Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references. / The benthic habitat is the terminal destination for marine animals in terms of their reproductive lifecycle. Recruitment dynamics relating to seasonal changes in the benthic habitat may be the best source of information for predicting recruit abundance and for marine resources management. The transition from the pelagic to the benthic phases is the last stage in the connectivity between benthic populations. The transition to the benthos may be a process that dominates recruitment dynamics to the exclusion of other characteristics of larvae such as their quality and their density. Recruitment of benthic marine animals is influenced by two seasonally varying factors of the benthic habitat. First, the availability of suitable habitat for recruitment can in large part determine the survival probability for settlers, a trend that is most pronounced for low or no survival when the settlement substrate is saturated by conspecifics from a recruitment cohort. Preemption is caused by the presence of current occupants from a recruit cohort, and it influences the settlement rate or the survival probability of conspecifics. Descriptive statistics (Chapter 2) and a field experiment (Chapter 4) highlight the role of preemption on barnacle recruitment. The second factor results from seasonal changes in environmental conditions that settlers experience in the benthic habitat, which could affect the physiology and survival probability of barnacle settlers. Highly unpredictable features of recruitment dynamics also play a role, such as wind that enhances wave action in the rocky intertidal that has been linked to the rate of settlement. Day to day variability in wind may cause patterns of settlement to be highly unpredictable. Predator induced mortality is spatially aggregated, and the random pattern of mortality in space is highly unpredictable. In contrast to these high frequency sources of recruitment variability, seasonal factors that vary at lower frequencies and that often change monotonically lend great predictive ability for recruitment dynamics. It appears that barnacles have evolved to compete for suitable habitat and have mechanisms to cope with seasonally varying environmental conditions in the benthic habitat, which may be the basis for why these features dominate the barnacle recruitment dynamic. / by Jonathan N. Blythe. / Ph.D.

Preservation of rare plant species often requires establishment of new populations. Survivorship surveys are the most common method of post-introduction monitoring. However, they provide an incomplete picture of establishment success. This study is an attempt to develop a model for determining establishment success by determining the factors affecting recruitment in introduced populations of a rare species. Erigeron decumbens is an endangered forb endemic to the Willamette Valley of western Oregon. Several populations of E. decumbens have been introduced by governmental and non-profit agencies. While there has been some monitoring of the survival of introduced plants, no systematic surveys have measured recruitment in the new populations. We monitored recruitment in five introduced populations, and compared abiotic and biotic characteristics in these and five stable natural populations. Seventy percent of introduced populations produced fewer than one recruit for every three survivors. Thirty percent produced at least one and one half recruits for every one survivor. The factors that affected recruitment were site specific. Low recruitment (less than one recruit per three survivors) was associated with dominance by exotic species (Dactylis glomerata, Rosa eglanteria, Vicia tetrasperma, and Leucanthemum vulgare), high litter cover, high soil electrical conductivity, and low silt levels. Recruitment was highest at sites with higher native plant species richness and soil characteristics falling within the variation of large natural populations. Viable seed number per individual had the strongest linear relationship with recruitment, demonstrating that seed viability could be a strong limitation for this species (r² = 0.83). The results of this study suggest numerous guidelines for future reintroductions of E. decumbens. This research also demonstrates the utility of recruitment surveys to determine factors important in the success of introduced populations of rare plant species. / Graduation date: 2013

It was previously thought that the South African chokka squid Loligo reynaudi is exclusively an inshore, shallow water spawner. Although spawning mostly within shallow bays (<60 m) the presence of squid eggs in trawls at depths up to 130 m indicates this species frequently makes use of deeper spawning areas on the mid-shelf. The extent of mid-shelf spawning (referred to as deep spawning) and the contribution to recruitment has yet to be assessed. Studies have shown mid-shelf bottom temperature to vary considerably from those inshore, suggesting chokka squid spawn in two very different oceanographic environments. Considering these apparent environmental differences, what leads to the mid-shelf environment becoming a suitable spawning habitat? Does a suitable benthic habitat, required for the attachment of egg pods, occur on the mid-shelf? These questions are not only important for determining the extent of deep spawning, but also to the understanding of factors “driving” deep spawning. The fate of deep spawned hatchlings is another unknown. It has been proposed that the main chokka squid inshore spawning grounds are positioned to exploit the net westward currents on the Eastern Agulhas Bank, i.e. paralarvae would be transported west from the hatching site to the cold ridge, an area of high primary and secondary productivity on the Central Agulhas Bank. This concept has come to be known as the Western Transport Hypothesis. Lagrangian ROMS-IBMs (regional ocean model system – individual-based model) predict the net westward transport of paralarvae from both the inshore and deep spawning grounds, to