Natacha Nikolic

French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE

Estimating and understanding the ratio between effective population size (Ne) and census population size (Nc) are pivotal in the conservation of large marine pelagic fish species, including bony fish such as tunas and cartilaginous fish such as sharks, given the challenges associated with obtaining accurate estimates of their abundance. The difficu...

Populations of marine top predators have been sharply declining during the past decades, and one‐third of chondrichthyans are currently threatened with extinction. Sustainable management measures and conservation plans of large pelagic sharks require knowledge on population genetic differentiation and demographic connectivity. Here, we present the...

Internship report by Chloé Bellanger, Léonard Ransan, Gaston Rognon (Master's in Bioinformatics and Environmental Genomics Tutored Project – KBIA8AEU). Supervised by: Sarah Maman-Haddad (INRAE Sigenae GenPhySE) & Natacha Nikolic (INRAE, AQUA & CRBE) This tutored project, named DeFIS (Detection of Fauna and Flora: Identification of Species), is par...

Understanding the evolution of wild species is crucial for developing effective population management strategies and predicting their future trajectories. In my doctoral research, we opted for genomics approaches to explore the demographic history of two iconic diadromous fishes: Anguilla anguilla (European eel) and Salmo salar (Atlantic salmon). W...

Humans are regularly cited as the main driver of current biodiversity extinction, but the impact of historic volcanic activity is often overlooked. Pre-human evidence of wildlife abundance and diversity are essential for disentangling anthropogenic impacts from natural events. Réunion Island, with its intense and well-documented volcanic activity,...

To clarify potential trans-oceanic connectivity and variation in the natal origin of albacore tuna (Thunnus alalunga) from the southwest Indian Ocean (SWI) and the southeast Atlantic (SA), lifetime otolith elemental signatures were assessed from 46 adults sampled from Reunion Island, and 26 juveniles(group 2+) sampled from two locations along the A...

Les Organismes Régionaux de Gestion des Pêcheries (ORGP) encouragent l’application de plusieurs méthodes complémentaires pour la gestion durable et l’évaluation de l’état de santé des stocks de grands pélagiques exploités par la pêche commerciale (thons, marlins, bonites) ou la pêche accessoire (requins, mammifères marins). La Commission des Thons...

Marius baroudeur intercontinental se lance dans sa deuxième aventure. Cet ambassadeur de la biodiversité s'en va découvrir les raies et les requins de l'océan Indien.

Description de la phase pilote et la phase d'inventaire du projet IRRAE "Inventaire des raies et des requins autour de La Réunion à partir d’analyses d’ADN environnemental avec une approche écosystémique (élasmobranches et poissons osseux) ".

French: Ce projet se divise en deux volets (Figure A). Le premier volet, appelé étude pilote, avait pour objectif d'optimiser une méthode non invasive, reproductible et standardisée pour réaliser l'inventaire et le suivi des requins autour de La Réunion, tout en complétant cette approche par une analyse écosystémique incluant les autres élasmobran...

Inférence taxonomique ichthyologique à partir de données en ADN environnemental : exemple d'écosystèmes mésophotiques et tropicaux « Le présent rapport constitue un exercice pédagogique qui ne peut en aucun cas engager la responsabilité de l'Entreprise ou du Laboratoire d'accueil » Encadrement : Natacha Nikolic (INRAE, ARBRE) Thierry Mulochau (spéc...

Mayotte is one of the places with one of the richest marine biodiversities of the territory. In order to preserve it and to evolve without altering it, it is important to know it better. Over the past recent years, a new molecular tool is increasingly used to carry out non-invasive to carry out non-invasive biodiversity inventories by detecting...

Albacore tuna (Thunnus alalunga) is an important portion for tuna fishing in all oceans. Over the past decade, commercial catches of albacore tuna have accounted for approximately 6% of world tuna catches. Assessing and managing this heavily exploited resource requires good knowledge of the species' biology and patterns of connectivity between mari...

