Integrating eDNA-inferred species diversity and amplicon-based phylogenetic alpha diversity to assess fish assemblages in the Araguaia River

Integrating eDNA-inferred species diversity and amplicon-based phylogenetic alpha diversity to assess fish assemblages in the Araguaia River | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL This is a preprint and has not been peer reviewed. Data may be preliminary. 3 January 2026 V1 Latest version Share on Integrating eDNA-inferred species diversity and amplicon-based phylogenetic alpha diversity to assess fish assemblages in the Araguaia River Authors : Diego Ortiz da Silva 0000-0003-2267-3727 [email protected] , Jocilaine Santos de Jesus 0009-0005-0167-5469 , Cíntia Pelegrineti Targueta 0000-0002-1964-8101 , Marcio Pie , Rhewter Nunes , José Alexandre Diniz-Filho 0000-0002-0967-9684 , Thannya Nascimento Soares , Fabrício Barreto Teresa , Daniel Carvalho , João Nabout 0000-0001-9102-3627 , Priscilla de Carvalho , and Mariana Pires de Campos Telles 0000-0002-9023-0007 Authors Info & Affiliations https://doi.org/10.22541/au.176744172.24812458/v1 232 views 100 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Environmental DNA (eDNA) is an efficient, non-invasive approach for monitoring aquatic biodiversity, enabling species detection from genetic material released into the environment and offering greater scalability than traditional surveys. The Araguaia River basin, a biodiversity-rich system in Central Brazil within the Cerrado biome, has been increasingly exposed to anthropogenic pressures. Here, we applied eDNA metabarcoding to investigate fish taxonomic and phylogenetic alpha diversity, as well as phylogenetic community structure, in floodplain lakes along the middle Araguaia River. Water samples (1,500 mL per site) were collected from 132 lakes during the flood season (February 2023), filtered through 0.45 µm membranes, and processed for DNA extraction. The 12S rRNA gene was amplified using MiFish primers and sequenced on an Illumina MiSeq platform. Amplicon sequence variants (ASVs) were inferred using DADA2, taxonomically assigned with the MIDORI2 database, and used to reconstruct an amplicon-based phylogeny under a maximum-likelihood framework. A total of 1,402 fish ASVs were detected, of which 384 were assigned to species level, including 67 species previously recorded for the Araguaia basin and 45 not listed in occurrence databases. Assemblages were dominated by Characiformes, followed by Cichliformes. Species alpha diversity, estimated using Shannon and Simpson indices, exhibited pronounced spatial heterogeneity, with higher values in the southern portion of the study area. Phylogenetic diversity (Faith’s PD) showed a similar spatial pattern and was strongly correlated with species richness (p < 0.001). Phylogenetic structure was predominantly random across lakes, although some communities showed significant clustering or overdispersion. Net Relatedness Index values indicated phylogenetic clustering at deeper evolutionary levels, whereas Nearest Taxon Index values were centered around zero, suggesting variable assembly processes near the phylogenetic tips. Variance partitioning revealed that spatial processes related to hydrological connectivity and geographic structure explained most variation in taxonomic and phylogenetic diversity, while local environmental variables had limited influence. Integrating eDNA-inferred species diversity and amplicon-based phylogenetic alpha diversity to assess fish assemblages in the Araguaia River Diego Ortiz da Silva 1 Jocilaine Santos de Jesus 1 Cíntia Pelegrineti Targueta 1,2 ; Marcio Roberto Pie 4 ; Rhewter Nunes 1,5 ; José Alexandre Felizola Diniz-Filho 6 , Thannya Nascimento Soares 1 ; Fabrício Barreto Teresa 7 ; Daniel Cardoso Carvalho 8 , João Carlos Nabout 7 , Priscilla de Carvalho 6 ; Mariana Pires de Campos Telles 1,9 1 Laboratório de Genética e Biodiversidade (LGBio) – Universidade Federal de Goiás, Goiânia, Goiás, Brasil. 2 Núcleo de Estudos e Pesquisas Ambientais e Limnológicas, Faculdade UnB Planaltina, Universidade de Brasília (UnB), 73345-010, Planaltina, Distrito Federal, Brasil. 3 Hospital Veterinário, Escola de Veterinária e Zootecnia, UFG, Goiânia, GO, Brasil. 4 Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, Brasil. 5 Laboratório de Bioinformática e Biodiversidade (LBB) - Instituto Acadêmico de Saúde e Ciências Biológicas, Universidade Estadual de Goiás, Iporá, GO, Brasil. 6 Departamento de Ecologia, ICB, UFG, Goiânia, Goiás, Brasil. 7 Campus Central, Universidade Estadual de Goiás, Universidade Estadual de Goiás (UEG), Anápolis, GO, Brasil 8 Laboratório de Genética da Conservação, Programa de Pós-Graduação em Biodiversidade e Meio Ambiente - PUC Minas, MG, Brasil 9 Faculdade de Ciências Médicas e da Vida - Pontifícia Universidade Católica de Goiás, Goiânia, GO, Brasil. Corresponding author: Diego Ortiz da Silva. Av. Esperança, s/n - Chácaras de Recreio Samambaia, Goiânia - GO, 74690-900. Laboratório de Genética e Biodiversidade (LGBio) – Universidade Federal de Goiás, Goiânia, Goiás, Brasil. Email: [email protected] . Supplementary Material File (alpha_diversity_araguaia_river.docx) Download 1.63 MB File (table1.docx) Download 1.61 MB Information & Authors Information Version history V1 Version 1 03 January 2026 Copyright This work is licensed under a Non Exclusive No Reuse License. Keywords community ecology freshwater molecular genetics vertebrate Authors Affiliations Diego Ortiz da Silva 0000-0003-2267-3727 [email protected] Universidade Federal de Goias View all articles by this author Jocilaine Santos de Jesus 0009-0005-0167-5469 Universidade de Brasilia View all articles by this author Cíntia Pelegrineti Targueta 0000-0002-1964-8101 Universidade Federal de Goiás View all articles by this author Marcio Pie Universidade Federal do Paraná View all articles by this author Rhewter Nunes Universidade Estadual de Goiás - Unidade Universitária de Iporá View all articles by this author José Alexandre Diniz-Filho 0000-0002-0967-9684 Universidade Federal de Goiás - Câmpus Samambaia View all articles by this author Thannya Nascimento Soares Universidade Federal de Goiás View all articles by this author Fabrício Barreto Teresa Universidade Estadual de Goiás View all articles by this author Daniel Carvalho Pontifícia Universidade Católica de Minas Gerais View all articles by this author João Nabout 0000-0001-9102-3627 Universidade Estadual de Goiás View all articles by this author Priscilla de Carvalho Universidade Federal de Goiás View all articles by this author Mariana Pires de Campos Telles 0000-0002-9023-0007 Pontifícia Universidade Católica de Goiás View all articles by this author Metrics & Citations Metrics Article Usage 232 views 100 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Diego Ortiz da Silva, Jocilaine Santos de Jesus, Cíntia Pelegrineti Targueta, et al. Integrating eDNA-inferred species diversity and amplicon-based phylogenetic alpha diversity to assess fish assemblages in the Araguaia River. Authorea . 03 January 2026. DOI: https://doi.org/10.22541/au.176744172.24812458/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . 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