complexity by implementing corridor reserves that facilitate the natural migration of organisms between different habitat types. I also recommend prioritizing preservation of species that possess functionally rare traits with few individuals (e.g., cleaner species) by preserving areas with greater functional diversity (e.g., Higher Relief Reefs and Forereef Deep Linear Reefs).

This study investigated the causes of high level of intra-and inter-population variation known to occur in the morphology of fish in the genus Hypseleotris Eleotride in southern Australia, particularly within the Murray-Darling river system. The three major objectives of the study were, identify the number and distribution of species,determine the genetic structure of the populations and analyse relationships between species and consider the process of speciation in this species complex. The investigation of morphological variation in Hypseleotris confirmed the presence of two well known species i.e. H. compressa and H. galli, in the coastal rivers and also of the inland species H. klunzingeri. Populations of Hypseleotris klunzigeri sensu lato in inland river were found to be very highly variable and analysis using discriminant functions and principle component analysis showed the widespread presence of three forms (A, B1 and B2). The analysis was confused by the presence of north/south clines and upstream/downstream variation in characteristic in each form. After these factors were removed, there was still a great deal of variation in each population. The presence of hybrids between each pair of inland species, identified by both morphological and genetic data, further confused the analysis and makes identification of all specimens to species in the field difficult. Examination of type material of H. Klunzingeri showed that this belonged to form B2. The other forms can be related to the undescribed species, Midgley's carp gudgeon and Lake's carp gudgeon. Keys to the species in the complex in southeastern Australia are given. The morphological and genetic data show that H. compressa and H. klunzingeri are sister species, primarily separated by the eastern uplands. Similarly, the coastal species, H. galli is related to form B1 and more distantly, to form A. Possible scenarios for the complex are given. / Doctor of Philosophy (PhD)

Humankind has redistributed a large number of species outside their native geographic ranges. Although the majority of introduction attempts fail to establish populations, the cumulative negative effect of successful non-native species has been and will continue to be large. Historical records of land bird introductions provide one of the richest sources of data for testing hypotheses regarding the factors that affect the successful establishment of non-native populations. However, despite comprehensive summaries of global avian introductions dating back two decades only very recent studies have examined the successful establishment of non-native bird species worldwide. It is clear that a non-random pattern exists in the types of land bird species that have been chosen by humans to be introduced outside their native range. Out of the 44 avian families from which species have been chosen for introduction almost 70% of introduction attempts have been from just five families (Phasianidae, Passeridae, Fringillidae, Columbidae, Psittacidae). Notably, these families include game species, insectivorous song birds, and species from the pet trade. It has been hypothesised that the fate of introduced species may be determined in part by heritable characteristics that are shared by closely related taxa. In my analyses, I have used current comparative methods to demonstrate that intrinsic eco-physiological characteristics are significant predictors of the worldwide success of introduced land bird species. The results of my analyses contribute to a greater ecological understanding of the traits that correlate with the successful establishment of non-native species. Notably, the three major conclusions that I have drawn from this thesis are: 1. Non-random patterns of successful establishment exist for introduced land bird taxa that have experienced a repeated number of introduction attempts. This result supports the idea that introduced species have an inherent likelihood of either succeeding or failing to establish non-native populations. 2. Eco-physiological traits are important correlates for determining the variability in introduction outcome for non-native land bird species. With reliable information on introduction attempts and taxa-specific traits predictive models are possible that quantify the outcome of repeated introduction attempts across non-native species. 3. Islands are not universally less resistant than mainland regions to the successful establishment of non-native species. This perception is a reflection of the greater number of introduction attempts to islands rather than an effect of biotic resistance. Any differences in the success of introduction attempts can be attributed largely to differences in the proportion of introductions that have been made across biogeographic regions. I have highlighted that data are accessible for global analyses of the variability in the successful establishment of non-native species. Although establishment success is not a deterministic process, the characteristics of an introduced species can influence the probability of its succeeding. I have shown that with adequate eco-physiological information, and for introduced land bird species at least, this probability can be predicted. These results refute previous suggestions that the stochastic component of species introductions will always overshadow any emerging patterns of successful establishment among non-native populations.

