Spatiotemporal variation of the abundance of calcareous green macroalgae in the Florida Keys: A study of synchrony within a macroalgal functional-form group

The abundance of calcareous green algae was recorded quarterly at 28 sites within the Florida Keys National Marine Sanctuary (FKNMS) for a period of 7 years as part of a sea grass monitoring program. To evaluate the validity of using the functional-form group approach, we designed a sampling method that included the functional-form group and the component genera. This strategy enabled us to analyze the spatiotemporal patterns in the abundance of calcareous green algae as a group and to describe synchronous behavior among its genera through the application of a nonlinear regression model to both categories of data. Spatial analyses revealed that, in general, all genera displayed long-term trends of increasing abundance at most sites; however, at some sites the long-term trends for genera opposed one another. Strong synchrony in the timing of seasonal changes was found among all genera, possibly reflecting similar reproductive and seasonal growth pattern, but the variability in the magnitude of seasonal changes was very high among genera and sites. No spatial patterns were found in long-term or seasonal changes; the only significant relation detected was for slope, with sites closer to land showing higher values, suggesting that some factors associated with land proximity are affecting this increase. We conclude that the abundances of genera behaved differently from the functional-form group, indicating that the use of the functionalform group approach may be unsuitable to detect changes in sea grass community structure in the FKNMS at the existing temporal and spatial scale of the monitoring program.

Patterns and ecosystem consequences of shark declines in the ocean

Whereas many land predators disappeared before their ecological roles were studied, the decline of marine apex predators is still unfolding. Large sharks in particular have experienced rapid declines over the last decades. In this study, we review the documented changes in exploited elasmobranch communities in coastal, demersal, and pelagic habitats, and synthesize the effects of sharks on their prey and wider communities. We show that the high natural diversity and abundance of sharks is vulnerable to even light fishing pressure. The decline of large predatory sharks reduces natural mortality in a range of prey, contributing to changes in abundance, distribution, and behaviour of small elasmobranchs, marine mammals, and sea turtles that have few other predators. Through direct predation and behavioural modifications, top-down effects of sharks have led to cascading changes in some coastal ecosystems. In demersal and pelagic communities, there is increasing evidence of mesopredator release, but cascading effects are more hypothetical. Here, fishing pressure on mesopredators may mask or even reverse some ecosystem effects. In conclusion, large sharks can exert strong top-down forces with the potential to shape marine communities over large spatial and temporal scales. Yet more empirical evidence is needed to test the generality of these effects throughout the ocean.

Influence of teleost abundance on the distribution and abundance of sharks in Florida Bay, USA

Understanding the factors that influence the distribution and abundance of predators, including sharks, is important for predicting the impacts of human changes to the environment. Such studies are particularly important in Florida Bay, USA where there are planned large-scale changes to patterns of freshwater input from the Everglades ecosystem. Studies of many marine predators suggest that links between predator and prey habitat use may vary with spatial scale, but there have been few studies of the role of prey distribution in shaping habitat use and abundance of sharks. We used longline catches of sharks and trawls for potential teleost prey to determine the influence of teleost abundance on shark abundance at the scale of regions and habitats in Florida Bay. We found that shark catch per unit effort (CPUE) was not linked to CPUE ofteleosts at the scale of sampling sites, but shark CPUE was positively correlated with the mean CPUE for teleosts within a region. Although there does not appear to be a strong match between the abundance of teleosts and sharks at small spatial scales, regional shark abundance is likely driven, at least partially, by the availability of prey. Management strategies that influence teleost abundance will have cascading effects to higher trophic levels in Florida Bay.

