Species‐level ichthyoplankton dynamics for 97 fishes in two major river basins of the Amazon using quantitative metabarcoding

Mariac, Cédric; Renno, Jean-François; García-Dávila, Carmen; Vigouroux, Yves; Mejía, Eduardo; Chávez, Carlos; Castro-Ruiz, Diana; Nolorbe, Christian; Vásquez, Aurea García; Núñez, Jesús; Cochonneau, Gérard; Flores, Mayra Padilla; Alvarado, Jhon; Vertiz, José; Chota-Macuyama, Werner; Sánchez, Homero; Miranda-Chumacero, Guido; Duponchelle, Fabrice

doi:10.1111/mec.15944

Cited by 20 publications

(22 citation statements)

References 86 publications

(119 reference statements)

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“…Mariac et al (2021) addresses well the bias that may arise from ichthyoplankton sampling and the unequal body size of fish larvae that may lead to differences in cell and DNA quantity from each species/specimen per bulk sample. Also, the authors were able to size fractionated specimens and extract DNA from individuals of similar size to minimize bias due to different initial amounts of DNA from each larva.…”

Section: Figurementioning

confidence: 99%

“…biomonitoring 2.0, DNA barcode, environmental genomics, high-throughput DNA sequencing, neotropical fish to mitigate bias during each stage in order to avoid constraints that hinder accurate quali-quantitative DNA metabarcoding analysis (Deagle et al, 2018;Ratcliffe et al, 2021;Thomas et al, 2016). Mariac et al (2021) addresses well the bias that may arise from ichthyoplankton sampling and the unequal body size of fish larvae that may lead to differences in cell and DNA quantity from each species/specimen per bulk sample. Also, the authors were able to size fractionated specimens and extract DNA from individuals of similar size to minimize bias due to different initial amounts of DNA from each larva.…”

Section: Introductionmentioning

confidence: 99%

“…However, several challenges remain open for its mainstream application in ecological studies, particularly when dealing with a quantitative approach. In a From the Cover article in this issue of Molecular Ecology, Mariac et al (2021) report species-level ichthyoplankton dynamics for 97 fish species from two Amazon river basins using a clever quantitative metabarcoding approach employing a probe capture method. They clearly show that most species spawned during the floods, although ~20% also spawned mainly during the receding period and some other year-round, but interestingly, species from the same genus reproduced in distinct periods (i.e., inverse phenology).…”

mentioning

confidence: 99%

“…Opportunistically, Mariac et al (2021) reported that during an intense hydrological anomaly, several species had a sharp reduction in spawning activity, demonstrating a quick response to environmental cues. This is an interesting result since the speed at which fish species can react to environmental changes, during the spawning period, is largely unknown.…”

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confidence: 99%

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Ichthyoplankton DNA metabarcoding: Challenges and perspectives

Carvalho

2022

Molecular Ecology

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DNA metabarcoding has been widely used to access and monitor species. However, several challenges remain open for its mainstream application in ecological studies, particularly when dealing with a quantitative approach. In a From the Cover article in this issue of Molecular Ecology, Mariac et al. (2021) report species‐level ichthyoplankton dynamics for 97 fish species from two Amazon river basins using a clever quantitative metabarcoding approach employing a probe capture method. They clearly show that most species spawned during the floods, although ~20% also spawned mainly during the receding period and some other year‐round, but interestingly, species from the same genus reproduced in distinct periods (i.e., inverse phenology). Opportunistically, Mariac et al. (2021) reported that during an intense hydrological anomaly, several species had a sharp reduction in spawning activity, demonstrating a quick response to environmental cues. This is an interesting result since the speed at which fish species can react to environmental changes, during the spawning period, is largely unknown. Thus, this study brings remarkable insights into basic life history information that is imperative for proposing strategies that could lead to a realistic framework for sustainable fisheries management practices and conservation, fundamental for an understudied and threatened realm, such as the Amazon River basin.

