The spatial and temporal distribution of macroalgal assemblages at 10 sites in the Baie de Ranobe and Baie de Toliara in southwestern Madagascar were investigated during warm (February to March) and cool (July to August) seasons. Algal species were identified and coverage estimated at six habitats between the shore and 15 m depth, based on surveys with 0.5 m x 0.5 m quadrats along transects of 30 m long by 5 m broad. Ninety eight taxa (53 red, 24 green, 21 brown) were identified of which 42 were edible. Species dominance varied by bay and season, with Sargassum latifolium dominating during the warm season, and Hypnea musciformis and Ulva lactuca prevalent during the cool season. Algal cover did not differ significantly between bays, but cover differed significantly between habitats. S. latifolium, U. lactuca, and H. musciformis were prominent on the algal shelf, Ulva reticulata on the inner shelf, and Amansia rhodantha on the outer shelf. Edible seaweed proportions increased during the cool season, particularly at algal and inner-shelf habitats. Generalized Linear Model analysis confirmed significant differences in edible algal cover across habitats and seasons. The potential of sustainably using macroalgae for aquaculture and human consumption in southwestern Madagascar is highlighted.

Size-spectra and taxonomic diversity are important indicators to study the dynamics of communities and to inform conservation in aquatic ecosystems. To date, few studies aimed at modelling the distribution of reef fish diversity at small spatial scales (∼10 km) have been done. Based on a one-year fish sampling using trawl nets, we described and modeled the distribution of fish diversity and their size spectra across various coastal habitats in the Toliara reef system (SW Madagascar). Our data revealed a significant spatial and seasonal change of taxonomic diversity. Beta-diversity was mainly driven by species turnover with up to 75 %, indicating the important conservation value of the sampled sites. Fish size spectra slope emphasized the high dominance of small-sized fish on the sites close to the shoreline indicating their potential nursery zones. By combining environmental and geographic data with the use of the machine learning algorithm Random Forest, we demonstrated the geographic position of sites and associated habitat features were the foremost drivers of alpha-diversity and size spectra patterns (50-64 % of variation). The use of Generalized Dissimilarity Models revealed sediment cover was the main predictor of species turnover patterns (62 % of explained variation), with a rapid increase of species replacement within the first 2 km from the coast. Beyond a confirmation of the role of habitat features on biodiversity, our study emphasized the importance of distance to the shoreline on the distribution of fish diversity across the lagoon. This unexpected driver is discussed in the light of various anthropogenic factors including fisheries and sedimentation.

Madagascar is renowned for its wide range of aquatic organisms, particularly crabs, octopus and fish. The latter are particularly abundant and are sold in a variety of forms (fresh, salted, smoked or dried) and sizes, ranging from large to small individuals. Small dried fish (SDF) are abundant and omnipresent across Malagasy markets. However, they remain poorly understood in terms of their cultural and taxonomic diversity, as well as their nutritional benefits. As an accessible and affordable food source, SDF could help alleviate micronutrient deficiencies, a major issue in Madagascar. In this study, we explored the diversity and nutritional importance of SDF sampled at 16 markets and 12 towns along the National Road 7, which connects Toliara (coast) to Antananarivo (inland). For that purpose, we combined: (i) a socio-economic survey of 112 vendors, (ii) taxonomic (traditional and molecular) analyses to identify the diversity of fish species sold across 131 batches of SDF, and (iii) nutritional and heavy metal analyses of the 10 most popular batches. We assessed their the potential intake of key nutrients and heavy metals from SDF and contribution to Recommended Dietary Allowance (RDA) and maximum Tolerable Weekly Intake (TWI), respectively, considering daily? portions of 10 g for infants (7-11 months) and 20 g for both children (1-3 years) and women of childbearing age (15-50 years). We identified 43,819 individual fish specimens corresponding to 8.1 kg across the 131 batches sampled. These specimens were classified into 233 morpho-species belonging to 110 genera and 61 families, with the Clupeidae, Engraulidae and Poeciliidae families being the most represented in terms of both biomass and abundance. Thirty distinct types of SDF were characterized, of which 19 are commonly consumed by humans, such as the freshwater fish varieties Pirina and Varilava, with appreciation rates of 89% and 83% respectively. SDF are mainly consumed with rice, cassava or maize, and are generally prepared in sauces, fried or mixed with leafy vegetables. Consumption of SDF provides essential nutrients for humans. Across the three population groups, SDF contribute at least 30% of the RDA for selenium, calcium, phosphorus, magnesium and iron. For infants, a 10g portion could meet more than 81% of daily calcium and selenium RDA. Most SDF also provide more than 42% of the RDA for iron and 29% for manganese. For children 1-3 and women of childbearing age, a 20 g portion covers more than 100% of the RDA for calcium, selenium and iron, particularly for the Matsiroky, Kalatambo and Ambotsika types of SDF. In all groups, contributions to potassium, copper and zinc RDA were moderate. Vitamin A was not detected in the ten SDF lots, except for a small trace in Ambotsika. Some types of SDF (Matsiroky) exhibited by significant traces of arsenic, cadmium and lead, requiring moderate consumption. This study enhances our understanding of the potential role of SDF in health and nutritional security and identifies the types most likely to improve nutritional outcomes for the population.Key words: Small dried fish, micronutrients, heavy metals, Recommended Dietary Allowance (RDA), food security, Madagascar

