Mud crab Scylla serrata is a crustacean that spends most of its life cycle in the mangrove environment throughout its range. Fishery and aquaculture of this crab are significant economic activities in coastal areas in the tropics and sub-tropics because of the meat quality and nutritional value. However there is a significant shortage of information on the ecology, fishery and aquaculture of these crabs in sub-Saharan Africa. This impacts the development of a sustainable aquaculture and fishery for the benefit of coastal communities. The present study analyses various aspects of mud crab ecology, fishery, aquaculture and social economics in East Africa using multidisciplinary approaches. The results are given in seven papers based on field and laboratory studies. The study established for the first time that high intertidal mangrove back-flats constitute a key habitat for the earliest instars of S. serrata (4 -30 mm CW). It also showed that diurnal tidal migration behaviour occurs in small juveniles that migrate to sub-tidal habitats during the day, possibly due to variable predation risks. Monthly sampling of juveniles in Kenya and Tanzania indicated continuous recruitment throughout the year. The large numbers of juvenile crabs along mangrove fringes indicate that these habitats could serve as sites suitable for collection of juvenile crabs for aquaculture. However, these areas must also be managed and protected to support the recruitment to the wild crab populations. An assessment of the crab fishery indicated that artisanal crab fishers possess significant traditional knowledge mainly inherited from their parents that enabled them to exploit the resource. Such knowledge could be useful for the development of the aquaculture and in management of the fishery. Mud crab fishing was found to be a male dominated activity, and fishers on foot practiced fishing in burrows at spring low tides. Interviews indicated that the average size of marketable crabs has declined over the years and a weak management system was observed with most fishers operating without a license. Due to the knowledge required regarding the local conditions, fishers are unable to shift to new areas. Furthermore fishers and could not fish at neap tides. Such limitations provide a “natural closure” of the fishery. Also foot fishers cover fairly limited distances in their daily operations, an aspect that can be utilized to effect site-specific management for the fishery if necessary. Laboratory and field experiments indicated that cannibalistic interactions are heavily influenced both by size differences of crabs and the availability of shelter but no significant effect was found for different stocking densities. Such information is of direct importance for crab farmers in East Africa, where seed from the wild are of multiple sizes and there is a need to grade juvenile crabs and provide shelter at stocking to ensure maximum survival. Experimental studies in earthen pond and mangrove pen cultures indicated high mortality rates. Comparing growth in earthen pond and mangrove pen systems indicated that growth rates were generally high in both systems, but significantly lower in pen systems without shelter, suggesting that shelter may have a stronger effect on growth than has been previously thought. Similar to artisanal mud crab fishery, an assessment of small-scale mud crab farming by organized community groups in Kenya indicated low level of women participation. A good knowledge of the market existed among the mud crab farming groups where hotels and exporters offered the highest prices. However there is a need for national policies to be directed to support small-scale aquaculture development by ensuring training and capacity building for women, operation and management of groups, data management and provision of user rights for communities working in the mangrove environment. Market analyses showed that the common market size of crabs in East Africa ranged between 500-1000 g and are thus larger than in Southeast Asia where the average size is reported at 300 g. Prices for mud crabs were over 50 % lower in Tanzania than in other East African countries and most of the profit was earned by middlemen and exporters. Cost revenue analysis showed that it would be more profitable to farm smaller commercial crabs, and develop a market for 300 g crabs to increase the profitability of crab farming in East Africa. Also, the same analyses found that farming large crabs in individual cages, which is the dominant culture form in East Africa today, had very low profitability due to high labor costs and low growth rates. Using a step-wise function of natural growth it was shown that growth rates of S. serrata cultured in cages was 40 % of the growth rates obtained in experimental pond and pen cultures, which were similar to natural growth. Therefore the good performance of grow-out cultures of juvenile mud crabs in earthen ponds and mangrove pens showed a potential to develop into a profitable and sustainable intervention. However, more work is needed to improve survival in culture systems and address the identified limitations of crab seeds and feed to enable development of sustainable mud crab aquaculture in East Africa.

