Multiple species of Phoreiobothrium from the blacktip shark, Carcharhinus limbatus, in the Gulf of Mexico

During a survey of the adult tapeworm fauna of sharks from the Gulf of Mexico, the blacktip shark, Carcharhinus limbatus (Müller and Henle, 1839), was found to host cestodes in the genus Phoreiobothrium. Carcharhinus limbatus inhabits the world's tropical and warm temperate waters. As yet, 34 species of cestodes representing the orders Tetraphyllidea, Cathetocephalidea, and Trypanorhyncha have been reported to parasitize the species throughout its range. Little is known about tetraphyllidean diversity in C. limbatus in the Gulf of Mexico; no records exist for Phoreiobothrium from C. limbatus in this region. Between 2005 and 2007, 6 specimens of C. limbatus were collected off Ocean Springs, Mississippi and 14 specimens were collected off Panama City, Florida, and their spiral intestines examined for cestodes. Whole mounts and histological sections of the cestode specimens were prepared for examination with light microscopy; scoleces were prepared for scanning electron microscopy. Overall, C. limbatus was found to host 4 species of Trypanorhyncha and 11 species of Tetraphyllidea. In addition to 1-2 species each in the tetraphyllidean genera Disculiceps, Anthobothrium, and Paraorygmatobothrium, C. limbatus hosted 6 species of Phoreiobothrium. The diversity of Phoreiobothrium species is of special interest: all are new to science and collectively represent an unusually high number of congeners in a single host species. The new species of Phoreiobothrium from C. limbatus can be distinguished from the known species and each other based on characters such as scolex dimensions, number of subloculi, presence or absence of papillae, and distribution of vitellaria. Despite its 11 cosmopolitan distribution, it has been suggested that several distinct populations of C. limbatus exist in the Gulf of Mexico. The complex species assemblage of Phoreiobothrium in C. limbatus in the Gulf of Mexico has the potential to inform us about its population structure of the host

MODELING SPECIES DISTRIBUTIONS: APPLICATIONS AND METHODS FOR MARINE BIOGEOGRAPHY AND CONSERVATION

I employed multidisciplinary approaches for understanding distributions of marine fishes in the present, past, and future, and for considering more broadly the historical role of primary research in policy decisions. In chapter 1, I generated ecological niche models (ENMs) for Latimeria chalumnae using two different modeling algorithms; these models anticipated occurrences of L. chalumnae's sister species, L. menadoensis, but sample sizes were not large enough to assess the statistical significance of these species' niche similarity. Furthermore, the range of coelacanths may extend beyond their presently known distributions; future exploration may reveal additional populations of these elusive fishes. In chapter 2, I developed a holistic biogeographic history of codfishes in the subfamily Gadinae. I found both ecological niche and geographic distributions of gadine fishes to be largely conservative, but two clades, tomcods and crown cods, included both Pacific and Atlantic species. Divergence in both clades was estimated to have begun in the Pliocene; environmental tolerance reconstructions support temperate origins of both clades, and cyclical Arctic ice formation may have driven divergence. In chapter 3, I addressed the role of general circulation model (GCM) bias as a significant source of uncertainty in estimates of species' potential distributional responses to climate change. ENMs of 15 gadine species calibrated using an observation-based dataset and a dataset derived from the CCSM4 GCM showed areas of disagreement concordant with known GCM biases. Consciousness of bias in GCM data will allow researchers and policy makers to identify areas of particular concern for biodiversity more realistically. Finally, in chapter 4, I explored the evolution of the relationship between policy makers and researchers through the lens of the U.S. Fisheries Service. Building cooperative capacity between these two groups led to a more systematic understanding of the oceans, and thus to success in reducing numbers of overfished stocks

Predicting suitable environments and potential occurrences for coelacanths (Latimeria spp.)