Madagascar harbors a rich marine biodiversity, yet detailed knowledge of its fish species remains limited. Of the 1689 species listed in 2018, only 22% had accessible cytochrome oxidase I (COI) sequences in public databases. In response to growing pressure on fishery resources, this study aims to strengthen biodiversity monitoring tools. Its objectives were to enrich the COI database for Malagasy marine fishes, create the first 12S reference library, and evaluate the taxonomic resolution of different 12S metabarcodes for eDNA analysis, namely MiFish, Teleo1, AcMDB, Ac12S, and 12SF1/R1. An integrated approach combining morphological, molecular, and phylogenetic analyses was applied for specimen identification of fish captured using various types of fishing gear in Toliara and Ranobe Bays from 2018 to 2023. The Malagasy COI database now includes 2146 sequences grouped into 502 Barcode Index Numbers (BINs) from 82 families, with 14 BINs newly added to BOLD (The Barcode of Life Data Systems), and 133 cryptic species. The 12S library comprises 524 sequences representing 446 species from 78 families. Together, the genetic datasets cover 514 species from 84 families, with the most diverse being Labridae, Apogonidae, Gobiidae, Pomacentridae, and Carangidae. However, the two markers show variable taxonomic resolution: 67 species belonging to 35 families were represented solely in the COI dataset, while 10 species from nine families were identified exclusively in the 12S dataset. For 319 species with complete 12S gene sequences associated with COI BINs (Barcode Index Numbers), 12S primer sets were used to evaluate the taxonomic resolution of five 12S metabarcodes. The MiFish marker proved to be the most effective, with an optimal similarity threshold of 98.5%. This study represents a major step forward in documenting and monitoring Madagascar’s marine biodiversity and provides a valuable genetic reference for future environmental DNA (eDNA) applications.

In Madagascar, food insecurity has increased considerably over the last ten years, affecting almost 33% of the population in 2022, or around 8.8 million people. To better understand the contribution of the coastal and inland small-scale fishery (SSF) sector to food supply, we carried out a multidisciplinary study in 2022 as part of the Illumating Hidden Harvest (IHH) worldwide program. We combined analysis of fishery statistics from the Ministry of Fisheries and the Blue Economy (MPEB), a review of previous research studies on small-scale fisheries in Madagascar, and a field survey in seven coastal and inland regions through in-depth interviews with fishers and community members about value chains, livelihoods, and food systems. The results showed that around 242,000 fishers (both men and women) are directly involved in small-scale fisheries in more than 2,500 villages across the country. Fish products form this sector accounted for 59% of national fish production and provided a vital source of nutrients (e.g., proteins, iron, calcium and omega-3s) to the Malagasy population, and more particularly in coastal fishing villages. In economic terms, the sector provided income for nearly 1.5 million people and contributed 6.6% of overall Malagasy exports. As an accessible, healthy, and major source for food, SSF also plays a fundamental role in food and nutritional security across the country through inland market networks. However, the sector faces major challenges, including coastal habitat degradation (e.g., in mangrove and coral reef ecosystems), the likely effects of climate change, and increasing fishing pressure due to population growth and rising domestic and export market demand. Appropriate management strategies and policy are therefore needed to enhance and sustain SSF and minimize post-harvest loss. Promoting the Voluntary Guidelines for Securing Sustainable Small-Scale Fisheries (SSF Guidelines) can support the establishment of inclusive governance frameworks and good resource management practices. Strengthening the commitment and implementation of these Guidelines can therefore help strengthening SSF’s contribution to food systems and, consequently, securing food security and sovereignty and poverty eradication in Madagascar. Key words: coastal communities, fish, poverty, sustainability