Commercial farming of mud crab Scylla serrata is a significant industry throughout South East Asia. The limited scientific knowledge of mud crab nutritional requirements and digestive processes, however, is recognised as a major constraint to the future growth of this industry. To better understand the mechanisms of digestion in the mud crab we have analysed the diversity of digestive enzymes from the hepatopancreas. Significant protease, amylase,cellulase and xylanase activities were detected in soluble extracts from this organ. Temperature profiles for all enzymes were basically similar with optimal activities observed at 500C. Examination of pH tolerance revealed optimal activities for protease and amylase at pH 7.0 while optimal activities for cellulase and xylanase were observed at pH 5.5. Under optimum conditions,protease and amylase activities were approximately two orders of magnitude greater than those seen for either cellulase or xylanase. Interestingly, hepatopancreatic extracts were able to liberate glucose from either starch or carboxymethyl (CM)-cellulose suggesting that a range of carbohydrates may be utilised as energy sources. The effects of dietary carbohydrates on feed digestibility, digestive enzyme levels and growth were also studied by inclusion of additional starch or CM-cellulose at the expense of casein in formulated diets. It was shown that amylase, cellulase and xylanase activities in extracts from the hepatopancreas were highest in mud crabs fed diets containing 47% carbohydrate. Based on the findings, we suggest that the ability of the mud crab to modulate digestive enzyme activities may represent a mechanism to maximise access to essential nutrients when the dietary profile changes.

It is often hypothesised that marine species with mobile planktonic phases are capable of widespread dispersal and may therefore be genetically homogenous throughout their distribution. Studies that have demonstrated positive correlation between duration of plankton phase and levels of gene flow reinforce the prediction that life history characteristics of marine species determine the potential extent of genetic and demographic connectivity throughout their distributions. This prediction has however been challenged by studies that have employed genetic markers highly sensitive to both historical and contemporary demographic changes. Disparities between dispersal potential and measured levels of gene flow have been demonstrated both among historically disconnected ocean basins and within semi-enclosed areas of strong hydraulic connectivity. These studies and others highlight a need for greater focus on factors that may influence population structure and distribution for marine species. In this thesis, I have examined genetic structure within and among populations of an estuarine species of mud crab Scylla serrata (Forskal, 1775) using a number of genetic markers and methods. The species is widely distributed throughout mangrove and estuarine habitats of the Indo - West Pacific (IWP); it is generally assumed that life-history characteristics of S. serrata promote high levels of population admixture and gene flow throughout its distribution. Alternatively, factors that have promoted population genetic structure for a variety of IWP marine species may also have affected S. serrata populations. By investigating genetic structure at several spatial scales of sampling, I was able to address a variety of hypotheses concerning the species distribution, dispersal, and genetic structure. Episodic changes to marine habitat and conditions experienced within the IWP during the Pleistocene may have affected genetic structure for a broad variety of marine taxa. The relative strength of this hypothesis may be assayed by comparative genetic studies of widespread IWP taxa with high dispersal capacity. In order to ascertain levels of historical and contemporary gene flow for S. serrata, I investigated the phylogeographic distribution of mitochondrial DNA haplotypes sampled throughout the species range. Adults were sampled from three west Indian ocean locations (N=21), six west Pacific sites (N=68), and two sites from northern eastern Australia (N=35). Temperature gradient gel electrophoresis and sequencing of 549 base pairs of the mitochondrial cytochrome oxidase I (COI) coding gene identified 18 distinct haplotypes. Apart from that seen in northern Australia, haplotype diversity was low (h < 0.36) at each of the locations. Total nucleotide diversity in the entire sample (excluding northern Australian locations) was also low (p = 0.09). Haplotypes clustered into two clades separated by approximately 2% sequence divergence. One clade was widespread throughout the IWP (clade 1) whereas the other was strictly confined to northern Australia (clade 2). Genealogical assessment of