This is the author's accepted manuscript. The original publication is available at www.springerlink.com.Extant coelacanths (Latimeria chalumnae) were first discovered in the western Indian Ocean in 1938; in 1998, a second species of coelacanth, Latimeria menadoensis, was discovered off the north coast of Sulawesi, Indonesia, expanding the known distribution of the genus across the Indian Ocean Basin. This study uses ecological niche modeling techniques to estimate dimensions of realized niches of coelacanths and generate hypotheses for additional sites where they might be found. Coelacanth occurrence information was integrated with environmental and oceanographic data using the Genetic Algorithm for Rule-set Production (GARP) and a maximum entropy algorithm (Maxent). Resulting models were visualized as maps of relative suitability of sites for coelacanths throughout the Indian Ocean, as well as scatterplots of ecological variables. Our findings suggest that the range of coelacanths could extend beyond their presently known distribution and suggests alternative mechanisms for currently observed distributions. Further investigation into these hypotheses could aid in forming a more complete picture of the distributions and populations of members of genus Latimeria, which in turn could aid in developing conservation strategies, particularly in the case of L. menadoensis

Experimental evidence of impacts of an invasive parakeet on foraging behavior of native birds

Resource competition is one potential behavioral mechanism by which invasive species can impact native species, but detecting this competition can be difficult due to the interactions that variable environmental conditions can have on species behavior. This is particularly the case in urban habitats where the disturbed environment can alter natural behavior from that in undisturbed habitats. The rose-ringed parakeet (Psittacula krameri), is an increasingly common invasive species, predominantly associated with large urban centers. Using an experimental approach, we tested the behavioral responses of native garden birds in response to the presence of a rose-ringed parakeet versus the presence of a similarly sized and dominant native bird, the great spotted woodpecker (Dendrocopos major). Parakeet presence significantly reduced feeding rates and increased vigilance among native birds compared with our control treatments. Of visits made by native birds in the presence of a parakeet, feeding was more likely to occur in sites within the parakeet range compared with sites outside, suggesting some habituation of native birds has occurred following prior exposure to parakeets but overall foraging behavior is still disrupted. The results of our study suggest that nonnative species can have complex and subtle impacts on native fauna and show that a nonnative competitor can impact native species simply through their presence near resources

Endemicity and climatic niche differentiation in three marine ciliated protists

The biogeographic pattern of single‐celled eukaryotes (protists), including ciliates, is poorly understood. Most marine species are believed to have a relatively high dispersal potential, such that both globally distributed and geographically isolated taxa exist. Primary occurrence data for three large, easily identified ciliate species, Parafavella gigantea, Schmidingerella serrata, and Zoothamnium pelagicum, and environmental data drawn from the National Oceanic and Atmospheric Administration's World Ocean Atlas were used to estimate each species’ spatial and environmental distributions using Maxent v3.3.3k. The predictive power of the models was tested with a series of spatial stratification studies, which were evaluated using partial receiver operating characteristic (ROC) statistics. Differences between niches occupied by each taxon were evaluated using background similarity tests. All predictions showed significant ability to anticipate test points. The null hypotheses of niche similarity were rejected in all background similarity tests comparing the niches among the three species. This article provides the first quantitative assessment of environmental conditions associated with three species of ciliates and a first estimate of their spatial distributions in the North Atlantic, which can serve as a benchmark against which to document distributional shifts. These species follow consistent, predictable patterns related to climate and environmental biochemistry; the importance of climatic conditions as regards protist distributions is noteworthy considering the effects of global climate change.We dedicate this paper to John Clamp, who was an integral part of the research and writing of this paper. Clamp passed while this manuscript was under review. He was a professor at North Carolina Central University for more than 30 yr, devoting his outstanding research to evolutionary biology, and particularly the study of ciliated protists. He was a larger‐than‐life character and will be greatly missed as friend and mentor. This work was supported by the Ministerio de Economía y Competitividad, Española (MINECO, grant number CGL2013‐40851‐P/ BOS) to MMC, and travel support from the Research Coordination Network for Biodiversity of Ciliates (National Science Foundation grant number DEB 1136580) from the U.S. National Science Foundation to JC. RAJW was supported by the Crafoord Foundation, Sweden (grant numbers 20160971 and 20170671), while completing this manuscript

