DNA barcoding highlights taxonomic uncertainties and cryptic lineages of São Francisco River basin fishes
Abstract The São Francisco River (SFR) is a watershed of extreme socioeconomic importance and rich biodiversity, notable for its unique ichthyofauna and high levels of endemism. However, human interference threatens several fish species, putting them at risk of extinction. Genetic knowledge about th...
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Sociedade Brasileira de Ictiologia
2025-01-01
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| Series: | Neotropical Ichthyology |
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| Online Access: | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1679-62252024000400206&lng=en&tlng=en |
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| author | Denis Bruno Santos Marques Nunes Alany Itala Pontes Leandro Ferreira dos Santos Leonardo Luís Calado Luciano Freitas Barros-Neto Silvia Yasmin Lustosa-Costa Sergio Maia Queiroz Lima Uedson Pereira Jacobina |
| author_facet | Denis Bruno Santos Marques Nunes Alany Itala Pontes Leandro Ferreira dos Santos Leonardo Luís Calado Luciano Freitas Barros-Neto Silvia Yasmin Lustosa-Costa Sergio Maia Queiroz Lima Uedson Pereira Jacobina |
| author_sort | Denis Bruno Santos Marques Nunes |
| collection | DOAJ |
| description | Abstract The São Francisco River (SFR) is a watershed of extreme socioeconomic importance and rich biodiversity, notable for its unique ichthyofauna and high levels of endemism. However, human interference threatens several fish species, putting them at risk of extinction. Genetic knowledge about the ichthyofauna of the SFR is still lacking. To address this gap, we used DNA barcoding of 94 taxa from six orders, 32 families, and 73 genera, sourced from the BOLD Systems platform and samples in the middle and lower SFR regions. Analyses revealed distinct patterns of genetic divergence. The BOLD platform identified 111 bins, 75 as MATCH, 32 as SPLIT, two as MERGE and two MIXTURE. We detected taxonomic confusions in the genera Astyanax and Psalidodon. Fourteen taxa exhibited high cryptic diversity, corroborated by lineage delimitation methods (BINs, ASAP, and GMYC). A significant portion of this cryptic diversity (eight lineages) is concentrated in the upper SFR, a region with tectonic faults, geomorphological reactivations, and the transposition of another basin, which likely contributed to genetically divergent lineages. Our data fill shortfalls in Linnaean and Darwinian knowledge about the SFR ichthyofauna, considering its hydrogeological formation. We hope this information will serve as a foundation for future management and conservation plans for this important ichthyofauna. |
| format | Article |
| id | doaj-art-2ede40fb1e2a47f2a2bee41eea4e6968 |
| institution | Kabale University |
| issn | 1982-0224 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Sociedade Brasileira de Ictiologia |
| record_format | Article |
| series | Neotropical Ichthyology |
| spelling | doaj-art-2ede40fb1e2a47f2a2bee41eea4e69682025-01-21T07:39:29ZengSociedade Brasileira de IctiologiaNeotropical Ichthyology1982-02242025-01-0122410.1590/1982-0224-2024-0059DNA barcoding highlights taxonomic uncertainties and cryptic lineages of São Francisco River basin fishesDenis Bruno Santos Marques Nuneshttps://orcid.org/0000-0003-2821-4839Alany Itala Ponteshttps://orcid.org/0000-0002-9457-1386Leandro Ferreira dos Santoshttps://orcid.org/0000-0002-9683-4602Leonardo Luís Caladohttps://orcid.org/0000-0003-2328-5267Luciano Freitas Barros-Netohttps://orcid.org/0000-0001-7568-6631Silvia Yasmin Lustosa-Costahttps://orcid.org/0000-0003-2405-7039Sergio Maia Queiroz Limahttps://orcid.org/0000-0001-9365-4879Uedson Pereira Jacobinahttps://orcid.org/0000-0002-5595-9812Abstract The São Francisco River (SFR) is a watershed of extreme socioeconomic importance and rich biodiversity, notable for its unique ichthyofauna and high levels of endemism. However, human interference threatens several fish species, putting them at risk of extinction. Genetic knowledge about the ichthyofauna of the SFR is still lacking. To address this gap, we used DNA barcoding of 94 taxa from six orders, 32 families, and 73 genera, sourced from the BOLD Systems platform and samples in the middle and lower SFR regions. Analyses revealed distinct patterns of genetic divergence. The BOLD platform identified 111 bins, 75 as MATCH, 32 as SPLIT, two as MERGE and two MIXTURE. We detected taxonomic confusions in the genera Astyanax and Psalidodon. Fourteen taxa exhibited high cryptic diversity, corroborated by lineage delimitation methods (BINs, ASAP, and GMYC). A significant portion of this cryptic diversity (eight lineages) is concentrated in the upper SFR, a region with tectonic faults, geomorphological reactivations, and the transposition of another basin, which likely contributed to genetically divergent lineages. Our data fill shortfalls in Linnaean and Darwinian knowledge about the SFR ichthyofauna, considering its hydrogeological formation. We hope this information will serve as a foundation for future management and conservation plans for this important ichthyofauna.http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1679-62252024000400206&lng=en&tlng=enGenetic divergenceMolecular delimitation of linagesDarwinian shortfallLinnean shortfallSpecies complex |
| spellingShingle | Denis Bruno Santos Marques Nunes Alany Itala Pontes Leandro Ferreira dos Santos Leonardo Luís Calado Luciano Freitas Barros-Neto Silvia Yasmin Lustosa-Costa Sergio Maia Queiroz Lima Uedson Pereira Jacobina DNA barcoding highlights taxonomic uncertainties and cryptic lineages of São Francisco River basin fishes Neotropical Ichthyology Genetic divergence Molecular delimitation of linages Darwinian shortfall Linnean shortfall Species complex |
| title | DNA barcoding highlights taxonomic uncertainties and cryptic lineages of São Francisco River basin fishes |
| title_full | DNA barcoding highlights taxonomic uncertainties and cryptic lineages of São Francisco River basin fishes |
| title_fullStr | DNA barcoding highlights taxonomic uncertainties and cryptic lineages of São Francisco River basin fishes |
| title_full_unstemmed | DNA barcoding highlights taxonomic uncertainties and cryptic lineages of São Francisco River basin fishes |
| title_short | DNA barcoding highlights taxonomic uncertainties and cryptic lineages of São Francisco River basin fishes |
| title_sort | dna barcoding highlights taxonomic uncertainties and cryptic lineages of sao francisco river basin fishes |
| topic | Genetic divergence Molecular delimitation of linages Darwinian shortfall Linnean shortfall Species complex |
| url | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1679-62252024000400206&lng=en&tlng=en |
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