<p>Many of the earth’s ecosystems are experiencing large species losses due to human impacts such as habitat destruction and fragmentation, climate change, species invasions, pollution, and overfishing. Due to the complex interactions between species in food webs the extinction of one species could lead to a cascade of further extinctions and hence cause dramatic changes in species composition and ecosystem processes. The complexity of ecological systems makes it difficult to study them empirically. The systems often consist of large species numbers with lots of interactions between species. Investigating ecological communities within a theoretical approach, using mathematical models and computer simulations, is an alternative or a complement to experimental studies. This thesis is a collection of theoretical studies. We use model food webs in order to explore how biodiversity (species number) affects the response of communities to species loss (Paper I-III) and to environmental variability (Paper IV).</p><p>In paper I and II we investigate the risk of secondary extinctions following deletion of one species. It is shown that resistance against additional species extinctions increases with redundancy (number of species per functional group) (Paper I) in the absence of competition between basal species but decreases with redundancy in the presence of competition between basal species (Paper II). It is further shown that food webs with low redundancy run the risk of losing a greater proportion of species following a species deletion in a deterministic environment but when demographic stochasticity is included the benefits of redundancy are largely lost (Paper II). This finding implies that in the construction of nature reserves the advantages of redundancy for conservation of communities may be lost if the reserves are small in size. Additionally, food webs show higher risks of further extinctions after the loss of basal species and herbivores than after the loss of top predators (Paper I and II).</p><p>Secondary extinctions caused by a primary extinction and mediated through direct and indirect effects, are likely to occur with a time delay since the manifestation of indirect effects can take long time to appear. In paper III we show that the loss of a top predator leads to a significantly earlier onset of secondary extinctions in model communities than does the loss of a species from other trophic levels. If local secondary extinctions occur early they are less likely to be balanced by immigration of species from local communities nearby implying that secondary extinctions caused by the loss of top predators are less likely to be balanced by dispersal than secondary extinctions caused by the loss of other species. As top predators are vulnerable to human-induced disturbances on ecosystems in the first place, our results suggest that conservation of top predators should be a priority. Moreover, in most cases time to secondary extinction is shown to increase with species richness indicating the decay of ecological communities to be slower in species-rich than in species-poor communities.</p><p>Apart from the human-induced disturbances that often force species towards extinction the environment is also, to a smaller or larger extent, varying over time in a natural way. Such environmental stochasticity influences the dynamics of populations. In paper IV we compare the responses of food webs of different sizes to environmental stochasticity. Species-rich webs are found to be more sensitive to environmental stochasticity. Particularly, species-rich webs lose a greater proportion of species than species-poor webs and they also begin losing species faster than species-poor webs. However, once one species is lost time to final extinction is longer in species-rich webs than in species-poor webs. We also find that the results differ depending on whether species respond similarly to environmental fluctuations or whether they are totally uncorrelated in their response. For a given species richness, communities with uncorrelated species responses run a considerable higher risk of losing a fixed proportion of species compared with communities with correlated species responses.</p>

