The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures ARMS and metabarcoding to measure cryptic diversity on Mo’orea coral reefs, French PolynesiaReportar como inadecuado




The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures ARMS and metabarcoding to measure cryptic diversity on Mo’orea coral reefs, French Polynesia - Descarga este documento en PDF. Documentación en PDF para descargar gratis. Disponible también para leer online.

The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures ARMS, have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four ARMS field processing methods, preservation media, and current bioinformatic pipelines in evaluating diversity from cytochrome c oxidase I metabarcoding data. Illustrating the ability of ARMS-based metabarcoding to capture a wide spectrum of biodiversity, 3,372 OTUs and twenty-eight phyla, including 17 of 33 marine metazoan phyla, were detected from 3 ARMS 2.607 m2 area collected on coral reefs in Mo’orea, French Polynesia. Significant differences were found between processing and preservation methods, demonstrating the need to standardize methods for biodiversity comparisons. We recommend the use of a standardized protocol NOAA method combined with DMSO preservation of tissues for sessile macroorganisms because it gave a more accurate representation of the underlying communities, is cost effective and removes chemical restrictions associated with sample transportation. We found that sequences identified at ≥ 97% similarity increased more than 7-fold 5.1% to 38.6% using a geographically local barcode inventory, highlighting the importance of local species inventories. Phylogenetic approaches that assign higher taxonomic ranks accrued phylum identification errors 9.7% due to sparse taxonomic coverage of the understudied cryptic coral reef community in public databases. However, a ≥ 85% sequence identity cut-off provided more accurate results 0.7% errors and enabled phylum level identifications of 86.3% of the sequence reads. With over 1600 ARMS deployed, standardizing methods and improving databases are imperative to provide unprecedented global baseline assessments of understudied cryptic marine species in a rapidly changing world.



Autor: Emma Ransome , Jonathan B. Geller, Molly Timmers, Matthieu Leray, Angka Mahardini, Andrianus Sembiring, Allen G. Collins, Christo

Fuente: http://plos.srce.hr/



DESCARGAR PDF




Documentos relacionados