Since the pioneering work in 70’, relatively few studies looked at the trophic niches of teleost reef fishes in Madagascar. The lagoon of Toliara (SW Madagascar) is facing threat from the use of mosquito net trawls, often practiced in seagrass and fringing reef habitats. These practices have the potential to induce alterations in the ecological dynamics of the species and in their feeding behaviors. The primary objective of this study is to investigate the dietary preferences and their potential interannual and spatial variation in two teleost fish species frequently found in mosquito net trawl: the rabbitfish Siganus sutor as juveniles and the goby Oplopomus oplopomus as adults. Sampling was conducted at two distinct sites, Ankilibe and Sarodrano, over a two-year period, in December of both 2017 and 2018. The diet composition of these two species was assessed through the examination of their stomach contents and the analysis of stable isotopes (δ13C and δ15N) from a sample of 40 individuals during each field campaign. A total of 22 different food items were identified in the stomach of young S. sutor, with seagrass and benthic mobile prey items being predominant. In adult O. oplopomus, 21 food items were identified, with a high representation of mobile benthic prey and zooplankton. Analyses of stomach contents and stable isotopes revealed significant variations in diet composition across different years and spatial locations. In addition, the results indicated a significant variation in diet according to the size of the individuals studied. The present study is one of the few documenting trophic variations in reef fishes, highlighting some feeding plasticity which could be highly valuable for a rapid adaptation in changing environments.

Publicly available Sentinel-2 satellite imagery was used to map the coral reef systems of Toliara in Madagascar, to standardize methods for monitoring reef health and guiding management decisions. Fieldwork conducted between March and December 2021 used georeferenced photoquadrats to assess benthic structure. The satellite image classification was based on the Object-Based Image Analysis (OBIA) and machine learning algorithms, with k-NN achieving the highest overall accuracy at 83 %, followed by the Bayes classifier (79 %), DT (68 %), RT (67 %) and SVM (42 %). The analysis identified distinct surface areas occupied by seagrass (21 km2), sand (73 km2), rubble (21 km2), coral (10 km2) and algae (6 km2). Comparative assessment with the Allen Coral Atlas underscored the importance of aligning satellite image analysis with in-situ data. The study emphasized the role of selecting appropriate classifier algorithms for precise mapping and stressed the importance of local data collection for accurate habitat mapping. It also showcased the successful application of OBIA with satellite imagery and field data for coral reef mapping, providing insights into habitat health and spatial changes essential for effective conservation.

This study explored the local knowledge, utilisation and consumption of seaweeds (lomotsy in Malagasy) among coastal communities in southwestern Madagascar. Primary data were collected in eight villages, through a survey questionnaire (with a total of 629 respondents) and daily focus group discussions, conducted between May and December 2022. The findings reveal widespread familiarity with seaweed, used predominantly for farming, cleaning fishing equipment, and shading fish during transport. A smaller proportion of respondents (9%) had experimented with seaweed as a food source, notably incorporating species like Kappaphycus alvarezii and Hydroclathrus clathratus into soups and sauces. Despite the coastal inhabitants' recognition of seaweed, the potential of the seaweed resource has not been fully developed, with utilisation restricted mainly to limited traditional practices. An interest in incorporating seaweed into a person's future diet or in seaweed cultivation was expressed by 58% and 45% of the respondents, respectively. This study underscores the importance of enhanced and sustainable use of the seaweed resource in Madagascar's coastal communities, presenting opportunities for economic development and ecological conservation.