Diel Patterns of Patch Reef Community Dynamics in a Caribbean Back-Reef System

Back-reef seascapes represent critical habitat for juvenile and adult fishes. Patch reef, seagrass, and mangrove habitats form a heterogeneous mosaic, often linked by species that use reefs as structure during the day and make foraging migrations into soft-bottom habitat at night. Artificial reefs are used to model natural patch reefs, however may not function equivalently as fish habitat. To study the relative value of natural and artificial patch reefs as fish habitat, these communities in the Sea of Abaco, Bahamas were compared using roving diver surveys and time-lapse photography. Diel turnover in fish abundance, recorded with time-lapse photography and illuminated by infrared light, was quantified across midday, dusk, and night periods to explore possible effects of reef type (artificial vs. natural) on these patterns. Diurnal communities on natural reefs exhibited greater fish abundance, species richness, and functional diversity compared to artificial reefs. Furthermore, both types of reef communities exhibited a significant shift across the diel period, characterized by a decline in total fish density at night, especially for grunts (Haemulidae). Cross-habitat foraging migrations by diurnal or nocturnal species, such as haemulids, are likely central drivers of this twilight turnover and can represent important energy and nutrient subsidies. Time-lapse surveys provided more consistent measures of reef fish assemblages for the smaller artificial reef habitats, yet underestimated abundance of certain taxa and species richness on larger patch habitats when compared to the roving diver surveys. Time-lapse photography complemented with infrared light represent a valuable non-invasive approach to studying behavior of focal species and their fine-scale temporal dynamics in shallow-reef communities.

Diatom-based Models for Inferring Hydrology and Periphyton Abundance in a Subtropical Karstic Wetland: Implications for Ecosystem-Scale Bioassessment

We developed diatom-based prediction models of hydrology and periphyton abundance to inform assessment tools for a hydrologically managed wetland. Because hydrology is an important driver of ecosystem change, hydrologic alterations by restoration efforts could modify biological responses, such as periphyton characteristics. In karstic wetlands, diatoms are particularly important components of mat-forming calcareous periphyton assemblages that both respond and contribute to the structural organization and function of the periphyton matrix. We examined the distribution of diatoms across the Florida Everglades landscape and found hydroperiod and periphyton biovolume were strongly correlated with assemblage composition. We present species optima and tolerances for hydroperiod and periphyton biovolume, for use in interpreting the directionality of change in these important variables. Predictions of these variables were mapped to visualize landscape-scale spatial patterns in a dominant driver of change in this ecosystem (hydroperiod) and an ecosystem-level response metric of hydrologic change (periphyton biovolume). Specific diatom assemblages inhabiting periphyton mats of differing abundance can be used to infer past conditions and inform management decisions based on how assemblages are changing. This study captures diatom responses to wide gradients of hydrology and periphyton characteristics to inform ecosystem-scale bioassessment efforts in a large wetland.

Contrasting patterns of individual specialization and trophic coupling in two marine apex predators

1. Apex predators are often assumed to be dietary generalists and, by feeding on prey from multiple basal nutrient sources, serve to couple discrete food webs. But there is increasing evidence that individual level dietary specialization may be common in many species, and this has not been investigated for many marine apex predators. 2. Because of their position at or near the top of many marine food webs, and the possibility that they can affect populations of their prey and induce trophic cascades, it is important to understand patterns of dietary specialization in shark populations. 3. Stable isotope values from body tissues with different turnover rates were used to quantify patterns of individual specialization in two species of ‘generalist’ sharks (bull sharks, Carcharhinus leucas, and tiger sharks, Galeocerdo cuvier). 4. Despite wide population-level isotopic niche breadths in both species, isotopic values of individual tiger sharks varied across tissues with different turnover rates. The population niche breadth was explained mostly by variation within individuals suggesting tiger sharks are true generalists. In contrast, isotope values of individual bull sharks were stable through time and their wide population level niche breadth was explained by variation among specialist individuals. 5. Relative resource abundance and spatial variation in food-predation risk tradeoffs may explain the differences in patterns of specialization between shark species. 6. The differences in individual dietary specialization between tiger sharks and bull sharks results in different functional roles in coupling or compartmentalizing distinct food webs. 7. Individual specialization may be an important feature of trophic dynamics of highly mobile marine top predators and should be explicitly considered in studies of marine food webs and the ecological role of top predators.

