End-to-end modelling for an ecosystem approach to fisheries in the Northern Humboldt Current Ecosystem

This work represents an original contribution to the methodology for ecosystem models' development as well as the rst attempt of an end-to-end (E2E) model of the Northern Humboldt Current Ecosystem (NHCE). The main purpose of the developed model is to build a tool for ecosystem-based management and decision making, reason why the credibility of the model is essential, and this can be assessed through confrontation to data. Additionally, the NHCE exhibits a high climatic and oceanographic variability at several scales, the major source of interannual variability being the interruption of the upwelling seasonality by the El Niño Southern Oscillation, which has direct e ects on larval survival and sh recruitment success. Fishing activity can also be highly variable, depending on the abundance and accessibility of the main shery resources. This context brings the two main methodological questions addressed in this thesis, through the development of an end-to-end model coupling the high trophic level model OSMOSE to the hydrodynamics and biogeochemical model ROMS-PISCES: i) how to calibrate ecosystem models using time series data and ii) how to incorporate the impact of the interannual variability of the environment and shing. First, this thesis highlights some issues related to the confrontation of complex ecosystem models to data and proposes a methodology for a sequential multi-phases calibration of ecosystem models. We propose two criteria to classify the parameters of a model: the model dependency and the time variability of the parameters. Then, these criteria along with the availability of approximate initial estimates are used as decision rules to determine which parameters need to be estimated, and their precedence order in the sequential calibration process. Additionally, a new Evolutionary Algorithm designed for the calibration of stochastic models (e.g Individual Based Model) and optimized for maximum likelihood estimation has been developed and applied to the calibration of the OSMOSE model to time series data. The environmental variability is explicit in the model: the ROMS-PISCES model forces the OSMOSE model and drives potential bottom-up e ects up the foodweb through plankton and sh trophic interactions, as well as through changes in the spatial distribution of sh. The latter e ect was taken into account using presence/ absence species distribution models which are traditionally assessed through a confusion matrix and the statistical metrics associated to it. However, when considering the prediction of the habitat against time, the variability in the spatial distribution of the habitat can be summarized and validated using the emerging patterns from the shape of the spatial distributions. We modeled the potential habitat of the main species of the Humboldt Current Ecosystem using several sources of information ( sheries, scienti c surveys and satellite monitoring of vessels) jointly with environmental data from remote sensing and in situ observations, from 1992 to 2008. The potential habitat was predicted over the study period with monthly resolution, and the model was validated using quantitative and qualitative information of the system using a pattern oriented approach. The nal ROMS-PISCES-OSMOSE E2E ecosystem model for the NHCE was calibrated using our evolutionary algorithm and a likelihood approach to t monthly time series data of landings, abundance indices and catch at length distributions from 1992 to 2008. To conclude, some potential applications of the model for shery management are presented and their limitations and perspectives discussed.

Strong connections, loose coupling: the influence of the Bering Sea ecosystem on commercial fisheries and subsistence harvests in Alaska

Human-environment connections are the subject of much study, and the details of those connections are crucial factors in effective environmental management. In a large, interdisciplinary study of the eastern Bering Sea ecosystem involving disciplines from physical oceanography to anthropology, one of the research teams examined commercial fisheries and another looked at subsistence harvests by Alaska Natives. Commercial fisheries and subsistence harvests are extensive, demonstrating strong connections between the ecosystem and the humans who use it. At the same time, however, both research teams concluded that the influence of ecosystem conditions on the outcomes of human activities was weaker than anticipated. Likely explanations of this apparently loose coupling include the ability of fishers and hunters to adjust to variable conditions, and the role of social systems and management in moderating the direct effects of changes in the ecosystem. We propose a new conceptual model for future studies that incorporates a greater range of social factors and their dynamics, in addition to similarly detailed examinations of the ecosystem itself.

Integrating a mobile accessible electronic system into dockside monitoring: How can small-scale fisheries data collection programs transition from paper-based to digital data collection?

Thesis (Master's)--University of Washington, 2016-06

Infection dynamics of Marteilia refringens in flat oyster Ostrea edulis and copepod Paracartia grani in a claire pond of Marennes-Oleron Bay

The protozoan parasite Marteilia refringens has been partly responsible for the severe decrease in the production of the European flat oyster Ostrea edulis Linnaeus in France since the 1970s. The calanoid copepod Paracartia grani Sars was recently found to be a host for M refringens in French shallow-water oyster ponds ('claires'). This study reconsidered M refringens transmission dynamics in the light of this finding, taking into account not only oyster infection dynamics and environmental factors but also data concerning the copepod host. P. grani population dynamics in the claire under study revealed that this species is the dominant planktonic copepod in this confined ecosystem. During winter, M refringens overwintered in O. edulis, with P. grani existing only as resting eggs in the sediment. The increase in temperature in spring controlled and synchronized both the release of M refringens sporangia in the oyster feces, and the hatching of the benthic resting eggs of the copepod. Infection of oysters by M refringens was limited to June, July and August, coinciding with (1) the highest temperature recorded in the claire, and (2) the highest abundance of P. grani. PCR detection of M refringens in P. grani during the summer period was linked to the release of parasite sporangia by the oyster. Our results are supported by previous results on the effective transmission of this parasite from the oyster to the copepod.

