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Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value


Spatial patterns of genetic variation compared across species provide information about the predictability of genetic diversity in natural populations, and areas requiring conservation measures. Due to their remarkable fish diversity, rivers in Neotropical regions are ideal systems to confront theory with observations and would benefit greatly from such approaches given their increasing vulnerability to anthropogenic pressures. We used SNP data from 18 fish species with contrasting life-history traits, co-sampled across 12 sites in the Maroni– a major river system from the Guiana Shield –, to compare patterns of intraspecific genetic variation and identify their underlying drivers. Analyses of covariance revealed a decrease in genetic diversity as distance from the river outlet increased for 5 of the 18 species, illustrating a pattern commonly observed in riverscapes for species with low-to-medium dispersal abilities. However, the mean within-site genetic diversity was lowest in the two easternmost tributaries of the Upper Maroni and around an urbanized location downstream, indicating the need to address the potential influence of local pressures in these areas, such as gold mining or fishing. Finally, the relative influence of isolation by stream distance, isolation by discontinuous river flow, and isolation by spatial heterogeneity in effective size on pairwise genetic differentiation varied across species. Species with similar dispersal and reproductive guilds did not necessarily display shared patterns of population structure. Increasing the knowledge of specific life history traits and ecological requirements of fish species in these remote areas should help further understand factors that influence their current patterns of genetic variation.

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Fig. 1: Map of French Guiana (inset) and the Upper Maroni River with the 12 sampling locations and their elevation (i.e., altitude, in meters).
Fig. 2: Estimated marginal means (EMM), with 95% confidence intervals (CIs, horizontal bars), for each fish species from the three analyses of covariance showing the relationship between upstream distance (explanatory factor) and the local polymorphism rate (P95), expected heterozygosity (HS), and local genetic isolation (FST.P) as response variables.
Fig. 3: Biplot of the principal component analysis used to describe the relative position of all species according to their patterns of overall genetic variation.

Data availability

Supplementary notes, figures, and tables for this article are provided in MARONI_Appendix1.pdf. Individual genotypes and genetic diversity data used in the current study are accessible through the Dryad repository, as well as sequence information about the 31 additional SNPs used for species C. meionactis. The R command lines used to analyze those data are provided and commented in MARONI_Appendix2.pdf. There are no financial benefits to report.


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We thank all residents and fishermen of villages in the Upper Maroni for their hospitality and support, including local mediators and fishermen who participated in sample collection: Pitoma Mekouanali, Janakale Makiloewala, Kutaka Aïtalé, Kuliwaïkë Menali, Moloko Atiwaïke, Palanaïwa Alikana, Sébastien Amaïpetit, Etulano Yamo, Mones Tokotoko, Marc Pinson, Hervé Tolinga, Kalou, and Alfred Djaba, with a particular thought for Raymond Essimon†. We thank all those involved in the fieldwork: Philippe Cerdan†, Sébastien Le Reun, Brian Senechal and Régis Vigouroux (Hydreco Guyane), Raphael Covain (MNHG), Jean-Luc Baglinière, Damien Fourcy, Catherine Le Penven and Marie Nevoux (UMR DECOD, INRAE). We also thank Anne-Laure Besnard and Thibaut Jousseaume for their help with DNA extraction, quantification, and dilution and we thank Raphael Covain for helping to identify a few ambiguous samples through COI barcoding. We are grateful to Oscar E. Gaggiotti (Scottish Ocean Institute), Olivier Lepais (UMR Biogeco, INRAE), and Ivan Paz-Vinas (EDB, Paul Sabatier University) for their greatly helpful advice throughout this study. Finally, we thank Daniel Ruzzante and two anonymous reviewers for their very constructive feedback about earlier versions of this manuscript.


This study was funded by the Parc Amazonien de Guyane under contract R&D-2003-06 to Pierre-Yves Le Bail and Jean-Marc Roussel, with financial support from the DREAL and the Office de l’Eau de Guyane. The genetic resources studied here were collected in accordance with ethical considerations defined in the convention APA-973-7 in relation with the Nagoya protocol.

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CD contributed to specimen and molecular data collection, designed and ran the analyses, and wrote the manuscript. EJP and SB contributed to the design of analyses and reviewed the manuscript. GL, RR, and RV organized fieldwork, contributed to specimen collection and reviewed the manuscript. J-MR, P-YLB, and SL conceptualized and supervised the research, contributed to specimen collection, contributed to the design of analyses and reviewed the manuscript. All authors contributed critically to the drafts and gave final approval for publication.

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Correspondence to Chrystelle Delord.

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Associate editor: Jane Hughes.

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Delord, C., Petit, E.J., Blanchet, S. et al. Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value. Heredity 131, 1–14 (2023).

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