sequenced haplotypes relative to their distributions suggested that a historical radiation of clade 1 S. serrata throughout the IWP occurred rapidly and recently (<1Myr bp) from a west Pacific origin. The evidence of fixed unique haplotypes at the majority of locations suggested that contemporary maternal gene flow between trans-oceanic sites was limited. Contrary to reports for other widespread species of IWP taxa, there was no evidence of lengthy periods of regional separation between Indian from Pacific Ocean populations. However, results may indicate a separation of northern Australian crabs from other locations before and during the IWP radiation. I speculated that this isolation might have resulted in the formation of a new species of Scylla. Additional sampling of mud crabs from the Australian coastline allowed an examination of the diversity and distribution of clade 1 and 2 haplotypes among recently formed shelf-connected coastal locations, and across a historical bio-geographic barrier. Over 300 individuals were sampled from multiple locations within coastal regions (western, northern and eastern) of Australia and analysed for mutational differences at the COI gene. Analysis of molecular variance partitioned by sampling scale (Among regions, within regions, and within all locations) indicated mitochondrial haplotypes were structured regionally (P < 0.001), which contrasted with evidence of genetic panmixia within regions. Regional genetic structure broadly correlated with hydrological circulation, supporting the contention that release and transport of propagules away from the estuary may allow genetic connectivity among widespread shelf-connected S. serrata populations. That similar patterns of maternal gene flow were absent among trans-oceanic populations may indicate that the spatial scale of effective dispersal for this species is generally limited to areas of coastal shelf. The two clades of haplotypes were geographically separated either side of the Torres Strait, a narrow sea channel connecting the northern and eastern regions of coastal Australia. This pattern of historical genetic separation was concordant with a number of other marine species across northern Australia, and might indicate a shared history of vicariance induced by eustasy. Alternatively, differences in diversity and distribution of the clades may be evidence of two independent expansions of clade 1 and 2 crab populations into Australian regions following post-glacial estuary formation. Overall, despite evidence of genetic panmixia within extensive sections of the Australian distribution, there was also evidence of significant barriers to maternal gene flow with both shallow and deep regional phylogeographic assortment of mtDNA haplotypes. The presence of these barriers indicated both historical and contemporary factors have imposed limits to effective dispersal by this species among coastal habitats. A subset of the Australian sample (8 locations, N = 188) was also examined for variation at five microsatellite loci developed specifically here for S. serrata. I examined variation among samples at each of the loci to: a) independently verify regional structure among crab populations previously detected using the mtDNA analysis; b) test for evidence of co-distributed non-interbreeding stocks of S. serrata within Australian waters by examining samples for segregation of alleles within microsatellite loci concordant with the two mtDNA clades. The frequency and distribution of alleles for each of the highly polymorphic microsatellites were homogenous at all levels of sample partitioning and contrasted sharply with the instances of both weak and strong regional phylogeographic assortment of mtDNA haplotypes. These contrasting results between different genomic markers were examined in relation to the species life history, and to differences in mutational rate and inheritance of the genetic markers. Several hypotheses may explain the disparity, however it is most likely that rampant homoplasy and high rates of mutation at the microsatellite in conjunction with large Ne at locations may be concerted to delay equilibrium between genetic drift and migration among populations at these highly polymorphic nuclear markers. There was also no evidence that alleles at microsatellite loci were co-segregated with mtDNA clades and therefore no evidence of segregated breeding between the clades of crabs. Whether or not this result was also driven by homoplasy at the microsatellites remains unknown. Recently established mud crab populations (~ 3-4 years old) observed in a number of southwest Australian estuaries are almost 1000 kilometres south of their previously recorded distribution on the Western Australian coast. Colonisation of the southwest region may have occurred either by a natural range expansion