Jorge Santos

Patterns of growth and lipid deposition in cod (Gadus morhua L.) fed natural prey and fish-based feeds

Abstract Groups of cod were fed two natural prey types, prawn and herring, and two herring-based wet diets, one with low and the other with high energy density. Cod fed upon whole herring and enriched-herring paste showed the highest growth rates but tended to store increasing amounts of lipid in the liver. Cod fed upon the leanest diet, prawn, showed, however, better efficiencies of energy and nutrient conversion. The effect of decreasing food particle size, by mincing the herring, was to slightly impair growth and to substantially lower the efficiency of food conversion. The fatty acid compositions of the body lipids tended to reflect dietary input. The major lipid class in the muscle was the phospholipid whereas the main lipid storage depot consisted of triacylglycerols in the liver. There were some indications that either 20:5 n −3 was chain elongated to 22:6 n −3, or was selective utilized. Dietary 22:1 appeared to have been used as an energy source by the cod, a predator that naturally feeds on prey such as herring which are rich in these fatty acids.

Trophic relationships in deep-water fish communities off Algarve, Portugal

A preliminary investigation was made of the trophic relationships of three species of cartilaginous fish and 12 species of bony fishes along the upper part of the continental slope off the Algarve. These fish, from the by-catch of crustacean bottom trawlers fishing between 190 and 650 m, were sampled for stomach content analysis. Three major predator assemblages were identified. Group 1 consumers preyed upon zooplankton, particularly euphausids, and micronekton usually associated with the deep scattering layers. Group 2 consumers were larger predators that fed largely on fish, particularly those of group 1, and several penaeid and pandalid shrimps. Group 3 consumers had a stronger benthic affinity, and their most important prey items were isopods, followed by crabs and shrimps. The euphausid Meganyctiphanes norvegica seems to play a key role in this food web. The results are discussed from a biogeographic perspective. The deep-water fishery off Algarve seems to be characterised by large technological (multi-fleet) and biological (multi-species) interactions.

Life-history traits of the common snook Centropomus undecimalis in a Caribbean estuary and large-scale biogeographic patterns relevant to management

The ecology of common snook Centropomus undecimalis in Amatique Bay, a tropical estuary in eastern Guatemala, was investigated and life-history traits were used to conduct a meta-analysis of the species from Florida to Brazil. The reproduction cycle of C. undecimalis in Amatique was strongly related to the precipitation cycle, with a lag of 2 months. Spawning occurred from April to November with a peak spawning after the onset of the summer rains. Protandric sex reversal occurred early in the dry season (December) before somatic recovery from spawning. The growth cycle preceded that of body condition by c. 1 month, and was out of phase with the reproductive cycle. Growth was fast, as many individuals reached >70% of the maximum observed total length (LT , 102 cm) after 3 years. Sex transition occurred within a relatively narrow LT range (70-79 cm), but over a wide range of ages, indicating plasticity in this respect. The meta-analysis indicated a latitudinal-temperature gradient in life-history traits, as well as different seasonal patterns relative to temperature and hydrographical cycles. Centropomus undecimalis from cooler winter waters (e.g. Florida) reach larger maximum LT and LT at sex change, as well as greater gonado-somatic indices and longer life spans. Further, increased fishing mortality results in younger age at sex reversal and male predominance in the populations compared. Recognition of large-scale biogeographic patterns in this important, but little studied, fish species helps in the formulation of management advice in other areas of its occurrence.

Spatial distribution patterns, abundance and population structure of deep-sea crab Chaceon macphersoni, based on complementary analyses of trap and trawl data

Marine species such as deep-sea geryonid crabs often exhibit high spatio-temporal variability in abundance and size over depth, substratum type and season, therefore data collected from a single gear type may not represent the whole population. Complementary data from trawl (soft substratum) and trap (hard substratum) fisheries were analysed within a general linear modelling (GLM) framework to assess distribution, abundance and population structure of Chaceon macphersoni off eastern South Africa. Catch rates, mean size, maturation size and sex ratio were modelled relative to year, month, depth, latitude and gear effects. Trap and trawl analyses indicated higher abundance as depth increased up to 500m, and during the austral spring and summer. The mean size of crabs remained constant at all depths sampled, and sex ratios were skewed towards females. Females were smaller than males, and achieved maturity at a smaller size. A standardised index based on trawl data (1988-2010) showed a long-term decline in abundance, with some recovery after 2002, whereas the trap index showed recent local depletions on hard substrata. Using data from two gear types confirmed broad gradients in abundance, but also emphasised subtle trends, such as local depletions on hard substrata, that would not have been apparent from trawl data only.

