No description available.

The scalloped spiny lobster, Panulirus homarus has a subspecies trio that are widely distributed in shallow-water habitats in the South West Indian Ocean. Subspecies are defined by differences in colour and abdominal sculptural pattern. A red variety with the megasculptural carapace pattern, P. h. rubellus is distributed along the south east coast of Africa and Madagascar, where they are endemic. Along the African coast P. h. rubellus stocks traverse political boundaries, Mozambique and South Africa. This project aimed to facilitate regional fisheries management of shared stocks by employing genetic tools to determine whether stocks (or populations) are indeed shared between countries. Lobster samples were collected from seven localities throughout the east African coast. The mitochondrial cyctochrome c oxidase subunit 1 region was sequenced to assess the genetic diversity 1) between different subspecies, P. h. homarus and P. h. rubellus and 2) between populations of P. h. rubellus across its African distribution range. Using DNA barcoding methods, genetic diversity was also found between morphologically distinct subspecies, Panulirus homarus homarus and P. h. rubellus which differed genetically by ca. 2-3% in sequence divergence. Both subspecies were monophyletic relative to the out-group taxa and formed well supported sister clades (BI: 1.00, ML: 93%, P: 100%, NJ: 100%). The distribution of P. h. rubellus along the African coast occurs adjacent to different current regimes and therefore varied larval transport modes (i.e. Agulhas Current and inshore countercurrents along the Eastern Cape). This may have driven the formation of subpopulations (ΦPT = 0.104, p = 0.010) which differ by ca. 1.7% in sequence difference. The pattern of gene flow of populations of P. h. rubellus lends support to the Agulhas Current being a major mode of larval transport as well as corroborates previous abundance and distribution records. Time since population expansion estimates for the P. h. homarus and P. h. rubellus subspecies as well as for the P. h. rubellus subpopulations dated back to the mid-Holocene Epoch in accordance with a warmer, more stable marine environment. Genetically distinct subspecies of P. homarus as well as differentiated subpopulations of P. h. rubellus calls for a re-visit of the current collective management of P. homarus as well as P. h. rubellus as a single genetic stock along the south east African coast. / Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2013.

Graduation date: 1998 / Best scan available for figures. Original is a black and white photocopy.

Thesis--Faculté des lettres de Paris. / Includes bibliographical references.

Thesis--Auburn University, 2009. / Abstract. Vita. Includes bibliographical references (p. 109-122).

As part of a long-term monitoring programme initiated by the South African Environmental Observation Network (SAEON) Elwandle Node, the spatio-temporal dynamics of mesozooplankton (200–2000 μm) community structure in Algoa Bay, on the Eastern Cape coastline of southern Africa, was investigated in summer and winter of 2008. Physical-chemical and biological variables were measured at selected sites in the eastern and western sectors of the Bay. During summer, nutrient rich waters upwelling into the eastern sector of the Bay contributed to significant spatial variation in selected physical-chemical variables. During winter, virtually no significant spatial patterns in the physical-chemical variables were observed (P>0.05 in all cases). For the majority of physical-chemical variables, no significant seasonal patterns in values were detected (P>0.05 in all cases). Notable exceptions were water column stability and water temperatures which were highest during summer, and seston, turbidity and ammonium concentrations which attained the highest values in winter. The striking seasonal pattern observed in the water column stability, coupled with the upwelling event, coincided with a strong seasonal pattern in the total surface and integrated chlorophyll-a concentrations within the Bay. During summer, the total surface phytoplankton biomass ranged from 1.87–3.11 μg.L⁻¹ and the integrated biomass values between 44.6 and 89.1 mg chl-a m⁻². In winter, surface chl-a concentrations ranged from 0.49 to 0.55 μg.L⁻¹ and integrated biomass from 13.5 to 13.8 mg chl-a m⁻². During both seasons, the large microphytoplankton (>20 μm) fraction contributed the most (>80%) to the total phytoplankton biomass suggesting that phytoplankton growth is not nutrient limited within the Bay. The total mesozooplankton abundance and biomass values during summer varied between 10088.92 and 28283.21 ind.m⁻³ and between 76.59 and 161.94 mg.m⁻³, respectively. During winter, total abundance and biomass of mesozooplankton within the Bay were significantly lower, ranging from 2392.49 to 11145.29 ind.m⁻³, and from 34.49 to 42.49 mg.m⁻³, respectively (P<0.05). During both seasons, cosmopolitan copepod species 200–500μm in size dominated the total mesozooplankton counts, numerically and in biomass. Hierarchical cluster analyses identified distinct zooplankton groupings within the Bay during both the summer (three groupings) and winter (four groupings) surveys. The different groupings identified during the two seasons were not associated with any specific geographic region or hydrological feature. Nonetheless, a distinct seasonal pattern in the mesozooplankton community was evident, largely reflecting the increased abundance of mesozooplankton during the summer survey. Canonical Correspondence Analyses (CCA) indicated that the zooplankton community structure within Algoa Bay reflected a complex interaction between physical-chemical (e.g. temperature, water column stability, turbidity, and nitrate, dissolved oxygen and nitrite concentrations) and biological factors (e.g. microphytoplankton and picophytoplankton concentrations). These data provide baseline information towards long-term monitoring programs that will be conducted in Algoa Bay, as part of the South African Environmental Observation Network (SAEON), in the near future.

