Fine-Scale Genomic Divergence in the Amazonian Pirarucu (Arapaima gigas) Highlights the Need for Local Management Strategies

Verba, Julia Tovar, Pereira, Ricardo J., Campos-Silva, João V., Farias, Izeni P., Hrbek, Tomas, Peres, Carlos A. and Hawes, Joseph E. (2026) Fine-Scale Genomic Divergence in the Amazonian Pirarucu (Arapaima gigas) Highlights the Need for Local Management Strategies. Freshwater Biology, 71 (3). ISSN 0046-5070

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Abstract

Freshwater habitats face significant human disturbances globally, impacting food security and ecosystems. Protected areas can mitigate biodiversity loss, but limited data on population connectivity hinders conservation management. This study examines pirarucu (Arapaima gigas), a heavily exploited and threatened Amazonian fish, using genomic data to assess fine-scale genetic structure and its implications for conservation. Samples from 187 pirarucu were collected across 5000 km2 of várzea floodplain in the Juruá River, Western Brazilian Amazon. Using single nucleotide polymorphism (SNP) data, isolation by distance and genetic population structure were tested. Genetic diversity, contemporary migration and effective population size were estimated. Six intergrading genetic clusters were identified, with stronger genetic separation between lakes upstream and downstream of a main town. Effective population sizes were larger upstream, with migration primarily following river flow. Current genetic differentiation was likely exacerbated by overexploitation near urban areas. These findings emphasise the need for tailored conservation strategies addressing genetic differentiation and overfishing impacts, particularly near towns. Management plans should account for fine-scale genetic structure to ensure sustainability. We propose protecting one-third of accessible lakes within 80 km of river sections through Fishing Agreements and better regulating fishing near Carauari to enhance connectivity between lake groups. This research underscores the importance of genetic monitoring and spatial zoning in community-based conservation efforts for pirarucu and other aquatic vertebrate populations.

Item Type:	Article
Additional Information:	Data Availability Statement: The data that support the findings of this study are openly available athttps://figshare.com/s/837a2b4dc80f818c8acd and the codes are avail-able at https://figshare.com/s/5a4b45e7b0 d09ad5d1b0.
Uncontrolled Keywords:	community-based management,fisheries genomics,floodplain connectivity,médio juruá,paiche,single nucleotide polymorphism,aquatic science,sdg 2 - zero hunger,sdg 15 - life on land ,/dk/atira/pure/subjectarea/asjc/1100/1104
Faculty \ School:	Faculty of Science > School of Environmental Sciences University of East Anglia Research Groups/Centres > Theme - ClimateUEA
UEA Research Groups:	Faculty of Science > Research Groups > Environmental Biology Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation
Related URLs:	https://www.scopus.com/pages/publication...
Depositing User:	LivePure Connector
Date Deposited:	13 May 2026 16:02
Last Modified:	14 May 2026 15:14
URI:	https://ueaeprints.uea.ac.uk/id/eprint/103016
DOI:	10.1111/fwb.70187

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