Several species of rays and sharks evolve in the waters of the Mascarene archipelago (La Réunion, Mauritius, Rodrigues) but they remain little known. To compensate this lack of knowledge, the Mascarene Archipelago Elasmobranch Observatory (MAEO) has been created in 2021 to collect data on elasmobranchs biodiversity and distribution. It combines non...

The blue shark Prionace glauca is a top predator with one of the widest geographic distributions of any shark species. It is classified as Critically Endangered in the Mediterranean Sea, and Near Threatened globally. Previous genetic studies did not reject the null hypothesis of a single global population. The blue shark was proposed as a possible...

The blue shark Prionace glauca is a top predator with one of the widest geographic distributions of any shark species, yet classified as critically endangered in the Mediterranean Sea, and Near Threatened globally. Previous genetic studies did not reject the null hypothesis of a single global population across the worldwide species range. Blue shar...

The aim of this study was to test whether the ichthyological diversity of one natural reserve in Reunion Island (Réserve de l'Etang de Saint-Paul) could be established with a molecular tool, environmental DNA (eDNA). We hence filtrated the water (2L) at 10 different areas around the reserve. For each sampling area, 12 PCR replicas were performed an...

Albacore tuna (Thunnus alalunga) is an important target of tuna fisheries in the Atlantic and Indian Oceans. The commercial catch of albacore is the highest globally among all temperate tuna species, contributing around 6% in weight to global tuna catches over the last decade. The accurate assessment and management of this heavily exploited resourc...

The blue shark Prionace glauca is a cosmopolitan species that inhabits all oceans worldwide except the poles. Several IUCN regional assessments have classified it as Near Threatened, mostly due to overfishing. Previous genetic studies that have used classical genetic markers failed to reject the hypothesis that the species is a single worldwide pop...

The blue shark Prionace glauca is a cosmopolitan species that inhabits all oceans worldwide except the poles. Several IUCN regional assessments have classified it as Near Threatened, mostly due to overfishing. Previous genetic studies that have used classical genetic markers failed to reject the hypothesis that the species is a single worldwide pop...

Efforts to conserve marine mammals are often constrained by uncertainty over their population history. Here, we examine the evolutionary history of a harbour seal (Phoca vitulina) population in the Moray Firth, northeast Scotland using genetic tools and microsatellite markers to explore population change. Previous fine-scale analysis of UK harbour...

The Mascarene petrel (Pseudobulweria aterrima ) is a critically endangered seabird endemic to Reunion Island, with an extremely small population suffering several threats. Fifteen polymorphic microsatellite loci were isolated from this species to analyse genetic diversity, estimate contemporary effective population size, search for evidence of a po...

Albacore tuna (Thunnus alalunga) is a highly economically important species in the western Indian Ocean. However, knowledge of its ecological and nutritional characteristics, essential for proper management of the species, is lacking in the region. The trophodynamics of the Indian Ocean albacore was thus examined using known fatty acid trophic mark...

The trophic ecology of albacore tuna in the western Indian Ocean and adjacent Atlantic waters based on stomach content analysis, using a reconstituted length and weight of prey approach, was studied. From a total of 686 non-empty stomachs, collected between 2001 and 2015 across three biogeographic provinces, we described the diet composition of alb...

Speciation in the ocean could differ from terrestrial environments due to fewer barriers to gene flow. Hence, sympatric speciation might be common, with American and European eel being candidates for exemplifying this. They show disjunct continental distributions on both sides of the Atlantic, but spawn in overlapping regions of the Sargasso Sea fr...

Les résultats présentés dans ce mémoire sont issus de données provenant d’un questionnaire spécialement élaboré pour cette étude et dont 1900 doctorants y ont répondu. Ces résultats révèlent une forte corrélation entre le « bien-être » des doctorant-e-s en France et i) le climat au travail, ii) la facilité de se projeter professionnelle, iii) la...

Dans le cadre du Diplôme Universitaire en Introduction à la Psychologie Positive, l’examen portait sur la question et le traitement thématique suivant : « En vous appuyant sur des éléments théoriques de votre choix, définissez ce que peut être l’optimisme en vous référant à un ou plusieurs auteurs, comment il est possible de le définir, donnez des...