Diversity Patterns of Amphibians in Lowland Amazonian Forests in Southeastern Peru

Biological diversity is threatened worldwide and it is a priority to generate more information that can be used both for understanding ecological processes and determining conservation strategies. For my dissertation, I focused on amphibian diversity patterns in lowland rainforests of southwestern Amazonia to evaluate the importance of habitat heterogeneity in the region. My main purpose was to test the hypothesis that amphibian communities in different forest types differ in species richness, composition, and abundance. I used standardized visual encounter surveys to quantify the species composition and abundance of amphibians at four sites, each containing four forest types (floodplain, terra firme, bamboo, and palm swamp). I used leaf-litter plots to evaluate the effect of soil and leaf-litter characteristics on species richness and abundance of leaf-litter frogs. I intensively sampled at one site and then sampled three other sites (distance among sites varied 3.5-105 km) to evaluate whether the patterns observed at one site were similar elsewhere. I also updated the information on threatened and potentially threatened amphibians in Peru and my study region. I found that no species appears to have experienced population declines in southeastern Peru, suggesting that the region still contains the original species pool. My results support the hypothesis that amphibian communities differ across forest types and that patterns observed at the local scale (one site) are similar at the regional scale (four sites). My data also indicate that there is no correlation between species composition and geographic distance among sites. Instead, an important proportion of the gamma diversity is represented by habitat-related beta diversity. My leaf-litter plot data showed that part of the variation in the leaf-litter community structure is explained by soil and litter characteristics. I found that soil total phosphorus and, to a lesser extent, humidity, leaf-litter mass, and pH is linked to species presence/absence and abundance. My study provides the first standardized, quantitative comparison of amphibian community structure across four major forest types in southwestern Amazonia and highlights the fact that forest types are complementary and necessary for maintaining high species richness in the region.

(Table I-II) Station details and isopoda abundance of samples taken during POLARSTERN cruise ANT-XV/3 to the eastern Weddell Sea and King George Island

Abundance, diversity, and distribution of suprabenthic Isopoda caught from a water layer between 0.27 to 0.60 m above the seafloor were analysed. The samples were taken during the ANT XV/3 cruise on RV Polarstern by means of an epibenthic sledge along two transects in the southern Weddell Sea (Vestkapp and Halley Bay) and another one east of King George Island. At each of these three bathymetric transects, five to six stations were sampled between 200 and 2000 m. In total, 4258 specimens of isopods were sampled at 14 stations standardized to 1000 m2 hauls. 114 species were identified from 49 genera and 23 higher taxa (families and suborders) of Isopoda. Most of them belonged to the suborder Asellota. Dominant families are Munnopsididae (Eurycopinae, Ilyarachninae), Joeropsidae, Munnidae, Paramunnidae, Ischnomesidae and Desmosomatidae. No striking differences were found between areas (Vestkapp, Halley Bay, Kapp Norvegia, and Bransfield Strait). Overall isopod abundances were highest at the shallowest station; species richness was slightly higher above 1000 m depth.

Diatom abundance in surface sediments of the northern North Pacific

In order to map the modern distribution of diatoms and to establish a reliable reference data set for paleoenvironmental reconstruction in the northern North Pacific, a new data set including the relative abundance of diatom species preserved in a total of 422 surface sediments was generated, which covers a broad range of environmental variables characteristic of the subarctic North Pacific, the Sea of Okhotsk and the Bering Sea between 30° and 70°N. The biogeographic distribution patterns as well as the preferences in sea surface temperature of 38 diatom species and species groups are documented. A Q-mode factor analysis yields a three-factor model representing assemblages associated with the Arctic, Subarctic and Subtropical water mass, indicating a close relationship between the diatom composition and the sea surface temperatures. The relative abundance pattern of 38 diatom species and species groups was statistically compared with nine environmental variables, i.e. the summer sea surface temperature and salinity, annual surface nutrient concentration (nitrate, phosphate, silicate), summer and winter mixed layer depth and summer and winter sea ice concentrations. Canonical Correspondence Analysis (CCA) indicates 32 species and species groups have strong correspondence with the pattern of summer sea surface temperature. In addition, the total diatom flux data compiled from ten sediment traps reveal that the seasonal signals preserved in the surface sediments are mostly from spring through autumn. This close relationship between diatom composition and the summer sea surface temperature will be useful in deriving a transfer function in the subarctic North Pacific for the quantitative paleoceanographic and paleoenvironmental studies. The relative abundance of the sea-ice indicator diatoms Fragilariopsis cylindrus and F. oceanica of >20% in the diatom composition is used to represent the winter sea ice edge in the Bering Sea. The northern boundary of the distribution of F. doliolus in the open ocean is suggested to be an indicator of the Subarctic Front, while the abundance of Chaetoceros resting spores may indicate iron input from nearby continents and shelves and induced productivity events in the study area.