Madagascar is a marine biodiversity hotspot. A recent checklist recorded 1689 marine or transitional water fish species, 2.5% being endemic. To date, studies in this country were mostly focused on adult fishes using morphological-based identification. The early life stages of fishes remain largely understudied. The present work aimed to improve knowledge of fish biodiversity in Madagascar by focusing on post-larval reef fishes and settled juveniles in seagrass meadows of southwest Madagascar by using either species identification keys or DNA barcoding. Up to 119,500 individuals were collected, and 1096 individuals were successfully barcoded. We identified 387 species—85 through their morphology (with 58 unsuccessfully sequenced) and 302 by using CO1 barcoding corresponding to 302 barcode index numbers (BINs). This study added 27 new BINs for the BOLD database, 120 new for Madagascar, but only 159 were assigned a precise species name. By referring to the updated checklist of Madagascar fishes, 10 new species were detected for Madagascar. This number will probably increase when all the barcoded specimens become assigned to precise species names. These preliminary findings stress our poor knowledge of marine fish biodiversity in Madagascar and demonstrate the relevance of DNA barcoding in improving this knowledge.

Understanding the interannual effect of various environmental factors on biodiversity distribution is fundamental for developing biological monitoring tools. The interannual variability of environmental factors on presettlement fish assemblages (PFAs) has been so far under investigated, especially in Madagascar. Numerous explanatory variables including local hydro-dynamic conditions recorded during the sampling night, characteristics of the benthic substrate and remotely sensed oceanic conditions (RSOC) were used to explain the spatio-temporal variability of PFAs in southwestern Madagascar. Gradient forest analyses were used to hierarchically classify the effect of these explanatory variables on the PFAs for two sites and during two different recruitment seasons. RSOC variables appeared to better explain the PFAs than the local variable and the characteristics of the benthic substrate. The PFAs caught in water masses with coastal characteristics were better explained than those with open water characteristics. This spatial variability is hypothesised to be linked to differences in feeding conditions among water masses. The gradient forest analyses also highlighted the complexity of predicting PFAs as the species for which abundances were better explained by RSOC variables varied between years. This interannual variability was mainly explained by the interannual variation of chlorophyll a (Chl a) concentration, wind and surface current, with better prediction obtained during the year with high Chl a values associated with high averaged sea surface temperature. These findings suggest the importance of forecasting Chl a concentrations, taking into account the impact of tropical storms and climate variability in order to predict PFAs in the future.

In order to provide biological evidence of the real impact of mosquito seine nets in southwestern Madagascar, an efficient procedure for determining the size at maturity of small-sized tropical fishes was developed. The fishes caught by two small-scale fishermen were studied between October 2017 and April 2018. One catch per day was analyzed three days per month during the full-moon period. In the laboratory, fishes were all sorted by morphospecies, photographed and measured. One individual per morphospecies was selected for being identified using CO1 DNA barcoding. A total of 34,051 individual fishes belonging to 144 DNA bacoded species from 48 families was obtained from 42 samples, 467 individuals from 22 morphospecies that had not been successfully barcoded were excluded from the analyses. The macroscopic observations of 8,143 individuals between 0.7 and 10 cm SL indicated the proportion of individuals with clearly observable gonads was 15% only.Among the 144 species identified via DNA barcoding, 83 consisted of individuals that were all without clearly observable gonads, seven of individuals that were all with clearly observable gonads and 54 included of individuals with and without clearly observable gonads. As the determination of L-50 using logistic general linear models failed for most species, the minimum size at maturity was retained to determine the proportion of juveniles and adults for these 54 species. Compared to the data available in FishBase, the minimum size at maturity appears more adequate to discrimine juvenile from adult fish of small-sized tropical species.