We compiled and analysed logbook data from the French trawl albacore fishery covering the period 1991–2015. The dataset comprised catch and effort data for the French fleet operating in the Bay of Biscay and Celtic Sea, as well as spatiotemporal and gear characteristics. Generalized linear modelling was used to model spatial, seasonal, environmenta...

Numerous species of marine megafauna are at risk of extinction and understanding their genetic population structure and demographic history is essential for their conservation. We used mitochondrial DNA and 18 nuclear microsatellite loci, on the largest genetic dataset compiled to date on Australian humpback dolphins (eight sampling sites, 159 samp...

Albacore is one of the most important commercially harvested species in the world’s oceans. Despite a long history of scientific research, there is no global review or synthesis of knowledge about the species across all oceanic regions. We analysed 613 published studies that report on albacore and summarize the current state of knowledge on biology...

The reproductive biology of albacore tuna, Thunnus alalunga, in the western Indian Ocean was examined through analysis of the sex ratio, spawning season, length-at-maturity (L50), spawning frequency and fecundity. From 2013 to 2015, a total of 923 female and 867 male albacore were sampled. A bias in sex ratio was found in favor of females with fork...

Number of fish per oocyte developmental stage or ovarian phase by 3-cm interval fork length (LF) used for maturity analysis of female albacore tuna in the western Indian Ocean based on histology. In the first criterion, immature fish were viewed as containing the most advanced oocyte stage the primary growth (PG) stage, cortical alveolar (CA) and v...

The GERMON project had several aims i) to understand the populations’ structure between albacore tuna southwest of the Indian Ocean and southeast Atlantic, ii) to determine the origin of juveniles observed in South Africa iii) to improve the understanding of the biology field (Size/Size and Size/Weight; reproduction and feeding area; trophic linkag...

This paper provides information on the length-length (fork-length, FL with pectoral length, PL and first dorsal length, LD1) and length-weight relationships of albacore tuna (Thunnus alalunga) in five regions of the Western Indian Ocean. Data were obtained for a total of 923 female and 867 male albacore, caught by different fishing gears, and sampl...

In this study, we confirmed that DNA control region can be used to identify potential spawning area from pelagic juveniles species. We used the mitochondrial DNA control region to identify tuna juveniles predated by common dolphinfish and sampled in surface waters around Reunion Island. These were skipjack juveniles at an early stage (small length...

Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we us...

The Nephrops fishery in the Bay of Biscay is an important commercial fishery which generates large amounts of discards owing to the use of small mesh trawls. To reduce discards, French trawlers were equipped with a variety of selective devices, from 2005 onwards. This study examines their efficacy using data from the French on-board observer progra...

Understanding and predicting population abundance is a major challenge confronting scientists. Several genetic models have been developed using microsatellite markers to estimate the present and ancestral effective population sizes. However, to get an overview on the evolution of population requires that past fluctuation of population size be trace...

The most comprehensive contribution to our understanding of albacore tuna, Thunnus alalunga, comes from studies in the Pacific and Atlantic Ocean. In the Indian Ocean, there is little information about this species in the literature. In the present paper, we propose a short review on albacore in the Indian Ocean with a particular attention on the b...

This document presents a characterization of the Reunion Island pelagic longline fishery, with a first description of the albacore catches, catch-at-size, and the standardized catch per unit of effort (CPUE) series for the period 1992-2013. The spatial catch and effort analysis revealed the major areas of operation of the fishery, and the identific...

Figure S1. Accuracy of population size estimates from the Mode and the Median as function of the diagonal λ parameter.

Data S1. Genetic diversity at microsatellite markers in a finite population. Data S2. The distribution of the TMRCA in a simple migration model.

Figure S5. Coefficients of variation of effective population size estimates after a transient increase.

Figure S3. Coefficients of variation of effective population size estimates after exponential expansion.

Figure S2. Accuracy of the estimation of the current population size from estimates in the past.

Figure S4. Coefficients of variation of effective population size estimates after a bottleneck.