from northwest Australian mud crab populations or by means of translocation from any number of mud crab sources within the Indo - West Pacific. I used mtDNA analysis to verify the species and determine the potential source population(s) of the colonists, by comparing sampled genetic material from the southwest (N = 32) against that previously described for the genus. I also compared levels of diversity at mtDNA and two microsatellite loci between the colonist and suspected source population(s) to qualitatively determine if the southwest populations experienced reductions in genetic diversity as a result of the colonisation process. All colonist samples had S. serrata mtDNA COI sequences identical to one previously described as both prevalent and endemic to northwest Australia. High levels of genetic diversity among source and colonist populations at two microsatellite loci contrasted to the mitochondrial locus which displayed an absence of variation among colonists compared to moderately diverse source populations. I argued that the southwest was recently colonised by large numbers of S. serrata propagules derived from the northwest of Australia, possibly due to an enhanced recruitment event coinciding with the reported strengthening of the Leeuwin Current during 1999. Contrasting levels of diversity among nuclear and mitochondrial loci may be attributed to a difference in response by the two genomes to the colonisation process. I predict that such differences may be generally prevalent among plankton-dispersed species. Finally, I discuss aspects of the species distribution and biogeography obtained as a composite of the various results and ideas expressed in this thesis. I propose that S. serrata populations in the IWP may have experienced several cycles of extinction and population retraction from temperate areas followed by subsequent periods of colonisation and rapid coastal expansion in response to the effects of glacial episodes on coastal habitats in the IWP. I propose that persistence of this species as remnant populations of clade 1 and 2 crabs at equatorial locations during low sea level stands provided source populations for later expansions by the species into a variety of coastal areas throughout the IWP. Further analysis is required to determine if mtDNA clade 1 and 2 crabs are non-interbreeding species of mud crab.

Mud crabs of the genus Scylla are widely exploited for aquaculture in the Asia- Pacific region. In the current study, a series of in vivo experiments were carried to assess the protein requirement, protein sparing effects of starch and the capacity of Scylla serrata to digest diets that contained different animal and plant-based feed meals and different levels and types of starch. Results from a protein requirement study indicated that juvenile S. serrata fed diets containing 45% or 55% protein demonstrated significantly higher growth responses than those fed the diet containing 25% protein. The subsequent study was carried out to determine if responses to dietary protein could be influenced by using purified wheat, potato, rice or corn starch to manipulate the gross energy level of fishmeal- based diets (18 or 15.5 MJ kg-1), i.e., to see if starch had a protein sparing effect in these animals. Overall, growth responses in this study appeared to be positively correlated with the level of protein in the diet with the highest growth rates achieved using diets containing 45% protein, regardless of the energy level of the diet. In addition, at a dietary protein level of 40% there was no evidence that the source of starch had any significant impact on growth performance or feed utilisation suggesting it had no protein sparing effect. By contrast, it was found that growth of juvenile S. serrata was strongly correlated with the intake of digestible dietary protein. The investigation of the capacity of sub-adult S. serrata to digest different animal and plant- based feed meals showed that apparent dry matter digestibility (ADMD) and apparent gross energy digestibility (AGED) values were not significant different for most selected feed meals (cotton seed, poultry, canola, fishmeal, soybean, and lupin meal). Apparent crude protein digestibility (ACPD) for all test feed meals were relatively high (86-96%). A subsequent study was carried out to determine if purified starch from different sources influenced the digestibility of fishmeal based diets. Overall, most diets containing starch were readily digested by mud crabs. In particular, there were no negative impacts on the digestibility of major nutrients (e.g. protein) observed following the inclusion of wheat, rice or corn starch in formulated feeds. Nevertheless, the apparent starch digestibility (ASD) of wheat starch decreased significantly as the inclusion level was increased from 15% to 