Genetic effect of domestication selective pressures on Pacific oyster at larval stage

Among bivalve species, the Pacific oyster, Crassostrea gigas, is the most economically important bivalve production over the world. Today, C. gigas is subject to an important production effort that leads to an intensive artificial selection. Larval stage is relatively unknown, specifically in a domestication context. Genetic consequence of artificial selection is still at a preliminary study. We aimed to tackle the consequence of inconscient domestication on the variance reproductive success focusing on larval stage, keystone of the life cycle. We studied two kinds of specific selective processes that common hatchery rearing practices exert : the effect of discarding the smallest larvae on genetic diversity and the artificial environment rearing effect via the temperature providing a contrast resembling wild versus hatchery conditions (20 and 26°C). In order to monitor the effect of the selection of fast growing larvae by sieving, growth variability and genetic diversity in a larval population descended from a factorial breeding was studied. We used a mixed-family approach to reduce potentially confounding environmental biais. The retrospective assignment of individuals to family groups has been performed using a three microsatellite markers set. Two different rearing were carried out in parallel. For three (replicates) 50-l tanks, the smallest larvae were progressively discarded by selective sieving, whereas for the three others no selective sieving was performed. The intensity of selective sieving was adjusted so as to discard 50% of the larvae over the whole rearing period in a progressive manner. As soon as the larvae reached the pediveliger stage, ready to settle larvae were sampled for genetic analysis. Regarding the artificial environment rearing effect via the temperature, we used a similar mixed-family approach. The progeny from a factorial breeding design was divided as follows: three (replicates) 50-l tanks were dedicaced to a rearing at 26°C versus 20°C for three others 50-l tanks. The whole size variability was preserved for this experiment. Individual growth measurements for larvae genetically identified have been performed at days 22 and 30 after fertilization for both conditions. In a same way, we collected individual measurements for genotyped juvenile oysters (80 days after fertilization). At a phenotypic scale, relative survival and settlement success for larvae with sieving were higher. Sieving appears as a time-saving process associated with a better relative survival ratio. But in the same time, our results confirm that a significant genetic variability exist for early developmental traits in the Pacific oyster. This is congruent with the results already obtained that investigated genetic variability and genetic correlations in early life-history traits of Crassostrea gigas. Discarding around 50% of the smallest larvae can lead to significant selection at the larval stage.

Fisheries Department Annual Report 1968

The year 1968 was yet another year of great success in the exploitation of the fishery resources. The total catch landed was estimated at 108,400 metric tons, worth approximately 77.2 million shillings at the lake shore, and about 220 million shillings in the retail market. This compared favorably with the 1967 catch of 97,000 metric tons, worth approximately 62 million shi11ings on the lake shore and 140 million shillings in the retail market. The 1968 catch exceeded the 1967 catch by 11,400 tons, and also exceeded the expected catch of 105,600 tons in 1971 by 2,800 tons. Most of the fish was consumed within Uganda, where shown a further increase and was estimated at 13 kg. Per head of population.

The past, present and projected scenarios in the Lake Albert and Albert Nile fisheries: implications for sustainable management

Lake Albert is one of the largest lakes in Uganda that still supports a multi-species fishery which as a result of variable adult sizes of the species, causes management challenges especially in relation to gear mesh size enforcement. Prior to the 1980s, commercial species were 17 large sized fishes especially Citharinus citharinus, Distichodus niloticus and Lates spp. that were confimed to inshore habitats of the lake and were thus rapidly over fished. Frame and catch assessment surveys conducted in this study revealed a >80% dominance of small size fish species (Neobola bredoi and Brycinus nurse) and a 40 -60% decrease in the contribution of the large commercial species. Sustainability of small size fish species is uncertain due to seasonal fluctuations and low beach value. At about 150,000 tons of fish recorded from Lake Albert and Albert Nile, the beach value was estimated at 55.3 million USD. Despite the noted decline in catches of the large sized fishes their contribution was more than 50% of total beach value. Therefore, management measures should couple value addition for the small sized species and maintain effort regulation targeting recovery of the large previously important commercial species.