the cold ridge. These simulations were used to investigate the transport of hatchlings to the cold ridge feeding grounds before the exhaustion of yolk reserves. The fate of paralarvae on reaching the feeding grounds has not yet been investigated. This work has contributed new knowledge to our understanding of deep spawning and its role in recruitment. Specific aims of this study were to (1) determine the extent, range and importance of the deep spawning grounds relative to those inshore; (2) investigate the deep spawning ground habitat (Agulhas Bank mid-shelf) morphology and oceanographic environment; (3) determine the transport and survival of deep spawned hatchlings; and (4) investigate the origin and distribution of chokka squid paralarvae on the Agulhas Bank. The extent, depth range and importance of the deep spawning grounds, relative to those inshore was assessed using 23 years of demersal trawl survey data. Data for both the west and south coasts of South Africa were examined for egg capsules. No spawning was found on the west coast. Data showed that chokka squid preferred the Eastern Agulhas Bank for spawning. Spawning occurred not only inshore but also on the mid-shelf extending to depths of 270 m near the shelf edge. The majority of deep spawned eggs however, were found in the depth range 71-130 m. Squid egg density markedly decreased beyond 70 m, suggesting delineation between the inshore and deep spawning grounds. Total egg biomass calculations for depths shallower and deeper than 70 m indicated the coastal area to be strongly favoured, i.e. 82 vs. 18%. These results contest the commonly accepted notion that chokka squid is an inshore spawner and redefine the spawning grounds to extend across the shelf. Apart from an initial study investigating bottom temperature on the mid-shelf, very little is known about the deep spawning habitat. St Francis Bay, a commonly used spawning location, was chosen as a demonstration area for further study. The deep spawning grounds (71-130 m) were mapped and benthic habitat described from underwater video footage. A study investigating cross-shelf bottom conditions was undertaken off Thys Bay. CTD data were used to compare seasonal bottom temperature and oxygen on the St Francis Bay inshore and deep spawning grounds. Squid movement between the two spawning habitats was assessed using filament tagging. Predation and fishing pressure across the spawning grounds was reviewed. The mid-shelf benthic habitat was found to be similar to that inshore and available for spawning. Despite the generally colder bottom temperatures on the mid-shelf, this study showed that bottom temperature in deeper waters can at times be warmer than inshore. Although mid-shelf warming events lasted from a few hours to a number of days, they resulted in similar conditions to those on the inshore spawning grounds. It is likely these events act to expand or shift spawning habitat. The movement of squid between the two spawning habitats makes it possible for them to seek patches of warm bottom water with appropiate substrate. This suggests they are spawning habitat opportunists. Predation and fishing pressure appear to be higher on the inshore spawning grounds. It is feasible that this also forces spawners to seek out more favourable habitat offshore. An individual-based model was used to predict the fate of mid-shelf and inshore hatched paralarvae. Within the model, both the highly productive cold ridge and inshore spawning grounds were considered feeding or nursery areas. Paralarvae were released from six inshore and six deep spawning sites, spanning the coast between Port Alfred and Knysna. All paralarvae not reaching the feeding areas before the exhaustion of yolk-reserves (≤5 days), not retained within the feeding grounds (≥14 days), and not retained on the Agulhas Bank after exiting the feeding grounds were considered lost. This work illustrated the dependence of paralarval transport success on both spawning location and time of hatching, as established in earlier studies. The current IBM has expanded on initial work, emphasizing the importance of the cold ridge and inshore spawning grounds as nursery areas for deep and inshore spawned paralarvae, respectively. This work has highlighted the complex interactions between processes influencing recruitment variability for chokka squid. Possible relationships between periods of highest recruitment success and spawning peaks were identified for both spawning habitats. Based on the likely autumn increase in deep spawning off Tsitsikamma, and the beneficial currents during this period, it can be concluded deep spawning may at times contribute significantly to recruitment. This is particularly true for years where the cold ridge persists into winter. Data on chokka squid paralarval distribution are scarce. Paralarval distribution and abundance, in relation to Agulhas Bank oceanography, was investigated using bongo caught paralarvae and corresponding oceanographic data. Individual-based models (IBMs) were used to predict the origin or spawning site of the wild caught paralarvae, with reference to inshore versus deep spawning. Although failing to predict realistic points of origin, this study provided evidence to support a number of scenarios previously assumed to influence chokka squid recruitment. First is the possible influence of coastal upwelling on the retention, and hence spatial distribution, of paralarvae on the inshore spawning grounds. The second factor thought to impact recruitment is the loss of paralarvae from the Agulhas Bank ecosystem. This study confirmed the removal of paralarvae from the Eastern Agulhas Bank due to Agulhas Current boundary phenomena and resultant offshelf leakage. In addition, data suggested that the formation of the cold ridge could enhance retention on the Central Agulhas Bank, and so prevent offshelf leakage from the Central and Western Agulhas Bank. A synthesis of the main conclusions is presented. Implications of the findings and directions for future research are discussed.