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Section: Figurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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confidence: 99%

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Ichthyoplankton DNA metabarcoding: Challenges and perspectives

Carvalho

2022

Molecular Ecology

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“… 2020 , Mariac et al. 2021 ). Monitoring data on egg and larval composition, distribution, and abundance can thus provide valuable early indicators of the effects of flood pulse change and ecosystem state change.…”

Section: Biotic Indicators Of Ecosystem State Change In Amazonian Flo...mentioning

confidence: 99%

Biotic Indicators for Ecological State Change in Amazonian Floodplains

et al. 2022

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Riverine floodplains are biologically diverse and productive ecosystems. Although tropical floodplains remain relatively conserved and ecologically functional compared to those at higher latitudes, they face accelerated hydropower development, climate change, and deforestation. Alterations to the flood pulse could act synergistically with other drivers of change to promote profound ecological state change at a large spatial scale. State change occurs when an ecosystem reaches a critical threshold or tipping point, which leads to an alternative qualitative state for the ecosystem. Visualizing an alternative state for Amazonian floodplains is not straightforward. Yet, it is critical to recognize that changes to the flood pulse could push tropical floodplain ecosystems over a tipping point with cascading adverse effects on biodiversity and ecosystem services. We characterize the Amazonian flood pulse regime, summarize evidence of flood pulse change, assess potential ecological repercussions, and provide a monitoring framework for tracking flood pulse change and detecting biotic responses.

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Assessing fish diversity in abandoned mining ponds in Madre de Dios, Peru, using environmental DNA

Timana‐Mendoza,

Reyes‐Calderon,

Venail

et al. 2024

Environmental DNA

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The Peruvian region of Madre de Dios is a biodiversity hotspot located in the Andean‐Amazon region. Since the 1970s, it has experienced the harsh effects of artisanal and small‐scale gold mining (ASGM), which has transformed the primary forests into numerous small mining ponds left abandoned after extraction. Preliminary surveys indicate that these ponds are being recolonized by surrounding biodiversity. These assessments are typically carried out using traditional methods that are costly, difficult to deploy at multiple locations, and have raised safety concerns. In this context, environmental DNA (eDNA) becomes a useful tool for biodiversity monitoring due to its simplicity for sample collection and performance to identify taxonomic groups. In this study, we evaluated fish biodiversity in two mining ponds created by ASGM along with two nearby pristine lakes, unimpacted by mining operations but also influenced by seasonal flooding. We compared two alternative eDNA processing methods and contrasted our results with historic data from traditional biodiversity monitoring. Both eDNA‐based methods yielded comparable results, varying only in logistic requirements and costs. In total, we detected 85 fish MOTUs (22 at the species level) from 5 orders, 22 families, and 41 genera. Some of the species identified with eDNA were rarely registered by traditional monitoring, and we could identify 6 genera associated with ASGM mining ponds only. A major restriction of the eDNA approach in this location was the insufficient local taxa registered in genomic databases which limited our taxonomic resolution. Despite this limitation, our results indicate that eDNA could be a powerful tool for biodiversity estimations in the Western Amazon, identifying more taxa, with much less time and money invested than traditional monitoring. Our results also confirm that abandoned mining ponds are being recolonized by surrounding ichthyofauna, reaching richness levels above nearby unmined oxbow lakes used as reference.

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Species‐level ichthyoplankton dynamics for 97 fishes in two major river basins of the Amazon using quantitative metabarcoding

Abstract: This study is dedicated to the memory of Aurea Garcia Vasquez, dearest colleague and friend who succumbed to covid-19. We miss you.

Cited by 20 publications

References 86 publications

Ichthyoplankton DNA metabarcoding: Challenges and perspectives

Ichthyoplankton DNA metabarcoding: Challenges and perspectives

Biotic Indicators for Ecological State Change in Amazonian Floodplains

Assessing fish diversity in abandoned mining ponds in Madre de Dios, Peru, using environmental DNA

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