60%, although there was no significant effect on ACPD values. At a 30% inclusion level, the ASD of diets containing different starches decreased in the order corn > wheat > potato = rice. Moreover, ACPD values were significantly higher for diets containing corn or rice starch than for those containing wheat or potato starch. The capacity of another species of mud crab commonly exploited for aquaculture in South East Asia, S. paramamosain, to digest the local plant-based ingredients (defatted soybean meal, rice bran, cassava and corn flour) was also conducted in Vietnam. Overall, the findings of this study showed that at a 30% inclusion level diets containing soybean meal or rice bran were well digested by mud crabs. In particular, the ACPD and AGED values for all diets containing soybean meal were not significantly different from the fishmeal based reference diet. Likewise, all digestibility values for the diet containing 30% rice bran were relatively high and not significantly different from the reference diet. By contrast, diets containing cassava flour appeared to be poorly utilised since their digestibility values for all parameters were lower than those from other testingredients. In summary, the apparent digestibility of dry matter, protein and energy was in the following order (from most to least digestible) soybean meal ~ rice bran > corn flour > cassava flour. In the next study the effects of attractants in diets (chicken meal, betaine, tuna oil and bait enhancer), temperature (26.5oC, 28.5oC and 30.5oC), sex (female and male) and size (small, medium and large) on feeding responses of S. serrata were investigated. Significant differences were observed in the behavioral responses of mud crabs to diets containing different attractants. Specifically, consumption of diets with chicken meal or betaine was significantly higher than for other treatments. With the exception of betaine, no significant difference in food consumption was observed when attractant inclusion levels were raised from 2% to 5%. Overall, small crabs consumed significantly more of the ration (as a percentage of body weight) than larger crabs. Temperature showed a significant impact on most behaviour of mud crabs, excepting continuation response and there was some evidence that females were significantly more active than males. Light intensity was considered as a main factor effect to crab response since there were extremely high percentage time of crab spent in half-shaded of the Y –maze which valued at 95.6%, 93.8 and 94.4% (corresponded to small, medium and large size respectively) in comparison to those of crabs spent in the unshaded side. Overall, the findings from these studies demonstrated that mud crabs have a high capacity to digest a range of plant based feed ingredients. In particular, soybean meal appeared to be well digested by both species of mud crabs examined. It was also shown that a range of purified starches were well digested by S. serrata although starch inclusion in diets did not appear to reduce the requirement for protein to promote growth. Subsequent attractant studies demonstrated that chicken meal and betaine produced significantly elevated feeding responses and food consumption when added to diets. Based on these results we propose that these ingredients can be utilised to increase the attractiveness and consumption of artificial mud crab feeds.

En Nouvelle-Calédonie il y a une forte volonté politique pour diversifier l'aquaculture qui repose encore aujourd'hui sur la crevetticulture. Dans ce contexte le crabe de palétuvier est considéré comme une espèce à fort potentiel. Un des principaux verrous au développement de la carcinoculture en Nouvelle-Calédonie est la disponibilité d'un aliment granulé commercial. Ainsi le principal objectif de cette thèse est d'améliorer notre connaissance des besoins nutritionnels du crabe de palétuvier afin d'être en mesure de formuler un aliment équilibré pour son élevage. Cependant avant d'aborder les études nutritionnelles nous avons vérifié le nombre d'espèces de crabes de palétuvier présentes en Nouvelle-Calédonie.Nos résultats d'études morphologiques et génétiques de 63 individus provenant de 9 sites des côtes Ouest et Nord-Est de la Nouvelle-Calédonie ont confirmé l'existence d'une unique espèce commercialisée: Scylla serrata. C'est donc sur cette espèce que nous avons travaillé en nutrition avec deux séries expérimentales ayant pour objectifs: i) d'évaluer le concentré protéique de soja (CPS) en comparaison avec la farine de poisson comme principale source en protéines et ii) de déterminer le taux optimum d'incorporation du CPS pour la mue et la croissance tissulaire des animaux. Nous avons ainsi observé deux phases de croissance tissulaire au cours d'un cycle de mue (CM): une phase rapide (CTR) qui démarre après la mue et dure