Population structure and biology of shortfin mako, Isurus oxyrinchus, in the south-west Indian Ocean

The population structure, reproductive biology, age and growth, and diet of shortfin makos caught by pelagic longliners(2005-10)andbatherprotectionnets(1978-2010)inthesouth-westIndianOceanwereinvestigated.Themean fork length (FL) of makos measured by observers on longliners targeting tuna, swordfish and sharks was similar, and decreased from east to west, with the smallest individuals occurring near the Agulhas Bank edge, June to November. Nearly all makos caught by longliners were immature, with equal sex ratio. Makos caught by bather protection nets were significantlylarger,malesweremorefrequent,and93%ofmalesand55%offemalesweremature.Agewasassessedfrom bandcountsofsectionedvertebrae,andavonBertalanffygrowthmodelfittedtosex-pooledlength-at-agedatapredicteda birth size (L0) of 90cm, maximum FL (LN) of 285cm and growth coefficient (k) of 0.113y � 1 . Males matured at 190cm FL,aged7years,andfemalesat250cm,aged15years.Littersizesrangedfromnineto14pups,andthepresenceofgravid females in bather protection nets suggested that some pupping occurred in shelf waters. Teleosts (mainly Trachurus capensis) occurred in 84% of stomachs collected on longliners, whereas elasmobranchs (63.5%) were most common in samples collected from bather protection nets, followed by teleosts (43.1%) and cephalopods (36.5%). Larger prey size may be a factor that attracts large makos to coastal waters. Additional keywords: demography, GLM, pelagic longline fisheries, shark bycatch, stomach contents.

Biology, fisheries and distribution of Thryssa vitrirostris (Gilchrist & Thompson 1908) and other Engraulidae along the coast of the Sofala Bank, western Indian Ocean

The Sofala Bank (16°–21° S) forms a major discontinuity in the gradients of engraulid distribution along the south-eastern African coast. Although the number of species declines southwards, the density and the catches of species associated with higher turbidity increases within the bank, particularly for Thryssa vitrirostris and a few other Thryssa and Stolephorus species. Thryssa vitrirostris forms a single demographic population on the Sofala Bank, as judged from spatial and seasonal catch-rate data from the beach-seine fishery, the largest fishery in Mozambique. The core of the exploitable population seems to migrate towards the coast at the onset of the rainy season (November–February), and then northwards. Our results indicate that reproduction is timed with the rain regime, and length frequency data show that this is also the onset of a fast (L ∞ = 19.0 cm, k = 0.66 y−1) and highly seasonal (C = 0.86) growth. The population is largely comprised of fish up to 2 years of age and the fisheries target mostly pre-spawners (L 50 = 13 cm). The decline in standing stocks offshore, and in the catches of this species by beach-seines, may be related to an excessive exploitation rate (40–60%) brought about by the directed fishery and trawl bycatch.

Abundance and Biology of the Langoustine Metanephrops Mozambicus (Nephropidae) on Deep-Water Trawl Grounds in Eastern South Africa

