Trade-off between morphological convergence and opportunistic diet behavior in fish hybrid zone

<p>Abstract</p> <p>Background</p> <p>The invasive <it>Chondrostoma nasus nasus </it>has colonized part of the distribution area of the protected endemic species <it>Chondrostoma toxostoma toxostoma</it>. This hybrid zone is a complex system where multiple effects such as inter-species competition, bi-directional introgression, strong environmental pressure and so on are combined. Why do sympatric <it>Chondrostoma </it>fish present a unidirectional change in body shape? Is this the result of inter-species interactions and/or a response to environmental effects or the result of trade-offs? Studies focusing on the understanding of a trade-off between multiple parameters are still rare. Although this has previously been done for Cichlid species flock and for Darwin finches, where mouth or beak morphology were coupled to diet and genetic identification, no similar studies have been done for a fish hybrid zone in a river. We tested the correlation between morphology (body and mouth morphology), diet (stable carbon and nitrogen isotopes) and genomic combinations in different allopatric and sympatric populations for a global data set of 1330 specimens. To separate the species interaction effect from the environmental effect in sympatry, we distinguished two data sets: the first one was obtained from a highly regulated part of the river and the second was obtained from specimens coming from the less regulated part.</p> <p>Results</p> <p>The distribution of the hybrid combinations was different in the two part of the sympatric zone, whereas all the specimens presented similar overall changes in body shape and in mouth morphology. Sympatric specimens were also characterized by a larger diet behavior variance than reference populations, characteristic of an opportunistic diet. No correlation was established between the body shape (or mouth deformation) and the stable isotope signature.</p> <p>Conclusion</p> <p>The Durance River is an untamed Mediterranean river despite the presence of numerous dams that split the river from upstream to downstream. The sympatric effect on morphology and the large diet behavior range can be explained by a tendency toward an opportunistic behavior of the sympatric specimens. Indeed, the similar response of the two species and their hybrids implied an adaptation that could be defined as an alternative trade-off that underline the importance of epigenetics mechanisms for potential success in a novel environment.</p

Emmanuel Corse, Le «barcoding alimentaire» : développement d’un nouvel outil d’écologie moléculaire pour les milieux d’eau douce. Exemple au travers de l’étude de la zone hybride Durance entre les deux Chondrostomes français, Thèse soutenue le 29 septembre 2010 à l’université de Provence

Corse Emmanuel. Emmanuel Corse, Le «barcoding alimentaire» : développement d’un nouvel outil d’écologie moléculaire pour les milieux d’eau douce. Exemple au travers de l’étude de la zone hybride Durance entre les deux Chondrostomes français, Thèse soutenue le 29 septembre 2010 à l’université de Provence. In: Ecologia mediterranea, tome 36 n°2, 2010. p. 122

Emmanuel Corse, Le «barcoding alimentaire» : développement d’un nouvel outil d’écologie moléculaire pour les milieux d’eau douce. Exemple au travers de l’étude de la zone hybride Durance entre les deux Chondrostomes français, Thèse soutenue le 29 septembre 2010 à l’université de Provence

Corse Emmanuel. Emmanuel Corse, Le «barcoding alimentaire» : développement d’un nouvel outil d’écologie moléculaire pour les milieux d’eau douce. Exemple au travers de l’étude de la zone hybride Durance entre les deux Chondrostomes français, Thèse soutenue le 29 septembre 2010 à l’université de Provence. In: Ecologia mediterranea, tome 36 n°2, 2010. p. 122

Inventaire de la diversité ichtyologique de l’étang de Saint-Paul à l’aide d’un outil génétique (ADNe).