Relative abundance of dinoflagellate cysts in surface sediments and dinoflagellate counts from three sediment cores from the Atlantic sector of the Southern Ocean

In this study we investigate the potential of organic-walled dinoflagellate cysts (dinocysts) as tools for quantifying past sea-surface temperatures (SST) in the Southern Ocean. For this purpose, a dinocyst reference dataset has been formed, based on 138 surface sediment samples from different circum-Antarctic environments. The dinocyst assemblages of these samples are composed of phototrophic (gonyaulacoid) and heterotrophic (protoperidinioid) species that provide a broad spectrum of palaeoenvironmental information. The relationship between the environmental parameters in the upper water column and the dinocyst distribution patterns of individual species has been established using the statistical method of Canonical Correspondence Analysis (CCA). Among the variables tested, summer SST appeared to correspond to the maximum variance represented in the dataset. To establish quantitative summer SST reconstructions, a Modern Analogue Technique (MAT) has been performed on data from three Late Quaternary dinocyst records recovered from locations adjacent to prominent oceanic fronts in the Atlantic sector of the Southern Ocean. These dinocyst time series exhibit periodic changes in the dinocyst assemblage during the last two glacial/interglacial-cycles. During glacial conditions the relative abundance of protoperidinioid cysts was highest, whereas interglacial conditions are characterised by generally lower cyst concentrations and increased relative abundance of gonyaulacoid cysts. The MAT palaeotemperature estimates show trends in summer SST changes following the global oxygen isotope signal and a strong correlation with past temperatures of the last 140,000 years based on other proxies. However, by comparing the dinocyst results to quantitative estimates of summer SSTs based on diatoms, radiolarians and foraminifer-derived stable isotope records it can be shown that in several core intervals the dinocyst-based summer SSTs appeared to be extremely high. In these intervals the dinocyst record seems to be highly influenced by selective degradation, leading to unusual temperature ranges and to unrealistic palaeotemperatures. We used the selective degradation index (kt-index) to determine those intervals that have been biased by selective degradation in order to correct the palaeotemperature estimates. We show that after correction the dinocyst based SSTs correspond reasonably well with other palaeotemperature estimates for this region, supporting the great potential of dinoflagellate cysts as a basis for quantitative palaeoenvironmental studies.

Distribution, density and abundance of Antarctic ice seals off Queen Maud Land and the eastern Weddell Sea

The Antarctic Pack Ice Seal (APIS) Program was initiated in 1994 to estimate the abundance of four species of Antarctic phocids: the crabeater seal Lobodon carcinophaga, Weddell seal Leptonychotes weddellii, Ross seal Ommatophoca rossii and leopard seal Hydrurga leptonyx and to identify ecological relationships and habitat use patterns. The Atlantic sector of the Southern Ocean (the eastern sector of the Weddell Sea) was surveyed by research teams from Germany, Norway and South Africa using a range of aerial methods over five austral summers between 1996-1997 and 2000-2001. We used these observations to model densities of seals in the area, taking into account haul-out probabilities, survey-specific sighting probabilities and covariates derived from satellite-based ice concentrations and bathymetry. These models predicted the total abundance over the area bounded by the surveys (30°W and 10°E). In this sector of the coast, we estimated seal abundances of: 514 (95 % CI 337-886) x 10**3 crabeater seals, 60.0 (43.2-94.4) x 10**3 Weddell seals and 13.2 (5.50-39.7) x 10**3 leopard seals. The crabeater seal densities, approximately 14,000 seals per degree longitude, are similar to estimates obtained by surveys in the Pacific and Indian sectors by other APIS researchers. Very few Ross seals were observed (24 total), leading to a conservative estimate of 830 (119-2894) individuals over the study area. These results provide an important baseline against which to compare future changes in seal distribution and abundance.

