Characterizing coral reef biodiversity: genetic species delimitation in brachyuran crabs of Palmyra Atoll, Central Pacific

Servis, Jennifer A.; Reid, Brendan N.; Timmers, Molly A.; Stergioula, Vasiliki; Naro‐Maciel, Eugênia

doi:10.1080/24701394.2020.1769087

Cited by 7 publications

(6 citation statements)

References 46 publications

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“…Only a few studies focused on the largest fraction of the reef biodiversity (the cryptobenthos) 59 , 60 . While ARMS have previously been used to investigate differences in the cryptobiome across spatial gradients (e.g., 5 , 16 , 48 , 49 , 51 , 53 , 54 , 61 , 62 , to the authors knowledge this is the first time a temporal aspect has been incorporated into the analysis of cryptobenthic communities associated with ARMS and across a bleaching event.…”

Section: Discussionmentioning

confidence: 99%

Inter-annual variability patterns of reef cryptobiota in the central Red Sea across a shelf gradient

Villalobos

Aylagas

Pearman

et al. 2022

Sci Rep

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The combination of molecular tools, standard surveying techniques, and long-term monitoring programs are relevant to understanding environmental and ecological changes in coral reef communities. Here we studied temporal variability in cryptobenthic coral reef communities across the continental shelf in the central Red Sea spanning 6 years (three sampling periods: 2013–2019) and including the 2015 mass bleaching event. We used a combination of molecular tools (barcoding and metabarcoding) to assess communities on Autonomous Reef Monitoring Structures (ARMS) as a standardized sampling approach. Community composition associated with ARMS for both methodologies (barcoding and metabarcoding) was statistically different across reefs (shelf position) and time periods. The partition of beta diversity showed a higher turnover and lower nestedness between pre-bleaching and post-bleaching samples than between the two post-bleaching periods, revealing a community shift from the bleaching event. However, a slight return to the pre-bleaching community composition was observed in 2019 suggesting a recovery trajectory. Given the predictions of decreasing time between bleaching events, it is concerning that cryptobenthic communities may not fully recover and communities with new characteristics will emerge. We observed a high turnover among reefs for all time periods, implying a homogenization of the cryptobiome did not occur across the cross shelf following the 2015 bleaching event. It is possible that dispersal limitations and the distinct environmental and benthic structures present across the shelf maintained the heterogeneity in communities among reefs. This study has to the best of our knowledge presented for the first time a temporal aspect into the analysis of ARMS cryptobenthic coral reef communities and encompasses a bleaching event. We show that these structures can detect cryptic changes associated with reef degradation and provides support for these being used as long-term monitoring tools.

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Section: Discussionmentioning

confidence: 99%

Inter-annual variability patterns of reef cryptobiota in the central Red Sea across a shelf gradient

Villalobos

Aylagas

Pearman

et al. 2022

Sci Rep

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“…The blue colouration represents diversity identified from water samples, the darker the shade of blue, the more MOTUs detected for that taxonomic order management strategies. This requires cost-effective and robust methods for surveying biodiversity in a timely manner, and eDNA metabarcoding has emerged as a promising method for survey- There is a knowledge gap regarding the optimum threshold for taxonomic assignments, as well as the taxonomic resolution/discriminative power of the gene fragments currently used in metabarcoding studies, particularly within megadiverse regions (Milan et al, 2020;Sales et al, 2021;Servis et al, 2020). Here, by performing a geneticdistance-threshold analysis, an optimum threshold value of 0.5% was obtained as a result of the lowest total cumulative errors (Figure 2a).…”

Section: Discussionmentioning

confidence: 99%

“…There is a knowledge gap regarding the optimum threshold for taxonomic assignments, as well as the taxonomic resolution/discriminative power of the gene fragments currently used in metabarcoding studies, particularly within megadiverse regions (Milan et al., 2020; Sales et al., 2021; Servis et al., 2020). Here, by performing a genetic‐distance‐threshold analysis, an optimum threshold value of 0.5% was obtained as a result of the lowest total cumulative errors (Figure 2a).…”

Section: Discussionmentioning

confidence: 99%

eDNA in a bottleneck: Obstacles to fish metabarcoding studies in megadiverse freshwater systems

et al. 2021

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“…There is a knowledge gap regarding the optimum threshold for taxonomic assignments, as well as the taxonomic resolution/discriminative power of the gene fragments currently used in metabarcoding studies, particularly within megadiverse regions (Milan et al, 2020;Servis, Reid, Timmers, Stergioula & Naro-Maciel, 2020;Sales et al, 2021). Here, by performing a geneticdistance-threshold analysis, an optimum threshold value of 0.5% was obtained as a result of the lowest total cumulative errors ( Fig.…”

Section: Discussionmentioning

confidence: 99%

eDNA in a bottleneck: obstacles to fish metabarcoding studies in megadiverse freshwater systems

Jackman

Benvenuto

Coscia

et al. 2021

Preprint

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The current capacity of environmental DNA (eDNA) to provide accurate insights into the biodiversity of megadiverse regions (e.g., the Neotropics) requires further evaluation to ensure its reliability for long-term monitoring. In this study, we first evaluated the taxonomic resolution capabilities of a short fragment from the 12S rRNA gene widely used in fish eDNA metabarcoding studies, and then compared eDNA metabarcoding data from water samples with traditional sampling using nets. For the taxonomic discriminatory power analysis, we used a specifically curated reference dataset consisting of 373 sequences from 264 neotropical fish species (including 47 newly generated sequences) to perform a genetic distance-based analysis of the amplicons targeted by the MiFish primer set. We obtained an optimum delimitation threshold value of 0.5% due to lowest cumulative errors. The barcoding gap analysis revealed only a 50.38% success rate in species recovery (133/264), highlighting a poor taxonomic resolution from the targeted amplicon. To evaluate the empirical performance of this amplicon for biomonitoring, we assessed fish biodiversity using eDNA metabarcoding from water samples collected from the Amazon (Adolpho Ducke Forest Reserve and two additional locations outside the Reserve). From a total of 84 identified Molecular Operational Taxonomic Units (MOTUs), only four could be assigned to species level using a fixed threshold. Measures of α-diversity analyses within the Reserve showed similar patterns in each site between the number of MOTUs (eDNA dataset) and species (netting data) found. However, β-diversity revealed contrasting patterns between the methods. We therefore suggest that a new approach is needed, underpinned by sound taxonomic knowledge, and a more thorough evaluation of better molecular identification procedures such as multi-marker metabarcoding approaches and tailor-made (i.e., order-specific) taxonomic delimitation thresholds.

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Characterizing coral reef biodiversity: genetic species delimitation in brachyuran crabs of Palmyra Atoll, Central Pacific

Cited by 7 publications

References 46 publications

Inter-annual variability patterns of reef cryptobiota in the central Red Sea across a shelf gradient

Inter-annual variability patterns of reef cryptobiota in the central Red Sea across a shelf gradient

eDNA in a bottleneck: Obstacles to fish metabarcoding studies in megadiverse freshwater systems

eDNA in a bottleneck: obstacles to fish metabarcoding studies in megadiverse freshwater systems

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