Subseasonal variability of tropical Indian Ocean sea surface temperature is thought to influence the active-break cycle of the Asian monsoon. There are several open questions related to the role of surface fluxes, large-scale ocean circulation and subsurface ocean processes in the subseasonal variability of upper ocean temperature. We present a unified study of the subseasonal (2-90 day) variability of surface heat flux and upper ocean temperature and salinity throughout the tropical Indian Ocean in all seasons. We focus on the relation between surface fluxes and ocean response using a new satellitebased daily heat flux. The role of ocean processes (advection, entrainment and mixing) in determining SST variability is diagnosed from the daily satellite SST. Before the onset of the summer monsoon, sea surface temperature (SST) of the north Indian Ocean warms to 30-32oC. Climatological mean mixed layer depth in spring (March-May) is 10-20 m, and net surface heat flux (Qnet) is 80-100 Wm 2 into the ocean. It has been suggested that observed spring SST warming is small mainly due to (a) penetrative flux of solar radiation through the base of the mixed layer (Qpen), (b) advective cooling by upper ocean currents and (c) entrainment of sub-mixed layer cool water. We estimate the role of the first two processes in SST evolution from a two-week ARMEX experiment in April-May 2005 in the the southeastern Arabian Sea. The upper ocean is stratified by salinity and temperature, and mixed layer depth is shallow (6 to 12 m). Current speed at 2 m depth is high even under light winds. Currents within the mixed layer are quite distinct from those at 25 m. On subseasonal scales, SST warming is followed by rapid cooling. The cooling occurs although the ocean gains heat at the surface - Qnet is about 105 Wm 2 in the warming phase, and 25 Wm 2 in the cooling phase; penetrative loss Qpen, is 80 Wm 2 and 70 Wm 2. In the warming phase, SST rises mainly due to heat absorbed within the mixed layer, i.e. Qnet minus Qpen; Qpen, reduces the rate of SST warming by a factor of three. In the second phase, SST cools rapidly because (a) Qpen, is larger than Qnet, and (b) advective cooling is _85 Wm 2. A calculation using time-averaged heat fluxes and mixed layer depth suggests that diurnal variability of fluxes and upper ocean stratification tends to warm SST on subseasonal time scale. Buoy and satellite data suggest that a typical premonsoon intraseasonal SST cooling event occurs under clear skies and weak winds, when the ocean is gaining heat. In this respect, premonsoon SST cooling in the north Indian ocean is different from that due to MJO or monsoon ISO. As a follow-up to ARMEX, we use a short dataset from a field campaign in the premonsoon north Bay of Bengal to study diurnal variability of SST. In addition to the standard meteorological and hydrographic parameters measured from shipborne instruments and buoy sensors, we obtained a two-hourly record of subsurface sunlight profiles. Heat fluxes are seen to drive the SST warming during the day while both advection and entrainment/mixing are important during the night. The simple heat balance based on heat flux shows that it drives the diurnal cycle of SST, though ocean processes contribute towards night time cooling; this has been confirmed using the Price-Weller-Pinkel mixing model forced by heat flux and wind stress. A similar analysis for mixed layer salinity revealed that the salt balance in the region is dominated by advection rather than freshwater flux or entrainment/mixing. Buoy and satellite data show pronounced subseasonal oscillations of sea surface temperature (SST) in the summertime north Indian Ocean. The SST oscillations are forced mainly by surface heat flux associated with the active-break cycle of the south Asian summer monsoon. The input of freshwater (FW) from summer rain and rivers to the Bay is large, but not much is known about subseasonal salinity variability. We use 2002-2007 observations from Argo floats with 5-day repeat cycle to study the subseasonal response of temperature and salinity to surface heat and freshwater flux in the central Bay of Bengal and central Arabian Sea. Estimates of surface heat and freshwater flux are based on daily satellite data sampled along the float trajectory. We find that intraseasonal variability (ISV) of mixed layer temperature is mainly a response to net surface heat flux minus penetrative radiation during the summer monsoon season. In winter and spring, however, temperature variability appears to be mainly due to ocean processes rather than local heat flux. Variability of mixed layer freshwater content is generally independent of local surface flux (precipitation minus evaporation) in all seasons. There are occasions when intense monsoon rainfall leads to local freshening, but these are rare. The large subseasonal fluctuations observed in FW appear to be due to advection, suggesting that freshwater from rivers and rain moves in eddies or filaments. We have developed a new daily satellite-based heat flux dataset for the tropical Indian Ocean (30oE 120oE; 30oS 30oN); satellite data include surface air temperature and relative humidity from the Atmospheric Infrared Sounder (AIRS). On the seasonal scale (> 90 days) the flux compares reasonably well with climatologies and other daily data. On the subseasonal scale, our flux product has realistic behaviour relative to buoy data at validation sites. An important result is that ocean processes (advection, entrainment/detrainment, mixing at the base of the mixed layer) cool the tropical Indian Ocean SST by 8oC over the year. The largest contribution of ocean processes (_20oC SST cooling over the year) is in the western equatorial Indian Ocean. Ocean processes generally cool the upper ocean in all seasons and all regions, except in boreal winter, when they warm the north Indian Ocean. This is likely due to entrainment of warm sub-mixed layer water in regions of inversions. On subseasonal (2-90 days) scales, the contribution of air temperature and humidity to latent heat flux is roughly equal to the contribution from wind speed variability: Another interesting finding is that the contribution of air temperature and humidity increases away from the equator. One of the most important contributions of this thesis is the demonstration that tropical Indian Ocean SST has a coherent response to intraseasonal changes in heat flux associated with organised convection in the summer hemisphere. SST responds to flux in (i) the northeast Indian Ocean during May-October and (ii) the 15oS-5oN region during November-April. In the winter hemisphere and in regions with no organised convection, it is ocean processes and not fluxes which drive the subseasonal changes in SST. This result suggests that SST ISV feeds back to organise and sustain organised convection in the tropical atmosphere.

