Dataset Information

Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle.

ABSTRACT: Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict (R² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.

SUBMITTER: Juhel JB

PROVIDER: S-EPMC7423466 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle.

Juhel Jean-Baptiste JB Utama Rizkie S RS Marques Virginie V Vimono Indra B IB Sugeha Hagi Yulia HY Kadarusman Pouyaud Laurent L Dejean Tony T Mouillot David D Hocdé Régis R

Proceedings. Biological sciences 20200708 1930

Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs ...[more]

PMID: 32635874

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Project description:Transcriptional profiling of gene responses in liver in the coral reef fish Pomacentrus moluccensis in response to different types of environmental stress: cold, heat, hypoxic and hyposmotic shock. Goal was to determine the common effects of different types of environmental stress on gene expression as well as responses unique to different stressors. Abstract from Kassahn et al. BMC Genomics (2007) 8:358 Background While our understanding of the importance of transcriptional regulation for biological function is continuously growing, we still know comparatively little about how environmentally-induced stress affects gene expression in vertebrates and how consistent transcriptional stress responses are across different types of environmental stress. Results In this study, we looked for a genetic measure of environmental stress and used a multi-stressor approach to identify components of a common stress response as well as components unique to different types of environmental stress. We exposed individuals of the coral reef fish Pomacentrus moluccensis to hypoxic, hyposmotic, cold and heat shock and measured the responses of approximately 16,000 genes in liver. We also compared winter and summer responses to heat shock to examine the capacity for such responses to vary with acclimation to different ambient temperatures. We identified a series of gene functions that were consistently involved in all stress responses examined here, suggesting common effects of stress on biological function. These common responses were achieved by the regulation of largely independent sets of genes and the responses of individual genes varied greatly across different stress types. However, we were able to identify groups of co-regulated genes, the genes within which shared similar functions. Given current estimates of climatic change, we were particularly interested in the response to prolonged heat exposure. In total, 324 gene loci were differentially expressed following exposure to heat over five days. The functions of these heat-responsive genes suggest that prolonged heat stress leads to oxidative stress and protein damage, challenge of the immune system, and a re-allocation of energy sources. Conclusion This is the first environmental genomic study to measure gene regulation in response to different environmental stressors in a natural population of a warm-adapted ectothermic vertebrate. This study offers insight into the effects of environmental stress on biological function and sheds light on the expected sensitivity of coral reef fishes to elevated temperatures in the future. Keywords: Stress response

Dataset Information

Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle.

Publications

Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle.

Similar Datasets

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