Factors mediating structure and trophic interactions of estuarine nekton communities

Understanding how communities and species assemblages persist is among the most fundamental objectives in ecology, particularly as human modifications to the landscape increase. Through application of traditional community metrics with emerging biochemical tracers in combination with community/food web ecology theory, I provide an evaluation of the effects of anthropogenically-altered freshwater flow disturbance on estuarine nekton community structure and trophic interactions. These two parameters are central toward understanding the functioning of aquatic communities and ensuring their persistence. This dissertation provides data regarding the effects of human-altered freshwater flow on estuarine nekton communities in tidal rivers and, in doing so, has fostered valuable findings regarding the application of stable isotopes to estuarine fishes and large vertebrates. Specifically, this research demonstrates that losses of estuarine nekton community biodiversity (Chapter 2), the shift in resource availability to lower trophic level species (Chapter 5), and changes to energy flow pathways leading to higher trophic level consumers (Chapter 6), are all associated with high flow events. This dissertation further demonstrates that the application of stable isotopes requires consideration of a species life history characteristics, as interpretation of a species diet and trophic roles can be complex (Chapters 3 and 4). Collectively, these findings suggest that high flow events affect the structure and trophic interactions of estuarine nekton communities and provide a greater understanding of the impacts of such anthropogenic-mediated stressors on these complex ecosystems. Whether altered high-flow disturbance events result in adverse or beneficial effects on the persistence of estuaries remains to be established. However, in order to maintain and/or restore the integrity of an ecosystem requires that conservation and management actions be firmly grounded in scientific understanding. This becomes especially relevant as worldwide changes to hydrologic connectivity continue with increasing anthropogenic pressures. This research demonstrates the potential for the simplification of food webs and changes to dominant trophic assemblages that are associated with flow alteration. For the commercially, recreationally and ecologically valuable species that define estuarine nekton communities, these observations emphasize the necessity of research and management programs aimed at maintaining the integrity of these highly-valued ecosystems

Spatial contrasts in hepatic and biliary PAHs in Tilefish (Lopholatilus chamaeleonticeps) throughout the Gulf of Mexico, with comparison to the Northwest Atlantic

A multinational demersal longline survey was conducted on the Gulf of Mexico continental shelf over the years 2015 and 2016 to generate a Gulf-wide baseline of polycyclic aromatic hydrocarbon (PAH) concentrations in demersal fishes. Tilefish (Lopholatilus chamaeleonticeps) were sampled in all regions of the Gulf of Mexico for biometrics, bile, and liver. Tilefish liver was also obtained from surveys in the northwest Atlantic Ocean for comparison. Liver tissues (n ¼ 305) were analyzed for PAHs and select alkylated homologs using QuEChERS extractions and gas chromatography tandem mass spectrometry. Bile samples (n ¼ 225) were analyzed for biliary PAH metabolites using high-performance liquid chromatography with fluorescence detection. Spatial comparisons indicate the highest levels of PAH exposure and hepatic accumulation in the north central Gulf of Mexico, with decreasing concentrations moving from the north central Gulf counterclockwise, and an increase on the Yucatan Shelf. Hepatic PAH concentrations were similar between the Gulf of Mexico and the northwest Atlantic, however, Tilefish from the northwest Atlantic had higher concentrations and more frequent detection of carcinogenic high molecular weight PAHs. Overall, results demonstrate that PAH pollution was ubiquitous within the study regions, with recent exposure and hepatic accumulation observed in Tilefish from both the Gulf of Mexico and northwest Atlantic

Separation of realized ecological niche axes among sympatric tilefishes provides insight into potential drivers of co-occurrence in the NW Atlantic