jusqu'au début de l'intermue (elle représente 30% du CM) suivi d'une phase de croissance lente (CTL) sur toute la durée de l'intermue et jusqu'à la mue suivante (elle représente 70% du CM). L'accumulation des protéines et des lipides au cours du CM a suivi le même profil de croissance tissulaire contrairement aux cendres qui ont augmenté de façon rapide durant 5 jours suivant l'ecdysis pour atteindre un plateau jusqu'à la prochaine mue. Les deux phases de croissance étaient corrélées avec une prise de l'aliment par les animaux maximale pendant les deux premières semaines suivant la mue. Elle a diminué de moitié sur les 5 semaines suivantes et s'est maintenue ensuite à un niveau de base jusqu'à la prochaine mue. L'énergie ingérée était allouée principalement à la croissance et à l'entretient respectivement durant les périodes CTR et CTL. Durant la phase de croissance lente, 28% de l'énergie ingérée étaient mise en réserve en prévision de la prochaine mue. Le remplacement de la farine de poisson par la CPS n'a pas modifié la croissance tissulaire,l'efficience de l'aliment et le bilan énergétique des animaux quelque soit la phase de croissance considérée. Le taux d'incorporation dans l'aliment de 42% de CPS a permis la meilleure croissance (fréquence de mue et croissance tissulaire, efficience de l'aliment et la rétention de l'énergie des protéines et des lipides. L'hypothèse d'une toxicité de l'ammonium issu de la dégradation des protéines en excès ou des facteurs antinutritionnels du soja est avancée pour expliquer les effets négatifs observés avec les aliments renfermant des taux d'incorporation élevés en CPS. En conclusion, nos travaux apportent des informations originales sur la croissance tissulaire et les dépenses énergétiques durant un cycle de mue et la capacité du crabe juvénile d'utiliser le CPS comme principale source de protéines. Sur ces bases nous somme en mesure de préconiser des contraintes nutritionnelles permettant de formuler un aliment équilibré sans farine de poissons pour l'élevage du crabe de palétuvier S.serrata. / In New Caledonia, there is the strong political will to diversify aquaculture which is mainly based on shrimp farming. In this context, mud crabs have been considered as a potential species for aquaculture development. One of the main constraints to develop crab farming is the availability of formulated feed. Thus, the main purpose of this thesis is to get information on the crab nutritional requirements in order to formulate a balanced diet. However, we had to clarify first how many species of mud crab were present in New-Caledonia. The result of our morphological and genetic investigations carried out on 63 specimens from 9 areas of the west and northeast coast of New-Caledonia confirmed that only one species, Scylla serrata, is commercialized in this country. Consequently, S. serrata was used in our nutritional study based on two experiments to: i) evaluate the soy protein concentrate (SPC) compared with the fishmeal as the main protein source and ii) determine the optimum level of SPC in the diet for molting and tissue growth. We observed two tissue growth phases within one molt cycle (MC): a fast tissue growth (FTG) occurred after ecdysis until early intermolt stage (30% of MC) which is followed by a slow tissue growth (STG) period from intermolt to ecdysis (70% of MC). Protein and lipid deposition followed the same trend than tissue growth while ash level increased quickly during five days after molt and then remained stable until the next molt. The two growth phases were correlated with the voluntary feed intakes (VFI) which was maximum during 2 weeks after ecdysis and then decreased by 50% over the five following weeks to reach a baseline until the next molt. Intake energy was allocated mainly for growth during FTG period and for maintenance during STG period. During STG, 28% of the ingested energy was accumulated for the next ecdysis. Replacement of fishmeal by SPC as main protein source did not affect tissue growth, efficiency of feed utilization and energy budget of crabs whatever the tissue growth period considered. The dietary SPC inclusion of 42% in the diet promoted growth (molt frequency and tissue growth), feed efficiency and retention of energy, protein and lipid. Hypothesis related to ammonia toxicity from catabolism of proteins in excess or anti-nutritional factors from soybean could explain the negative effects of higher inclusion of SPC in the diet for juvenile crabs. In conclusion, our work brings novel information on tissue growth, energy budget during a molt cycle and the ability of juvenile crab to use SPC as a main source of protein. On this basis we suggest to formulate nutritionally balanced diet without fishmeal to farm juvenile mud crabs S. serrata.

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