Socio-economic aspects of the fisheries of Nabugabo lakes and implications for management

Fisheries are very important to Uganda's economy. The sector provides a vital source of food, recreation, trade and socioeconomic well being for the people and community globally. The fisheries of small lakes are important for producing fish for local populations who are not near the large lakes. These satellite lakes support important fisheries and other economic activities like fishing, water for domestic purposes and tourism, besides socio-cultural values. A number-of fish;- species, some of which were found only in Lake Victoria have been depleted through over-exploitation, introduction of exotics especiaily Nile perch and environmental degradation. Some of these fishes have been observed to survive in satellite lakes in the Victoria and Kyoga Lake basins. The Nabugabo satellite lakes (Manywa, Kayugi and Kayanja) contain endemic Cichlid fish species acting as reservoirs and therefore very important for conservation of fish biodiversity. Despite the socio-economic importance and uniqueness of these satellite lakes little research on socio-economic studies has been carried out. The sustainability of the lake is being threatened by increasing human activities. The fish stocks and species diversity are declining and this poses a threat to the livelihood of the people who depend on fish for food and income. Arising from this need a study was carried out to establish the socio-economic aspects of Nabugabo fisheries and implications for management, on which basis resource users would be made aware of the impacts of their activities. It was hoped that this would go further to ensure wise use and management of the resources by the users. The specific objectives were identifying activities around the lake, establishing socioeconomic values attached to the lake, identifying problems of the lake and resource users and examining existing local based management institutions. Results show that the activities taking place around the lakes include fishing, farming, watering of animals, deforestation and charcoal burning, brick making, resort beach development and food and refreshment. The major problem facing the lake was found to be encroachment of Hippo grass (Vossia) on the lake, which is decreasing the size of the lake, and limiting open waters for fishing (this only applied to Lake Nabugabo). Other important problems include use of illegal fishing methods, declining fish stocks and loss of cultural identity. The resource users are most pressed by the low incomes resulting from poor fish catches, theft of gears and lack of market. On examining the resource base for the lakes, it was only Lake Nabugabo that had a Landing Management Committee. The other three lakes did not have leadership institutions in place except the local councils for the respective villages. This was probably due to observed limited fisheries activities. Majority of the respondents agreed that Government and other service providers should work jointly to supplement local beach management committees in the management of the lakes resources. This is a good gesture because with increase in fishing effort and rampant use of illegal fishing methods, there is need to strengthen management institutions present on the lake. This would require Government, local community and other service providers to work together in a participatory way to control environment-degrading activities and stop the use of illegal fishing methods. Burning of vegetation on the lake should be stopped since it enhances growth of this grass. Finally, traditional taboos; which are present on some of the Nabugabo lakes, should be enhanced, as away of preserving them.

Fisheries Department Annual Report 1969

During the year 1969, the fishing industry maintained a rate of increase that had been witnessed in the three previous years. The total catch landed was estimated at 125300 metric tons, valued at shs 130,500,000/-at the lakeside,and about shs 260,000,000/-in the retail market. This was an increase of 16,900 metric tons over the 1968 figure. The largest increases again came from the Lake Kyoga area, where the Nile Perch and the introduced Tilapia species are still expanding. Large numbers of fishermen from other regions (i.e. from Lake Victoria) moved to Lake Kyoga where catches were high and remunerative. This intensified fishing on this lake, resulting in the high figure of catches recorded. As in the previous year, there was a marked increase in the use of large-mesh gill-nets for catching Nile Perch and Tilapia. Individual Tilapia nilotica of up to 5 kg were quite common, and Nile Perch weighing over 50 kg were also regularly taken. The marketing and distribution side of the industry was as active as ever: 87 people took out specific licences, and 640 fishmongers were licensed by different urban authorities. Elsewhere in the Districts, 7,950 fishmongers were licensed. Host of the fish landed was consumed within Uganda and exports accounted for dnly a very small fraction of the market, mainly composed of frozen fiilets to Kenyai and salted fish to the Republic of the Congo. Kampala market was the most important one, serving also as a central market from where fishmongers bought fish for distribution to rural areas.

Some biological and ecological considerations for research in the management of the fisheries of Lakes Victoria and Kyoga