Golden and Blueline Tilefish (Lopholatilus chamaeleonticeps and Caulolatilus microps) are keystone taxa in northwest (NW) Atlantic continental shelf-edge environments due to their biotic (trophic-mediated) and abiotic (ecosystem engineering) functional roles combined with high-value fisheries. Despite this importance, the ecological niche dynamics (i.e., those relating to trophic behavior and food-web interactions) of these sympatric species are poorly understood, knowledge of which may be consequential for maintaining both ecosystem function and fishery sustainability. We used stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) to build realized ecological niche hypervolumes to serve as proxies for diet and production use patterns of L. chamaeleonticeps and C. microps. We hypothesized that: (a) species exhibit ontogenetic shifts in diet and use of production sources; (b) species acquire energy from spatially distinct resource pools that reflect a sedentary life-history and differential use of the continental shelf-edge; and (c) species exhibit differentiation in one or more measured niche axes. We found evidence for ontogenetic shifts in diet (δ15N) but not production source (δ13C) in both species, suggesting a subtle expansion of measured ecological niche axes. Spatial interpolation of stable isotope ratios showed distinct latitudinal gradients; for example, individuals were 13C enriched in northern and 15N enriched in southern regions, supporting the assertion that tilefish species acquire energy from regional resource pools. High isotopic overlap was observed among species (≥82%); however, when hypervolumes included depth and region of capture, overlap among species substantially decreased to overlap estimates of 15%–77%. This suggests that spatial segregation could alleviate potential competition for resources among tilefish species inhabiting continental shelf-edge environments. Importantly, our results question the consensus interpretation of isotopic overlap estimates as representative of direct competition among species for shared resources or habitats, instead identifying habitat segregation as a possible mechanism for coexistence of tilefish species in the NW Atlantic

Variable δ15N Diet-Tissue Discrimination Factors among Sharks: Implications for Trophic Position, Diet and Food Web Models

The application of stable isotopes to characterize the complexities of a species foraging behavior and trophic relationships is dependent on assumptions of δ15N diet-tissue discrimination factors (∆15N). As ∆15N values have been experimentally shown to vary amongst consumers, tissues and diet composition, resolving appropriate speciesspecific ∆15N values can be complex. Given the logistical and ethical challenges of controlled feeding experiments for determining ∆ 15N values for large and/or endangered species, our objective was to conduct an assessment of a range of reported ∆ 15N values that can hypothetically serve as surrogates for describing the predator-prey relationships of four shark species that feed on prey from different trophic levels (i.e., different mean δ 15N dietary values). Overall, the most suitable species-specific ∆ 15N values decreased with increasing dietary-δ 15N values based on stable isotope Bayesian ellipse overlap estimates of shark and the principal prey functional groups contributing to the diet determined from stomach content analyses. Thus, a single ∆ 15N value was not supported for this speciose group of marine predatory fishes. For example, the ∆ 15N value of 3.7‰ provided the highest percent overlap between prey and predator isotope ellipses for the bonnethead shark (mean diet δ 15N = 9‰) whereas a ∆ 15N value \u3c 2.3‰ provided the highest percent overlap between prey and predator isotope ellipses for the white shark (mean diet δ 15N = 15‰). These data corroborate the previously reported inverse ∆ 15N-dietary δ 15N relationship when both isotope ellipses of principal prey functional groups and the broader identified diet of each species were considered supporting the adoption of different ∆ 15N values that reflect the predators’ δ 15N-dietary value. These findings are critical for refining the application of stable isotope modeling approaches as inferences regarding a species’ ecological role in their community will be influenced with consequences for conservation and management actions