Post-larval prediction is important, as post-larval supply allows us to understand juvenile fish populations. No previous studies have predicted post-larval fish species richness and abundance combining molecular tools, machine learning, and past-days remotely sensed oceanic conditions (RSOCs) obtained in the days just prior to sampling at different scales. Previous studies aimed at modeling species richness and abundance of marine fishes have mainly used environmental variables recorded locally during sampling and have merely focused on juvenile and adult fishes due to the difficulty of obtaining accurate species richness estimates for post-larvae. The present work predicted post-larval species richness (identified using DNA barcoding) and abundance at 2 coastal sites in SW Madagascar using random forest (RF) models. RFs were fitted using combinations of local variables and RSOCs at a small-scale (8 d prior to fish sampling in a 50 × 120 km2 area), meso-scale (16 d prior; 100 × 200 km2), and large-scale (24 d prior; 200 × 300 km2). RF models combining local and small-scale RSOC variables predicted species richness and abundance best, with accuracy around 70 and 60%, respectively. We observed a small variation of RF model performance in predicting species richness and abundance among all sites, highlighting the consistency of the predictive RF model. Moreover, partial dependence plots showed that high species richness and abundance were predicted for sea surface temperatures <27.0°C and chlorophyll a concentrations <0.22 mg m-3. With respect to temporal changes, these thresholds were solely observed from November to December. Our results suggest that, in SW Madagascar, species richness and abundance of post-larval fish may only be predicted prior to the ecological impacts of tropical storms on larval settlement success.

Les écosystèmes marins qui fournissent de multiples services écosystémiques indispensables au bien-être de l’humanité sont actuellement menacés par la surexploitation des ressources et l’utilisation d’engins destructifs. Ceci conduit à une perte à l’échelle globale de 20% des mangroves, 19% des récifs coralliens et 110 km2 par an des herbiers. Les habitats côtiers qui soutiennent jusqu’à 20% de la production globale de la pêche sont les plus touchés, notamment dans les pays les moins avancés comme Madagascar. Dans ce pays, 87% des écosystèmes récifaux sont menacés, notamment dans le sud-ouest où les petits pêcheurs utilisent des engins prohibés capturant les juvéniles. Une meilleure connaissance de l’écologie des jeunes poissons est donc un point clé pour la mise en place des mesures de gestion efficaces et robustes. D’où l’objet de ce présent travail centré sur les jeunes stades de développement des poissons, identifiés en utilisant le barcoding ADN. Les identifications à l’espèce ont permis de prédire l’approvisionnement en post-larves et de découvrir la variabilité du recrutement en juvéniles qui semble liée à l’altération des apports en post-larves. Au total, 387 espèces ont été observées avec 9 nouvelles espèces pour Madagascar. L’intérêt et les limites du barcoding ADN sont largement discutés (chapitre 1). L’approvisionnement en post-larves a été mieux prédit par les conditions océaniques obtenues par télédétection avec une précision de 60% pour la richesse et 50% pour l’abondance. Pourtant, la performance des modèles pour prédire l’abondance semble influencée par les caractéristiques des masses d'eau qui sont différentes entre les deux sites, tandis que la performance pour prédire la richesse parait similaire entre ces deux sites (chapitre 2). Les conditions océaniques obtenues par télédétection expliquent mieux les assemblages de post-larves. Pourtant, ces conditions océaniques structurent davantage les assemblages de post-larves dans les masses d'eau présentant des caractéristiques d’eaux côtières que ceux dans les eaux présentant des caractéristiques océaniques (chapitre 3). La période de recrutement et les assemblages de juvéniles diffèrent entre les années. Ces variabilités interannuelles ont été aussi observées dans l’approvisionnement en post-larves qui semble conditionné par les variations des conditions océaniques. Ce qui suggère que les altérations des apports en post-larves influencent la distribution temporelle des juvéniles (chapitre 4). Le cas du recrutement des juvéniles de Siganidae, qui semble être fortement en lien avec les apports en post-larves, est développé dans la discussion générale. De même, la localisation des zones de nourriceries a permis de proposer des mesures de gestion tenant compte du contexte local qui sont aussi discutées.