Understanding and predicting population abundance is a major challenge confronting scientists. Several genetic models have been developed using microsatellite markers to estimate the present and ancestral effective population sizes. However, to get an overview on the evolution of population requires that past fluctuation of population size be trace...

Albacore tuna (Thunnus alalunga) is an economically valuable species worldwide. However information on this species is sparse in some scientific fields according to oceans. This disparity has been revealed from bibliometric analysis. Here, we presented the clustering map and the classification of scientific fields by ocean.

Discards refer to the part of the catch not retained on board during commercial fishing operations, but returned to the sea. The proposed European Union Common Fisheries Policy reform, to be implemented in 2014, sets out a gradual elimination of discards by reducing unwanted catches and ensuring that all catches are landed. To develop successful di...

While the stocking of captive-bred fish has been occurring for decades and has had substantial immediate genetic and evolutionary impacts on wild popula-tions, its long-term consequences have only been weakly investigated. Here, we conducted a spatiotemporal analysis of 1428 Atlantic salmon sampled from 1965 to 2006 in 25 populations throughout Fra...

Because one of the most common problems in fisheries is the definition of management units, we propose in this paper a bibliometric review focusing on the differentiation of Albacore populations, Thunnus alalunga, among and within oceanic regions (Atlantic, Pacific and Indian Oceans, and Mediterranean Sea). This paper is the first step of a current...

This short video details an effective way for collecting albacore (Thunnus alalunga) otoliths from headed.

Tunas are important commercial species that represent a share of about 8 percent of total fish exports. In 2010, the total catch of tuna in three oceans was about 6.6 million tons, 4.3 million tons for the most marketed species, a level roughly stable since 2002 (FAO 2012). Among these tuna species, there are in descending order of capture: skipjac...

The aim of this study was to explore the research trends and the evolution of publications covered on diadromous fish from 1970s to 2010. We conducted a bibliometric analysis on seven patrimonial species: Atlantic salmon (Salmo salar), Brown and Sea trout (Salmon trutta), Allis shad (Alosa alosa), Twaite shad (Alosa fallax), Eel (Anguilla Anguilla)...

The aim of this work was to explore the study covered by the research on diadromous fish.

The aim of this work was to explore the study covered by the research on diadromous fish.

The aim of this work was to explore the study covered by the research on diadromous fish.

Detect past changes in the effective size to better understand the populations conservation status.

We investigate the effects of past changes of the effective population size on the present allelic diversity at a microsatellite marker locus. We first derive the analytical expression of the generating function of the joint probabilities of the time to the Most Recent Common Ancestor for a pair of alleles and of their distance (the difference in a...

Effective population size (Ne) is an important parameter in the conservation of genetic diversity. Comparative studies of empirical data that gauge the relative accuracy of Ne methods are limited, and a better understanding of the limitations and potential of Ne estimators is needed. This paper investigates genetic diversity and Ne in four populati...

Assess the added value of the unsupervised approach given by Artificial Neural Networks (Self-Organizing Map), compared with classical approaches.

General and genetic statistical methods are commonly used to deal with microsatellite data (highly variable neutral genetic markers). In this paper, the self-organizing map (SOM) that belongs to the unsupervised artificial neural networks (ANNs) was applied to analyse the structure of 58 European and two Chinese pig populations (Sus scrofa) includi...

Atlantic salmon Salmo salar microsatellite markers from a large database were analysed and selected with technical, economic and genetic criteria to provide an optimized set of polymorphic DNA markers for the analysis of the genetic diversity and the structure of anadromous Atlantic salmon populations. A set of 37 microsatellite markers was identif...

Ces travaux de thèse se sont intéressés principalement à la diversité génétique et à la taille efficace (Ne) de stocks de poissons sauvages amphihalins migrateurs en danger, le Saumon atlantique (Salmo salar). Pour cela, quatre populations ont été choisies en Europe du Nord (Ecosse) et en Europe du Sud (France) pour leurs différences de structure e...

Pourquoi les populations de saumon de l’Atlantique (Salmo salar) diminuent-elles en Europe? Projet de thèse 2005-2008: Problématique, Objectifs et Réalisation