Evolution of realized Eltonian niches across Rajidae species

The notion that closely related species resemble each other in ecological niche space (i.e., phylogenetic dependence) has been a long-standing, contentious paradigm in evolutionary biology, the incidence of which is important for predicting the ecosystem-level effects of species loss. Despite being examined across a multitude of terrestrial taxa, many aspects of niche conservatism have yet to be explored in marine species, especially for characteristics related to resource use and trophic behavior (Eltonian niche characteristics, ENCs). We combined ENCs derived from stable isotope ratios at assemblage- and species-levels with phylogenetic comparative methods, to test the hypotheses that benthic marine fishes (1) exhibit similar assemblage-wide ENCs regardless of geographic location and (2) display phylogenetically dependent ENCs at the species level. We used a 12-species sub-set of the monophyletic group Rajidae sampled from three independent assemblages (Central California, Gulf of Alaska, and Northwest Atlantic), which span two ocean basins. Assemblage-level ENCs implied low trophic diversity and high evenness, suggesting that Rajidae assemblages may exhibit a well-defined trophic role, a trend consistent regardless of geographic location. At the species level, we found evidence for phylogenetic dependence of ENCs relating to trophic diversity (i.e., isotopic niche width; SEAc). Whether individuals can be considered functional equivalents across assemblages is hard to ascertain because we did not detect a significant phylogenetic signal for ENCs relating to trophic function (e.g., trophic position). Thus, additional, complimentary approaches are required to further examine the phylogenetic dependence of species functionality. Our approach illustrates the potential of stable isotope-derived niche characteristics to provide insight on macroecological processes occurring across evolutionary time, which could help predict how assemblages may respond to the effects of species loss

Telemetry-validated nitrogen stable isotope clocks identify ocean-to-estuarine habitat shifts in mobile organisms

Throughout their life history, many animals transition among heterogeneous environments to facilitate behaviours such as reproduction, foraging and predator avoidance. The dynamic environmental and biological conditions experienced by mobile species are integrated in the chemical composition of their tissues, providing retrospective insight into movement. Here, we present a unique application of nitrogen stable isotope clocks (‘isotopic clocks’), which integrate tissue turnover rates, consumer stable isotope ratios and habitat-specific isotope baselines to predict time-since-immigration and the timing of habitat shifts in a migratory species. Nitrogen stable isotope values of blood plasma collected from juvenile sand tiger sharks Carcharias taurus, a species known to undertake seasonal movements between ocean and estuarine environments, were used to derive estimates of time-since-immigration and the timing of seasonal habitat shifts undertaken by this species. Nitrogen isotopic clocks estimated for 65 juvenile sand tiger sharks sampled across 6 years indicated that individual sharks predominantly arrived to estuarine habitats between June and July, with some individuals arriving as early as mid-May. These estimates were validated by comparing isotope-derived estuarine arrival times with those from acoustically tracked individuals. The median estuarine arrival day estimates from our isotopic approach aligned with estimates from acoustic telemetry for each sampling population. Sensitivity analyses indicated that isotopically inferred time-since-immigration and estuarine arrival estimates were robust to variation in isotopic turnover rate and diet tissue discrimination factors under multiple modelling scenarios. This suggests that parameterization of the nitrogen isotopic clock provides reliable estimates of time-since-immigration and day of arrival into new habitats if isotopic variation exists between origin and new locations. Our study presents a unique application of telemetry-validated isotope clocks to derive retrospective estimates of time-since-immigration and timing of habitat shifts for animals that seasonally traverse heterogeneous environments. This approach can be readily applied across many temporal and spatial scales, and to other species and ecosystems, to facilitate rapid assessment of changes in animal habitat use and broader ecosystem structure

Coastal Wetland Restoration through the lens of Odum\u27s theory of ecosystem development

Advancing ecological restoration assessments requires a more detailed consideration of species interactions and ecosystem processes. Most restoration projects rely on a few metrics not always directly linked with ecological theory. Here, we used Odum\u27s theory of ecosystem development to assess and compare the ecosystem structure and services of created marshes (4–6 years old) with preexisting, reference marshes in a brackish water region of the Mississippi River Delta. We built ecosystem models for created and reference marshes that integrated large datasets of stomach contents, stable isotopes, and taxa abundances. Despite strong resemblance in community structure, created marshes were at an earlier succession stage compared to the reference marshes, having lower biomass (including exploited species), higher biomass turnover and production, less dependence on detritus, lower material cycling, and less energy flowing through specialist pathways. Although preserving preexisting marshes should be a priority, created marshes may still be an important tool for the restoration of coastal areas and their ecosystem services. In addition, our results show that comparisons of species biodiversity alone may fail to capture essential differences in ecosystem processes between habitats, which reinforces the importance of ecosystem modeling approaches to assess restoration projects