This thesis aims to improve our understanding of how riverine ecosystems respond to dam removal. Riverine and particularly riparian ecosystems are among the most variable and important features of all landscapes. They connect landscape elements both longitudinally and laterally, and are governed by processes such as flooding, erosion and deposition that create dynamic, diverse and heterogeneous habitats. In fact, riparian zones are among the world’s most species-rich habitats. Worldwide there are millions of dams that fragment stream and river systems, regulate flows and degrade ecosystems. Dams impact freshwater, marine and terrestrial ecosystems and threaten biodiversity by disrupting organism movements and energy flows in the landscape. An important upstream effect of dams is inundation of habitats and development of new shorelines around impounded areas. Effects downstream of dams are mainly caused by changed hydrological regimes and retention of organic and inorganic materials in reservoirs, leading to reduced transport and dispersal of for example seeds to reaches downstream. The removal of dams create expectations that biota will eventually recover. We have studied a number of dam removal projects in Sweden. Our experimental results showed that following dam removal, newly exposed soils in former impoundments were rapidly colonized by pre-removal species. Their species richness increased slightly with time and their species composition indicated a slow change towards that in the reference site. In addition, the vegetation in formerly impounded areas showed a direction of change from lentic riparian plants (high proportion of aquatics) towards lotic ones, consisting of native perennials typical of free-flowing streams. We also found that the apprehensions that former impoundments would turn into pools of mud did not come true; in fact, a process towards more pristine channel morphology was observed. After removal there was erosion and downstream transport of sediment. We found only minor effects on macroinvertebrate communities. For example, a few species decreased over the years, suggesting that dam removal in itself might cause a temporary disturbance. This highlights the importance of long-term studies after dam removal, and also the importance of comparisons with pre-removal conditions and stretches unaffected by dams. Thorough documentation of executed dam removal projects and distribution of the results and experiences are tremendously important in the planning process of future decommissioning projects. Also, our experiences have taught us that in order to attain a successful dam removal it is important to involve stakeholders such as non-governmental organizations and local inhabitants in the process.

Many of the earth’s ecosystems are experiencing large species losses due to human impacts such as habitat destruction and fragmentation, climate change, species invasions, pollution, and overfishing. Due to the complex interactions between species in food webs the extinction of one species could lead to a cascade of further extinctions and hence cause dramatic changes in species composition and ecosystem processes. The complexity of ecological systems makes it difficult to study them empirically. The systems often consist of large species numbers with lots of interactions between species. Investigating ecological communities within a theoretical approach, using mathematical models and computer simulations, is an alternative or a complement to experimental studies. This thesis is a collection of theoretical studies. We use model food webs in order to explore how biodiversity (species number) affects the response of communities to species loss (Paper I-III) and to environmental variability (Paper IV). In paper I and II we investigate the risk of secondary extinctions following deletion of one species. It is shown that resistance against additional species extinctions increases with redundancy (number of species per functional group) (Paper I) in the absence of competition between basal species but decreases with redundancy in the presence of competition between basal species (Paper II). It is further shown that food webs with low redundancy run the risk of losing a greater proportion of species following a species deletion in a deterministic environment but when demographic stochasticity is included the benefits of redundancy are largely lost (Paper II). This finding implies that in the construction of nature reserves the advantages of redundancy for conservation of communities may be lost if the reserves are small in size. Additionally, food webs show higher risks of further extinctions after the loss of basal species and herbivores than after the loss of top predators (Paper I and II). Secondary extinctions caused by a primary extinction and mediated through direct and indirect effects, are likely to occur with a time delay since the manifestation of indirect effects can take long time to appear. In paper III we show that the loss of a top predator leads to a significantly earlier onset of secondary extinctions in model communities than does the loss of a species from other trophic levels. If local secondary extinctions occur early they are less likely to be balanced by immigration of species from local communities nearby implying that secondary extinctions caused by the loss of top predators are less likely to be balanced by dispersal than secondary extinctions caused by the loss of other species. As top predators are vulnerable to human-induced disturbances on ecosystems in the first place, our results suggest that conservation of top predators should be a priority. Moreover, in most cases time to secondary extinction is shown to increase with species richness indicating the decay of ecological communities to be slower in species-rich than in species-poor communities. Apart from the human-induced disturbances that often force species towards extinction the environment is also, to a smaller or larger extent, varying over time in a natural way. Such environmental stochasticity influences the dynamics of populations. In paper IV we compare the responses of food webs of different sizes to environmental stochasticity. Species-rich webs are found to be more sensitive to environmental stochasticity. Particularly, species-rich webs lose a greater proportion of species than species-poor webs and they also begin losing species faster than species-poor webs. However, once one species is lost time to final extinction is longer in species-rich webs than in species-poor webs. We also find that the results differ depending on whether species respond similarly to environmental fluctuations or whether they are totally uncorrelated in their response. For a given species richness, communities with uncorrelated species responses run a considerable higher risk of losing a fixed proportion of species compared with communities with correlated species responses.