Abundance trends, population structure, and biology of the langoustine Metanephrops mozambicus (Macpherson, 1990) were investigated, based on commercial logbook information (1988-2010; 49 990 trawls) and biological samples collected off eastern South Africa. A generalized linear model (GLM) framework was used to model variation in catch rates, carapace length (CL), sex ratio, and maturation size. Standardized catch rates were inversely related to fishing effort, gradually increasing between 2002 and 2010, when fishing effort was lower. Catch rates were greatest in trawls made at 300 to 599 m depth and between June and December. Langoustines ranged in size from 17.5 to 72.6 mm CL, and the mean CL decreased with increasing depth. Males predominated in November, but equal numbers of males and females were observed in other months. The smallest egg-bearing female had a CL of 33.5 mm, and L50 was estimated at 49.4 mm, based on the incidence of external eggs. Females with freshly spawned eggs were most abundant in August, and the incidence of egg-bearing remained high until March, where after it declined. Eggs about to hatch occurred mainly in May. Growth parameter estimates (L∞ and K) were 65.5 mm and 0.7 year−1 for sexes combined, based on modal progression and the standard von Bertalanffy growth function, and longevity was estimated to be 3-4 years. Combining analyses of fisheries data with biological samples yielded insights into spatio-temporal population trends, as well as the correlation of reproduction and moulting in M. mozambicus.

Patterns in abundance, population structure and biology of knife prawn Haliporoides triarthrus on deep-water trawl grounds off eastern South Africa

The deep-water trawl fishery along the KwaZulu-Natal coast of South Africa targets several crustacean species, with the knife (or pink) prawn Haliporoides triarthrus contributing most of the catch. Logbook data of fishing effort and catch between 1988 and 2010 were used to assess the distribution and abundance of H. triarthrus on fishing grounds. Generalised linear models were used to quantify the effects of year, month and depth on catch rates. Standardised trends indicated a general decline in abundance between 1990 and 1998, followed by an increase between 2001 and 2008. Catch rates peaked in March, and they were highest between 200 and 499 m depth. Biological samples collected during commercial fishing were used to assess size and sex composition, growth rates and reproductive activity of H. triarthrus. Females became larger than males and mean carapace length (CL) varied by month. The youngest female cohort appeared in November (modal CL of 25 mm), and dissipated after two years (39 mm). Sex ratios were equal for all data combined, but fluctuated by month and CL. Few reproductively active females were recorded. Length-based methods and the standard von Bertalanffy growth function were used to estimate growth parameters (L∞ and K) of females (40.6 mm CL and 1.06 y–1) and males (35.2 mm and 1.27 y–1) respectively. Our findings were compared with information on H. triarthrus from Mozambican waters.

Effects of inconsistent reporting, regulation changes and market demand on abundance indices of sharks caught by pelagic longliners off southern Africa

The assumption of a proportional relationship between catch-per-unit-effort (CPUE) and the abundance of sharks caught by pelagic longliners is tenuous when based on fisher logbooks that report only retained specimens. Nevertheless, commercial logbooks and landings statistics are often the only data available for stock status assessments. Logbook data collected from local and foreign pelagic longline vessels operating in four areas off southern Africa between 2000 and 2015 were used to construct standardized CPUE indices for blue sharks Prionace glauca and shortfin makos Isurus oxyrinchus. Generalized linear mixed models were used to explore the effects of year, month, vessel, fleet and presence of an observer on blue shark and shortfin mako variability. Landing statistics and auxiliary information on the history of the fishery, regulation changes, and market factors were superimposed on the CPUE indices, to test hypotheses that they would influence CPUE trends. Indices in the West and Southwest (Atlantic) areas were elevated for both species, compared to the South and East (Indian Ocean). The scale of year-on-year CPUE increments, up to an order of magnitude for blue sharks, reflected occasional targeting and retention, interspersed with periods where blue sharks were not caught, or discarded and not reported. Increments were smaller for higher value shortfin makos, suggesting that indices were less affected by unreported discarding. CPUE indices and landings of both shark species have increased in recent years, suggesting increased importance as target species. Analysis of logbook data resulted in unreliable indicators of shark abundance, but when trends were interpreted in conjunction with landings data, disaggregated by area and month, and with hindsight of market demand and regulation changes, anomalies could be explained.

Chapter 3. Excel basics

This introductory chapter of CONΣERV IT deals with the following preparatory skills: - How to lose the fear of using a spreadsheet? - How to do basic repetitive calculations? - How to present figures and reports in scientific style? - How to efficiently select and summarize sub-groups of data? Excel basics