Can biodiversity of preexisting and created salt marshes match across scales? An assessment from microbes to predators

Coastal wetlands are rapidly disappearing worldwide due to a variety of processes, including climate change and flood control. The rate of loss in the Mississippi River Delta is among the highest in the world and billions of dollars have been allocated to build and restore coastal wetlands. A key question guiding assessment is whether created coastal salt marshes have similar biodiversity to preexisting, reference marshes. However, the numerous biodiversity metrics used to make these determinations are typically scale dependent and often conflicting. Here, we applied ecological theory to compare the diversity of different assemblages (surface and below-surface soil microbes, plants, macroinfauna, spiders, and on-marsh and off-marsh nekton) between two created marshes (4–6 years old) and four reference marshes. We also quantified the scale-dependent effects of species abundance distribution, aggregation, and density on richness differences and explored differences in species composition. Total, between-sample, and within-sample diversity (γ, β, and α, respectively) were not consistently lower at created marshes. Richness decomposition varied greatly among assemblages and marshes (e.g., soil microbes showed high equitability and α diversity, but plant diversity was restricted to a few dominant species with high aggregation). However, species abundance distribution, aggregation, and density patterns were not directly associated with differences between created and reference marshes. One exception was considerably lower density for macroinfauna at one of the created marshes, which was drier because of being at a higher elevation and having coarser substrate compared with the other marshes. The community compositions of created marshes were more dissimilar than reference marshes for microbe and macroinfauna assemblages. However, differences were small, particularly for microbes. Together, our results suggest generally similar taxonomic diversity and composition between created and reference marshes. This provides support for the creation of marsh habitat as tools for the maintenance and restoration of coastal biodiversity. However, caution is needed when creating marshes because specific building and restoration plans may lead to different colonization patterns

Integrating data types to estimate spatial patterns of avian migration across the Western Hemisphere

For many avian species, spatial migration patterns remain largely undescribed, especially across hemispheric extents. Recent advancements in tracking technologies and high-resolution species distribution models (i.e., eBird Status and Trends products) provide new insights into migratory bird movements and offer a promising opportunity for integrating independent data sources to describe avian migration. Here, we present a three-stage modeling framework for estimating spatial patterns of avian migration. First, we integrate tracking and band re-encounter data to quantify migratory connectivity, defined as the relative proportions of individuals migrating between breeding and nonbreeding regions. Next, we use estimated connectivity proportions along with eBird occurrence probabilities to produce probabilistic least-cost path (LCP) indices. In a final step, we use generalized additive mixed models (GAMMs) both to evaluate the ability of LCP indices to accurately predict (i.e., as a covariate) observed locations derived from tracking and band re-encounter data sets versus pseudo-absence locations during migratory periods and to create a fully integrated (i.e., eBird occurrence, LCP, and tracking/band re-encounter data) spatial prediction index for mapping species-specific seasonal migrations. To illustrate this approach, we apply this framework to describe seasonal migrations of 12 bird species across the Western Hemisphere during pre- and postbreeding migratory periods (i.e., spring and fall, respectively). We found that including LCP indices with eBird occurrence in GAMMs generally improved the ability to accurately predict observed migratory locations compared to models with eBird occurrence alone. Using three performance metrics, the eBird + LCP model demonstrated equivalent or superior fit relative to the eBird-only model for 22 of 24 species–season GAMMs. In particular, the integrated index filled in spatial gaps for species with over-water movements and those that migrated over land where there were few eBird sightings and, thus, low predictive ability of eBird occurrence probabilities (e.g., Amazonian rainforest in South America). This methodology of combining individual-based seasonal movement data with temporally dynamic species distribution models provides a comprehensive approach to integrating multiple data types to describe broad-scale spatial patterns of animal movement. Further development and customization of this approach will continue to advance knowledge about the full annual cycle and conservation of migratory birds

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century