L’objectif de ce projet était de i) tester cette approche non invasive, reproductible et standardiséepour effectuer le suivi ichtyologique dans la Réserve Naturelle de l’Étang de Saint-Paul (RNNESP)et ii) d’en évaluer le potentiel et les limites afin d’identifier les pistes et les actions dedéveloppement possibles. À ce jour, ces approches n’ont jamais été utilisées à La Réunion

Le "barcoding alimentaire" (développement d'un nouvel outil d'écologie moléculaire pour les milieux d'eau douce)

Le principal objet de cette thèse a été d'étudier les régimes alimentaires des chondrostomes dans la Durance et de les comparer à d'autres populations évoluant dans des rivières non aménagées. Pour cela nous avons échantilloné des populations provenant de zones allopatriques nous permettant de définir des comportements alimentaires de référence. Afin de dissocier l'effet de l'aménagement de la rivière de l'effet sympatrie dans la zone Durance, nous avons échantilloné une seconde zone hybride considérée comme faiblement aménagée, l'Ardèche. L'acquisition d'une information fine de la nature des proies ingérées étant complexe à partir des techniques non invasives traditionnellement utilisées (isotopes stables), nous avons développé une méthode d'écologie moléculaire non invasive, basée sur la détermination de l'ADN présent dans les excréments du prédateur. Cette méthode repose sur des PCR spécifiques (réaction de polymérisation en chaîne) permettant de détecter 34 clades à hautes informations écologiques ("Clade Ecologique").. Les analyses des résultats nous ont permis de valider le "barcoding alimentaire" et ont montré que l'aménagement de la Durance affectait les populations de chondrostomes selon plusieurs modalités d'actions. Les résultats ont montré également que le Cnn était plus sensible par l'aménagement de la rivière que le Ctt. A l'issue de ce travail, nous proposons donc que le Cnn soit considéré comme une espèce sentinelle en vue des suivis de l'impact du débit régulé sur les communautés biologiques en Durance. En outre, cette thèse a permis le développement d'une méthode non invasive en écologie. Elaborée dans le but d'optimiser son accessibilité autant financière que technique tout en ayant permis de définir finement le comportement alimentaire des chondrostomes à travers plusieurs zones d'études, le barcoding alimentaire apparait comme une méthode très prometteuse en écologie des eaux douces.Hydroelectric settlement could lead to affect trophic resources availability for sh populations, mainly for benthos feeder species. Previous works demonstrated that in the Durance River (an highly man-impacted river), many morphological and ecological characteristics were moved in compare to reference station's populations for the two benthic feeders species, Chondrostoma toxosroma toxostoma (Ctt, endemic species) and Chondrostoma nasus nasus (Cnn, introduced species) and their hybrids. To better understand which environmental factors are responsible of these differences, we studied the diet behavior of the two Chondrostoma species. The main goal of this thesis was so to study the diet behavior of the two Chondrostoma species and their hybrids in the Durance River and to compare with i) the diet behavior of the species in allopatric stations, ii) the diet behavior of the species sampled in another hybrid zone (Ardeche River) which is less disturbed. This approach allowed distinguishing the effects played by the River anthropisation to the effect played by the species interactions. In the rst part of this work we used the stable isotope analysis (SIA) of carbon and nitrogen on several Chondrostoms populations. This approach was performed to determine the inter and intra populations variability of the diet behavior in different environments (allopatry/sympatry). However, the acquisition of taxonomic determination about ingested preys using the SIA method is difficult. To obtain this qualitative information we developed a non-invasive molecular methodology, based on DNA determination from feces. This method is based on clade speci c PCR allowing the detection of 34 taxa, with high ecological relevant information (called Ecological Clade). In order to highlights some suspected links between morphology and diet, we also studied the body and the lower lip morphologies of the Chondrostoms samples. The obtained results allowed to conclude that environmental conditions (regulated flow and substrate clogging) of the Durance River affected Chondrostomes through different process. For example we observed that Cnn are more sensitive to environmental conditions of Durance than Ctt. In this way, Cnn could be considered as a sentinel species to study impacts of a regulated river on freshwater community. More than the biological conclusions we obtained on the Chondrostoms complex, we demonstrated the usefulness of the non-invasive method we developed. This method, designed with the concern to reduce nancial and technical costs compared to other protocols (using cloning step or systematic sequencing of PCR products) could have lots of applications in ecology. Furthermore, because we take into account a high taxonomic ranks (family or order), allowing to describe diet behavior of Chondrostoms in different environments, the alimentary bar coding is not constrained to our studied sites. Thus, this method appears as a promising tool to study trophics interactions on freshwater environment.AIX-MARSEILLE1-BU Sci.St Charles (130552104) / SudocSudocFranceF