There is little doubt that the exploitation of the current fisheries of Lakes Victoria and Kyoga requires close monitoring with a view to enforce adherence to prudent management practices. Many indigenous fishes have gradually disappeared from the commercial fishery of both lakes. In the Uganda portion of Lake Victoria for instance Okaronon and Wadanya (in press) have shown that:- 1. The once preponderant haplochromiine taxon ceased to feature in the commercial catches in 1979. 2. The lung-fish (Protopterus aethiopicus) which formerly contributed significantly to the commercial landings had declined to minor species status by the mid 1980s. 3. The catfishes Clarias mossambicus and Bagrus docmac, formerly major fish species, contributed insignificant quantities to the commercial fishery since the early and mid 1980s, respectively. Similar trend have been "reported in the Kenya and Tanzania portions of Lake Victoria (Bwathondi, 1985; Mainga, 1985, Witte and Goudswaard, 1985). On the other hand since their establishment all round the lake in the early to mid 1980s some introduced fishes namely Nile perch (Lates niloticus) and Nile tilapia (Oreochromis niloticus) built up impressive stocks in Lake Victoria (Ssentongo and Welcomme, 1985, Okaronon et al. 1985; Okaronon and Wadanya, in press). Togetther with the native pelagic cyprinid Rastrineobola argentea or Dagaa/Mukene the introduced fishes have contributed unprecidented catches, stimulating vibrant commercial fisheries which have yielded significant social economic benefits to the peoples of the three states riparian to the Lake (Reynolds and Greboval, 1988; Kudhongania et al in press). The impressive landings particularly of the Nile perch and Nile tilapia have also led to rapid industrialisation of fish processing in East Africa mainly for the export market. Fish export has now the potential of a major foreign exchange enterprise in the region.

The fisheries resources of Lake Nakivali: report of a rapid assessment of the Lake Nakivali fishery

Lake Nakivali is one of the four small lakes that form what is known as the Koki lakes system. It is 14 km long, 6 km wide, 26 km2 in area and has maximum depth of 3.5 m at high water level. The lake is located in a lake-swamp complex with River Rwizi as the principle inflow, and a number of peripheral lakes among which are four major ones, i.e. Lakes Nakivali, Mburo, Kachira, and Kijanebalola. The survey therefore established that Lake Nakivali is a healthy ecosystem capable of sustaining fisheries production. While stock enhancement through restocking with fry could boost fish stocks, especially of the Nile tilapia, effective management measures that allow natural regeneration of stocks of indigenous fish species is paramount. This may require closed fishing seasons and control of fishing effort. Tank aquaculture is a viable option for increasing fish production and Ngege (O. niloticus) and Male (C. gariepinus) are candidate fish species for fish farming.

Desk Review of Queensland shark stock assessment for Fisheries Queensland

An independent desk review of the document entitled “Stock assessment of whaler and hammerhead sharks (Carcharhinidae and Sphyrnidae) in Queensland” commissioned by the Queensland’s Department of Agriculture and Fisheries was undertaken during January 15-February 12, 2016.

Evaluating conservation and fisheries management strategies by linking spatial prioritization software and ecosystem and fisheries modelling tools

Well-designed marine protected area (MPA) networks can deliver a range of ecological, economic and social benefits, and so a great deal of research has focused on developing spatial conservation prioritization tools to help identify important areas. However, whilst these software tools are designed to identify MPA networks that both represent biodiversity and minimize impacts on stakeholders, they do not consider complex ecological processes. Thus, it is difficult to determine the impacts that proposed MPAs could have on marine ecosystem health, fisheries and fisheries sustainability. Using the eastern English Channel as a case study, this paper explores an approach to address these issues by identifying a series of MPA networks using the Marxan and Marxan with Zones conservation planning software and linking them with a spatially explicit ecosystem model developed in Ecopath with Ecosim. We then use these to investigate potential trade-offs associated with adopting different MPA management strategies. Limited-take MPAs, which restrict the use of some fishing gears, could have positive benefits for conservation and fisheries in the eastern English Channel, even though they generally receive far less attention in research on MPA network design. Our findings, however, also clearly indicate that no-take MPAs should form an integral component of proposed MPA networks in the eastern English Channel, as they not only result in substantial increases in ecosystem biomass, fisheries catches and the biomass of commercially valuable target species, but are fundamental to maintaining the sustainability of the fisheries. Synthesis and applications. Using the existing software tools Marxan with Zones and Ecopath with Ecosim in combination provides a powerful policy-screening approach. This could help inform marine spatial planning by identifying potential conflicts and by designing new regulations that better balance conservation objectives and stakeholder interests. In addition, it highlights that appropriate combinations of no-take and limited-take marine protected areas might be the most effective when making trade-offs between long-term ecological benefits and short-term political acceptability.

Lake Victoria fisheries catch assessment survey (CAS) information, Uganda 2005-2007

Management of fisheries resources requires information on the fish stocks; the magnitude, distribution and trends of fishing effort and the trends of fish catches. Catch Assessment Surveys (CAS) in Lake Victoria are one of the ways through which the partner states sharing the lake are generating the key information required. In the Uganda part of the lake, CAS activities are carried out at 54 fish landing sites in the 11 riparian districts. The National Fisheries Resources Research Institute (NaFIRRI), the Department of Fisheries Resources (DFR), and the Districts of Busia, Bugiri, Mayuge, Jinja, Mukono, Wakiso, Kampala, Mpigi, Masaka, Kalangala and Rakai jointly conduct the surveys, The CAS enumerators are recruited from the fishing communities and work under direct supervision of sub-county fisheries officers. This fact sheet presents catch statistics for the period 2005 to 2007