occCite: Tools for querying and managing large biodiversity occurrence datasets

The amount of observational and specimen-based biodiversity data available to researchers is increasing exponentially, yet the ability to manage and cite large, complex biodiversity datasets lags behind. This management and citation gap impedes reproducibility for data users and the ability for data publishers to track use and accumulate use citations, ultimately harming the longer-term sustainability of the still-emerging enterprise of research data-sharing. Here we present an R package, occCite (v. 0.4.7), to aid researchers in querying large species occurrence data aggregators (specifically, the Global Biodiversity Information Facility, GBIF, and the Botanical Information and Ecology Network, BIEN), and store metadata such as primary data providers, database accession dates, DOIs, and the taxonomic source used for search terms. occCite also includes tools to summarize and visualize query results and generate citation lists of all data providers and software packages used during the query process. We provide examples of a basic occurrence search and citation workflow as well as an advanced workflow using features for custom optimized searches, visualization, and summary procedures. occCite improves upon existing R packages by uniting data from powerful API-based query packages (rgbif and BIEN) into a unified object-based framework, while maintaining metadata vital to best-practice recommendations for documenting biodiversity analysis workflows. occCite aims to efficiently close the gap in the citation cycle between primary data providers and final research products, allowing researchers to meet dataset documentation standards without sacrificing time and resources to the demands of providing increasing levels of detail on their datasets

Automated identification of insect vectors of Chagas disease in Brazil and Mexico: the Virtual Vector Lab

Identification of arthropods important in disease transmission is a crucial, yet difficult, task that can demand considerable training and experience. An important case in point is that of the 150+ species of Triatominae, vectors of Trypanosoma cruzi, causative agent of Chagas disease across the Americas. We present a fully automated system that is able to identify triatomine bugs from Mexico and Brazil with an accuracy consistently above 80%, and with considerable potential for further improvement. The system processes digital photographs from a photo apparatus into landmarks, and uses ratios of measurements among those landmarks, as well as (in a preliminary exploration) two measurements that approximate aspects of coloration, as the basis for classification. This project has thus produced a working prototype that achieves reasonably robust correct identification rates, although many more developments can and will be added, and—more broadly—the project illustrates the value of multidisciplinary collaborations in resolving difficult and complex challenges

Acknowledging uncertainty in evolutionary reconstructions of ecological niches

Reconstructing ecological niche evolution can provide insight into the biogeography and diversification of evolving lineages. However, comparative phylogenetic methods may infer the history of ecological niche evolution inaccurately because (a) species' niches are often poorly characterized; and (b) phylogenetic comparative methods rely on niche summary statistics rather than full estimates of species' environmental tolerances. Here, we propose a new framework for coding ecological niches and reconstructing their evolution that explicitly acknowledges and incorporates the uncertainty introduced by incomplete niche characterization. Then, we modify existing ancestral state inference methods to leverage full estimates of environmental tolerances. We provide a worked empirical example of our method, investigating ecological niche evolution in the New World orioles (Aves: Passeriformes: Icterus spp.). Temperature and precipitation tolerances were generally broad and conserved among orioles, with niche reduction and specialization limited to a few terminal branches. Tools for performing these reconstructions are available in a new R package called nichevol

Acknowledging uncertainty in evolutionary reconstructions of ecological niches

Reconstructing ecological niche evolution can provide insight into the biogeography and diversification of evolving lineages. However, comparative phylogenetic methods may infer the history of ecological niche evolution inaccurately because (a) species' niches are often poorly characterized; and (b) phylogenetic comparative methods rely on niche summary statistics rather than full estimates of species' environmental tolerances. Here, we propose a new framework for coding ecological niches and reconstructing their evolution that explicitly acknowledges and incorporates the uncertainty introduced by incomplete niche characterization. Then, we modify existing ancestral state inference methods to leverage full estimates of environmental tolerances. We provide a worked empirical example of our method, investigating ecological niche evolution in the New World orioles (Aves: Passeriformes: Icterus spp.). Temperature and precipitation tolerances were generally broad and conserved among orioles, with niche reduction and specialization limited to a few terminal branches. Tools for performing these reconstructions are available in a new R package called nichevol

Updating the Secondary Transition Research Base: Evidence- and Research-Based Practices in Functional Skills

Transition education should be grounded in quality research. To do so, educators need information on which practices are effective for teaching students with disabilities transition-related skills. The purpose of this systematic literature review was to identify evidence-based and research-based practices in secondary special education and transition for students with disabilities. This systematic review resulted in the identification of nine secondary transition evidence-based practices and 22 research-based practices across more than 45 different transition-related skills. The range of effects for each of the secondary transition evidence-based and research-based practices identified are also included. Limitations and implications for future research, policy, and practice are discussed