The Abundance and Behavioral Ecology of Cape Cod Gray Seals Under Predation Risk From White Sharks

The ultimate goal of wildlife recovery is abundance growth of a species, though it must also involve the reestablishment of the species’ ecological role within ecosystems frequently modified by humans. Reestablishment and subsequent recovery may depend on the species’ degree of adaptive behavior as well as the duration of their functional absence and the extent of ecosystem alteration. In cases of long extirpations or extensive alteration, successful reestablishment may entail adjusting foraging behavior, targeting new prey species, and encountering unfamiliar predatory or competitive regimes. Recovering species must also increasingly tolerate heightened anthropogenic presence, particularly within densely inhabited coastal zones. In recent decades, gray seals (Halichoerus grypus) recovered from exploitation, depletion, and partial extirpation in the Northwest Atlantic. On Cape Cod, MA, USA, gray seals have reestablished growing breeding colonies and seasonally interact with migratory white sharks (Carcarodon carcharias). Though well-studied in portions of their range due to concerns over piscivorous impacts on valuable groundfish, there are broad knowledge gaps regarding their ecological role to US marine ecosystems. Furthermore, there are few studies that explicitly analyze gray seal behavior under direct risk of documented shark predation.

In this dissertation, I apply a behavioral and movement ecology approach to telemetry data to understand gray seal abundance and activity patterns along the coast of Cape Cod. This coastal focus complements extensive research documenting and describing offshore movement and foraging behavior and allows me to address questions about movement decisions and risk allocation. Using beach counts of seals visible in satellite imagery, I estimate the total regional abundance of gray seals using correction factors from haul out behavior and demonstrate a sizeable prey base of gray seals locally. Analyzing intra-annual space use patterns, I document small, concentrated home ranges utilizing nearshore habitats that rapidly expand with shifting activity budgets to target disperse offshore habitats following seasonal declines in white sharks. During the season of dense shark presence, seals conducted abbreviated nocturnal foraging trips structured temporally around divergent use of crepuscular periods. The timing of coastal behavior with different levels of twilight indicate risk allocation patterns with diel cycles of empirical white shark activity. The emergence of risk allocation to explain unique behavioral and spatial patterns observed in these gray seals points to the importance of the restored predator-prey dynamic in gray seal behavior along Cape Cod.

Spatial Relationships among Hydroacoustic, Hydrographic and Top Predator Patterns: Cetacean Distributions in the Mid-Atlantic Bight

Effective conservation and management of top predators requires a comprehensive understanding of their distributions and of the underlying biological and physical processes that affect these distributions. The Mid-Atlantic Bight shelf break system is a dynamic and productive region where at least 32 species of cetaceans have been recorded through various systematic and opportunistic marine mammal surveys from the 1970s through 2012. My dissertation characterizes the spatial distribution and habitat of cetaceans in the Mid-Atlantic Bight shelf break system by utilizing marine mammal line-transect survey data, synoptic multi-frequency active acoustic data, and fine-scale hydrographic data collected during the 2011 summer Atlantic Marine Assessment Program for Protected Species (AMAPPS) survey. Although studies describing cetacean habitat and distributions have been previously conducted in the Mid-Atlantic Bight, my research specifically focuses on the shelf break region to elucidate both the physical and biological processes that influence cetacean distribution patterns within this cetacean hotspot.

In Chapter One I review biologically important areas for cetaceans in the Atlantic waters of the United States. I describe the study area, the shelf break region of the Mid-Atlantic Bight, in terms of the general oceanography, productivity and biodiversity. According to recent habitat-based cetacean density models, the shelf break region is an area of high cetacean abundance and density, yet little research is directed at understanding the mechanisms that establish this region as a cetacean hotspot.

In Chapter Two I present the basic physical principles of sound in water and describe the methodology used to categorize opportunistically collected multi-frequency active acoustic data using frequency responses techniques. Frequency response classification methods are usually employed in conjunction with net-tow data, but the logistics of the 2011 AMAPPS survey did not allow for appropriate net-tow data to be collected. Biologically meaningful information can be extracted from acoustic scattering regions by comparing the frequency response curves of acoustic regions to theoretical curves of known scattering models. Using the five frequencies on the EK60 system (18, 38, 70, 120, and 200 kHz), three categories of scatterers were defined: fish-like (with swim bladder), nekton-like (e.g., euphausiids), and plankton-like (e.g., copepods). I also employed a multi-frequency acoustic categorization method using three frequencies (18, 38, and 120 kHz) that has been used in the Gulf of Maine and Georges Bank which is based the presence or absence of volume backscatter above a threshold. This method is more objective than the comparison of frequency response curves because it uses an established backscatter value for the threshold. By removing all data below the threshold, only strong scattering information is retained.