Abstract not available

Today, ocean modeling is fast developing as a versatile tool for the study of earth’s climate, local marine ecosystems and coastal engineering applications. Though the field of ocean modeling began in the early 1950s along with the development of climate models and primitive computers, even today, the state-of-the-art ocean models have their own limitations. Many issues still remain such as the uncertainity in the parameterisation of essential processes that occur on spatial and temporal scales smaller than that can be resolved in model calculations, atmospheric forcing of the ocean and the boundary and initial conditions. The advent of data assimilation into ocean modeling has heralded a new era in the field of ocean modeling and oceanic sciences. “Data assimilation” is a methodology in which observations are used to improve the forecasting skill of operational meteorological models. The study in the present thesis mainly focuses on obtaining a four dimensional realization (the spatial description coupled with the time evolution) of the oceanic flow that is simultaneously consistent with the observational evidence and with the dynamical equations of motion and to provide initial conditions for predictions of oceanic circulation and tracer distribution. A good implementation of data assimilation can be achieved with the availability of large number of good quality observations of the oceanic fields as both synoptic and in-situ data. With the technology in satellite oceanography and insitu measurements advancing by leaps over the past two decades, good synoptic and insitu observations of oceanic fields have been achieved. The current and expected explosion in remotely sensed and insitu measured oceanographic data is ushering a new age of ocean modeling and data assimilation. The thesis presents results of analysis of the impact of data assimilation in an ocean general circulation model of the North Indian Ocean. In this thesis we have studied the impact of assimilation of temperature and salinity profiles from Argo floats and Sea Surface height anomalies from satellite altimeters in a Sigma-coordinate Indian Ocean model. An ocean data assimilation system based on the Regional Ocean Modeling System (ROMS) for the Indian Ocean is used. This model is implemented, validated and applied in a climatological simulation experiment to study the circulation in the Indian Ocean. The validated model is then used for the implementation of the data assimilation system for the Indian Ocean region. This dissertation presents the qualitative and quantitative comparisons of the model simulations with and without subsurface temperature and salinity profiles and sea surface height anamoly data assimilation for the Indian Ocean region. This is the first ever reported data assimilation studies of the Argo subsurface temperature and salinity profile data with ROMS in the Indian Ocean region.

[Truncated abstract] This work was the first large-scale biological oceanographic study to be undertaken in the coastal eastern Indian Ocean adjacent to Western Australia, and covered both northwest (Exmouth Peninsula to the Abrolhos Islands) and southwest (Cape Naturaliste to Cape Leeuwin) regions. The study area was dominated by the Leeuwin Current (LC), an anomalous eastern boundary current that transports tropical water poleward and prevents deep nutrients from reaching the surface by creating large-scale downwelling. Indeed, LC and offshore waters were consistently associated with low nitrate concentrations and low phytoplankton biomass and production (< 200 mg C m-2 d-1). However, the physical forcing of the LC was offset, during the summer months, by upwelling associated with wind-driven inshore countercurrents (Ningaloo and Capes Currents), which provided a mechanism to access high nutrient concentrations normally confined to the base of the LC. ... Limited seasonal investigations off the Capes region of southwestern Australia showed that the winter production scenario can be very different than summer conditions, with strong Leeuwin Current flow that meanders onto the continental shelf and entrains seasonally nutrient-enriched shelf waters. However, production in the LC was still low (≤450 mg C m-2 d-1) due to light limitation resulting from both increased light attenuation and reduced surface irradiance characteristic of the winter months. This investigation provides fundamental knowledge on physical-biological coupling off Western Australia, with implications for fisheries management in view of seasonal and inter-annual variability in the strength of both the Leeuwin Current and inshore countercurrents.