Ichtyological diversity in a tropical nature reserve (Etang de Saint-Paul, Réunion Island) from environmental DNA (eDNA) metabarcoding

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 and the identification of fish species was carried out by metabarcoding through a primer over a mitochondrial region (12S). This study showed the importance of reference sequencing databases as well as improvements through phylogenetic analyses. This first fish study by eDNA in La Réunion also revealed the coherence of the distribution of species and their habitat.See the Poster in Suppl. material 1.Collection : 1st DNAQUA International Conference - poster session

Etude du régime alimentaire de l'apron du Rhône dans le Verdon

International audienc

Data from: Improving PCR detection of prey in molecular diet studies: importance of group-specific primer set selection and extraction protocol performances

While morphological identification of prey remains in feces of predators is the method most commonly used to study trophic interactions, many studies indicate that this method does not detect all consumed prey. Polymerase Chain Reaction based methods are increasingly used to detect prey DNA in the predator food bolus and have proved themselves efficient, with high accuracy. When studying complex diet samples, the extraction of total DNA is a critical step, as PCR inhibitors may be co-extracted. Another critical step consist in carefully select suitable group-specific primer sets that should only amplify prey DNA from the targeted taxon. In this study, the food boluses of five Rattus rattus and seven Rattus exulans were analyzed using both morphological and molecular methods. We tested a panel of 30 PCR specific primer sets targeting Bird, Invertebrate and Plant sequences and four were finally selected to be use as group-specific primer pairs in PCR protocols. The performances of four DNA extraction protocols (QIAamp DNA stool mini kit, DNeasy mericon food kit and two CTAB-based methods) were compared using four variables: DNA concentration, A260/A280 absorbance ratio, food compartment analyzed (stomach or fecal contents), total number of prey specific PCR amplification per sample. Our results clearly indicate that the A260/A280 absorbance ratio, which varies between extraction protocols, is positively correlated to the number of PCR amplifications of each prey taxon. We recommend using the DNeasy mericon food kit (Qiagen), which yielded results very similar to those achieved with the morphological approach

VTAM: A robust pipeline for validating metabarcoding data using optimized parameters based on internal controls

Metabarcoding has become a powerful approach to study biodiversity from environmental samples but it is still prone to some pitfalls. Several papers have called for good practice in study design, data production and analyses to ensure repeatability and comparability between studies. Notably, the importance of mock community samples, negative controls, and replicates is frequently highlighted (Alberdi et al. 2018, O'Rourke et al. 2020). However, their use in bioinformatics pipelines is often limited to post hoc verification of expectations by the user. Indeed, one of the biggest challenges in metabarcoding analyses is to take into account the trade-off between false positive (FP) and false negative (FN) occurrences. We thus developed the VTAM (Validation and Taxonomic Assignation of Metabarcoding data) pipeline, which is the first tool to use explicitly the negative control and mock samples to find optimal parameters to minimize false positive and negative occurrences. In addition, VTAM addresses all known technical error types including tag-jumps, repeatability among replicates, and also it is able to integrate more than one overlapping markers to further minimize false negative occurrences.In order to evaluate VTAM, we compared it with two other pipelines: a pipeline based on DADA2 (Callahan et al. 2016) and LULU (Frøslev et al. 2017), and a pipeline based on OBITools3 (Boyer et al. 2016) and metabaR (Zinger et al. 2020). Two datasets from fish and bat diet studies were analysed with the three different pipelines. Based on mock and negative samples, we demonstrate that VTAM showed the best precision for mock samples in both datasets, while specificity in negative controls were comparable among the three pipelines (Fig. 1).VTAM therefore constitutes a complete pipeline to filter and validate metabarcoding data, from raw FASTQ data to Amplicon Sequence Variant tables with taxonomic assignments. Our pipeline aggregates a series of features rarely grouped in a single pipeline and performs a non-arbitrary parameter optimization based on internal control samples to generate conservative but informative metabarcoding datasets. We believe VTAM provides a very valuable tool for the validation of metabarcoding data, which is essential for conducting robust analyses of biodiversity