In Chapter Three I analyze the distribution of the categorized acoustic regions of interest during the daytime cross shelf transects. Over all transects, plankton-like acoustic regions of interest were detected most frequently, followed by fish-like acoustic regions and then nekton-like acoustic regions. Plankton-like detections were the only significantly different acoustic detections per kilometer, although nekton-like detections were only slightly not significant. Using the threshold categorization method by Jech and Michaels (2006) provides a more conservative and discrete detection of acoustic scatterers and allows me to retrieve backscatter values along transects in areas that have been categorized. This provides continuous data values that can be integrated at discrete spatial increments for wavelet analysis. Wavelet analysis indicates significant spatial scales of interest for fish-like and nekton-like acoustic backscatter range from one to four kilometers and vary among transects.

In Chapter Four I analyze the fine scale distribution of cetaceans in the shelf break system of the Mid-Atlantic Bight using corrected sightings per trackline region, classification trees, multidimensional scaling, and random forest analysis. I describe habitat for common dolphins, Risso’s dolphins and sperm whales. From the distribution of cetacean sightings, patterns of habitat start to emerge: within the shelf break region of the Mid-Atlantic Bight, common dolphins were sighted more prevalently over the shelf while sperm whales were more frequently found in the deep waters offshore and Risso’s dolphins were most prevalent at the shelf break. Multidimensional scaling presents clear environmental separation among common dolphins and Risso’s dolphins and sperm whales. The sperm whale random forest habitat model had the lowest misclassification error (0.30) and the Risso’s dolphin random forest habitat model had the greatest misclassification error (0.37). Shallow water depth (less than 148 meters) was the primary variable selected in the classification model for common dolphin habitat. Distance to surface density fronts and surface temperature fronts were the primary variables selected in the classification models to describe Risso’s dolphin habitat and sperm whale habitat respectively. When mapped back into geographic space, these three cetacean species occupy different fine-scale habitats within the dynamic Mid-Atlantic Bight shelf break system.

In Chapter Five I present a summary of the previous chapters and present potential analytical steps to address ecological questions pertaining the dynamic shelf break region. Taken together, the results of my dissertation demonstrate the use of opportunistically collected data in ecosystem studies; emphasize the need to incorporate middle trophic level data and oceanographic features into cetacean habitat models; and emphasize the importance of developing more mechanistic understanding of dynamic ecosystems.

Abundance, biomass and secondary production of benthic megafauna on the Barents Sea shelf in 2008 and 2009

Megabenthos plays a major role in the overall energy flow on Arctic shelves, but information on megabenthic secondary production on large spatial scales is scarce. Here, we estimated for the first time megabenthic secondary production for the entire Barents Sea shelf by applying a species-based empirical model to an extensive dataset from the joint Norwegian? Russian ecosystem survey. Spatial patterns and relationships were analyzed within a GIS. The environmental drivers behind the observed production pattern were identified by applying an ordinary least squares regression model. Geographically weighted regression (GWR) was used to examine the varying relationship of secondary production and the environment on a shelfwide scale. Significantly higher megabenthic secondary production was found in the northeastern, seasonally ice-covered regions of the Barents Sea than in the permanently ice-free southwest. The environmental parameters that significantly relate to the observed pattern are bottom temperature and salinity, sea ice cover, new primary production, trawling pressure, and bottom current speed. The GWR proved to be a versatile tool for analyzing the regionally varying relationships of benthic secondary production and its environmental drivers (R² = 0.73). The observed pattern indicates tight pelagic? benthic coupling in the realm of the productive marginal ice zone. Ongoing decrease of winter sea ice extent and the associated poleward movement of the seasonal ice edge point towards a distinct decline of benthic secondary production in the northeastern Barents Sea in the future.