Semi-natural grasslands, which are a declining and fragmented habitat in Europe, contain a high biodiversity, and are therefore of interest to conservation. This thesis examines how plant diversity is influenced by the landscape context, and how plant and fungal diversity can be targeted by practical conservation using indicator species and congruence between species groups. Reproduction and recruitment of the dioecious herb Antennaria dioica was also investigated, providing a case study on how fragmentation and habitat degradation may affect grassland plants. Grassland size and heterogeneity were of greater importance for plant diversity in semi-natural grassland, than present or historical connectivity to other grasslands, or landscape characteristics. Larger grasslands were more heterogeneous than smaller grasslands, being the likely reason for the species-area relationship. A detailed study on A. dioica discovered that sexual reproduction and recruitment may be hampered due to skewed sex-ratios. Sex-ratios were more skewed in small populations, suggesting that dioecious plants are likely to be particularly sensitive to reduced grassland size and fragmentation. A study on indicators of plant species richness, used in a recent survey of remaining semi-natural grasslands in Sweden, revealed several problems. A high percentage of all indicator species were missed by the survey, removing an otherwise significant correlation between indicator species and plant species richness. Also, a null model showed that the chosen indicator species did not perform significantly better than species chosen at random from the available species pool, questioning the selection of the indicators in the survey. Diversity patterns of the threatened fungal genus Hygrocybe were not congruent with plant species richness or composition. Plants are thus a poor surrogate group for Hygrocybe fungi, and probably also for other grassland fungi. Implications from this thesis are that conservation of semi-natural grasslands should target several species groups, and that an appropriate scale for plant conservation may be local rather than regional.

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.

Humans are modifying the global landscape at an unprecedented scale and pace. As a result, species are declining and going extinct at an alarming rate. Here, I investigate two main aspects of species’ declines: what factors are contributing to their declines and how effective our conservation efforts have been. I assessed one of the main mechanisms for protecting species by looking at the Endangered Species Act (ESA) in the United States. I examined three separate indicators of species declines for different groups of species: range contractions in Canadian imperilled species, declines in abundance in global amphibian populations and increases in temporal variability in abundance in North American breeding birds. I found that change in recovery status of ESA listed species was only very weakly related to the number of years listed, number of years with a recovery plan, and funding. These tools combined explained very little of the variation in recovery status among species. Either these tools are not very effective in promoting species’ recovery, or species recovery data are so poor that it is impossible to tell whether the tools are effective or not. I examined patterns of species’ declines in three different groups in relation to a number of anthropogenic variables. I found high losses of Canadian imperiled bird, mammal, amphibian and reptile species in regions with high proportions of agricultural land cover. However, losses of imperiled species are significantly more strongly related to the proportion of the region treated with agricultural pesticides. This is consistent with the hypothesis that agricultural pesticide use, or something strongly collinear with it (perhaps intensive agriculture more generally), has contributed significantly to the decline of imperiled species in Canada. Global increases in UV radiation do not appear to be a major cause of amphibian population declines. At individual sites, temporal changes in amphibian abundance are not predictably related to changes in UV intensity. Variability in species’ abundance of North American breeding birds, after accounting for mean abundance, is not systematically higher in areas of high human-dominated land cover or climate change. Rather, it appears that areas with a high proportion of human-dominated cover come to have a higher proportion of highly abundant, and thus more variable, species.