Prioritizing taxa for genetic reference database development to advance inland water conservation

Monchamp, Marie‐Ève; Taranu, Zofia E.; Garner, Rebecca E.; Rehill, Tessa; Morissette, Olivier; Iversen, Lars; Fugère, Vincent; Littlefair, Joanne E.; Costa, Naíla Barbosa da; Desforges, Jessica E.; Schacht, Joe R. Sánchez; Derry, Alison M.; Cooke, Steven J.; Barrett, Rowan D. H.; Walsh, David A.; Ragoussis, Jiannis; Albert, Monique; Cristescu, Melania E.; Gregory‐Eaves, Irene

doi:10.1016/j.biocon.2023.109963

Cited by 9 publications

(2 citation statements)

References 55 publications

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“…Sequencing priority species is an important task to be conducted at a fast pace, as it will enable them to be properly detected and their populations monitored across the landscape (Monchamp et al 2023). Moreover, it can make a significant difference in terms of increasing endangered species detection to combat poaching and wildlife trade, but also improving species identification after roadkills, which can help in elaborating strategies for preventing these accidents.…”

Section: Prioritization Of Species Sequencingmentioning

confidence: 99%

Barcoding Brazilian mammals to monitor biological diversity and threats: trends, perspectives, and knowledge gaps

Oliveira,

Freire-Jr.,

Silva

et al. 2024

Preprint

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DNA barcoding and environmental DNA (eDNA) represent an important advance for biomonitoring the world's biodiversity and its threats. However, these methods are highly dependent on the presence of species sequences on molecular databases. Brazil is one of the largest and most biologically diverse countries in the world. However, many knowledge gaps still exist for the description, identification, and monitoring of its mammalian biodiversity using molecular methods. We aimed at unraveling the patterns related to the presence of Brazilian mammal species on molecular databases to improve our understanding on how effectively it would be to monitor them using DNA barcoding and environmental DNA, and contribute to the conservation of this flagship zoological group. We found that many gaps exist in molecular databases, with many taxa being poorly represented, particularly from the Amazon biome, the order Lagomorpha, and arboreal, gomivorous, near extinct, and illegally traded species. Moreover, our analyses revealed that the year of species description was the most important factor determining the probability of a species to have been sequenced. Primates are the group with the highest number of species considered to be priority for sequencing due to their high level of combined threats. We highlight where investments are needed to fill knowledge gaps and increase the representativity of species on molecular databases to enable a better monitoring ability of Brazilian mammals encompassing different traits using DNA barcoding and environmental DNA.

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Section: Prioritization Of Species Sequencingmentioning

confidence: 99%

Barcoding Brazilian mammals to monitor biological diversity and threats: trends, perspectives, and knowledge gaps

Oliveira,

Freire-Jr.,

Silva

et al. 2024

Preprint

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“…Combining short‐ and long‐strand sequencing of environmental metagenomes may also be an alternative, allowing thorough investigation of fragmented and thus poorly preserved DNA from the sediments, but can be costly and time‐consuming (Pedersen et al, 2016). Importantly, all these methods are dependent upon adequate DNA sequence resources and reference databases (Monchamp et al, 2023). Overall, further research is required to meet ecological and methodological challenges, but in the meantime, it is essential to consolidate best practices from existing workflows to enable higher success in detecting fish DNA from sediment samples.…”

Section: Troubleshooting Fish Seddna Workflowsmentioning

confidence: 99%

Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities

Huston,

Lopez,

Cheng

et al. 2023

Environmental DNA

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Environmental DNA studies have proliferated over the last decade, with promising data describing the diversity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery of DNA present in the sediment of aquatic systems (sedDNA) has provided short‐ and long‐term data on a wide range of biological groups (e.g., photosynthetic organisms, zooplankton species) and has advanced our understanding of how environmental changes have affected aquatic communities. However, substantial challenges remain for recovering the genetic material of macro‐organisms (e.g., fish) from sediments, preventing complete reconstructions of past aquatic ecosystems, and limiting our understanding of historic, higher trophic level interactions. In this review, we outline the biotic and abiotic factors affecting the production, persistence, and transport of fish DNA from the water column to the sediments, and address questions regarding the preservation of fish DNA in sediment. We identify sources of uncertainties around the recovery of fish sedDNA arising during the sedDNA workflow. This includes methodological issues related to experimental design, DNA extraction procedures, and the selected molecular method (quantitative PCR, digital PCR, metabarcoding, metagenomics). By evaluating previous efforts (published and unpublished works) to recover fish sedDNA signals, we provide suggestions for future research and propose troubleshooting workflows for the effective detection and quantification of fish sedDNA. With further research, the use of sedDNA has the potential to be a powerful tool for inferring fish presence over time and reconstructing their population and community dynamics.

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Diatom DNA from Lake Sediments

Dulias,

Epp,

R. Stoof-Leichsenring

2023

Developments in Paleoenvironmental Research

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Prioritizing taxa for genetic reference database development to advance inland water conservation

Cited by 9 publications

References 55 publications

Barcoding Brazilian mammals to monitor biological diversity and threats: trends, perspectives, and knowledge gaps

Barcoding Brazilian mammals to monitor biological diversity and threats: trends, perspectives, and knowledge gaps

Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities

Diatom DNA from Lake Sediments

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