In the seagrass zone of Toliara (southwestern Madagascar), the local small-scale fishermen deploy seine mosquito nets that likely affect the structure of seagrass meadow systems and associated fishes. Nevertheless, the responses of these associated fishes communities to the intense marine resource exploitation using such destructive fishing gear remain unknown for the WIO region, especially in southwestern Madagascar. The present study aims to evaluate the trophic diversity of fishes living in seagrass beds and to assess their trophic plasticity. More specifically, we compared the diet of two dominant species in the catches of local fishermen (the rabbitfish Siganus sutor and the goby Oplopomus oplopomus) and we evaluated the potential variation in their trophic ecology. The sampling of fishes was achieved by collecting the catches of two small-scale fishermen using seine mosquito nets off Ankilibe only in December 2017, off Ankilibe and Sarodrano in December 2018. This sampling strategy allowed us to make spatial and temporal comparisons. In order to assess the diet of these two dominant fish species, stomach content analyses were performed on 40 specimens/species/village/year. Using a binocular microscope, animal preys were identified at class level and assigned to planktonic or benthic compartment. Plant items were classified as either phytoplankton, fragments of algae, or seagrass. The trophic niche of each fish population was quantified in two ways: as a percentage of occurrence and as a mean percent composition of each item in the gut content. The rabbitfish has gut filled by 50% of detritus, 40% of fragments of seagrass, and 10% of phytoplankton. The diet of the goby was more diversified and composed of 40% of detritus, 25% of copepods, 30% of gastropods (body or just operculum) and 5% of ostracods. The results of isotopic analyses (in progress), will improve our knowledge of the diet of these two fish species, which are decreasing progressively in small-scale fishermen catches due to heavy fishing pressure.

An annotated checklist of the fish species of the Madagascar EEZ (southwestern Indian Ocean) comprises a total of 1,798 species in 247 families. 158 species are recorded from Madagascar for the first time. The majority of the species is autochthonous; 28 species have been introduced, mainly in freshwater habitats. The fish fauna is mostly marine (95.4% of the total number of native fish species), with the Gobiidae, Labridae, Serranidae, Pomacentridae and Apogonidae being the families with most representatives; among the 90 native freshwater fish species (adults mainly occurring in freshwater), the Cichlidae are the dominating family, but there are also two endemic families, the Bedotiidae (16 species) and Anchariidae (6 species). The fish fauna at Madagascar is typical for offshore, high islands in the southwestern Indian Ocean. Zoogeographically, the main element of the marine fish fauna of Madagascar consists of widespread tropical Indo-Pacific species (978 species, 58.3% of the total native marine species). A total of 13 species (3.3%) are found worldwide, either circumtropical or circumtropical including warm temperate zones. A total of 215 species (12.8%) are found worldwide, either circumtropical or circumtropical including warm temperate zones. An additional 453 species (27.0%) are Indian Ocean endemics, including 233 western Indian Ocean endemics (13.9%), 73 southwestern Indian Ocean endemics (4.4%), 16 species endemic to Madagascar and Mascarenes (1.0%), 4 species endemic to Madagascar and Comoros (0.2%), 3 species endemic to Madagascar and Madagascar Ridge (0.2%), and 37 marine species endemic to Madagascar (2.2%). Most of the autochthonous freshwater fishes are endemic to Madagascar (87 species, 96.7% of the native freshwater species).

The temporal structure of reef fish post-larvae assemblages were examined at two sites on the southwest coast of Madagascar: Nosy Ve Island, off Anakao, where every forms of fishing have been banned since 1999, and the north of the Great Barrier Reef of Toliara which has been impacted by overfishing for years. Fish post-larvae were collected using light traps during five nights of the new moon periods from August 2013 to February 2014. A total of 34 and 36 families grouping 95 and 101 different morphospecies were collected from the two sites respectively. At both sites, fish post-larvae were more abundant and diverse from December to January. Significant differences in the assemblage structure of reef fish post-larvae were detected between seasons due to the Pomacentridae (Pomachromis richardsoni and Parma spp1), Mullidae (Parupeneus spp), Siganidae (Siganus sutor) and Blenniidae (Istiblennius edentulus). The relationship between fish post-larval assemblage and abiotic factors differed between the two sites. At the Anakao site, temperature and water transparency explained 26.4% of the variability observed in fish post-larvae assemblages when at the Great Barrier Reef site, these two variables and salinity explained 20.7% only. All these results are discussed in the context of the development of post-larvae capture and culture for ornamental fish market and food fish rearing.