In anticipation of the current biodiversity crisis, it has become critical to rapidly and accurately assess biodiversity. DNA barcoding has proved efficient in facilitating the discovery and description of thousands of species and also provides insight into the dynamics of biodiversity. Here, we sequenced a portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene from all morphospecies of reef brittle stars collected during a large-scale biodiversity survey in the southwestern Indian Ocean (SWIO). Three methods of species delineation (Automatic Barcode Gap Discovery, Generalized Mixed Yule Coalescent model, and Bayesian Poisson Tree Processes) showed concordant results and revealed 51 shallow reef species in the region. Mean intraspecific genetic distances (0.005-0.064) and mean interspecific genetic distances within genera (0.056-0.316) were concordant with previous echinoderm studies. This study revealed that brittle-star biodiversity is underestimated by 20% within SWIO and by >40% when including specimens from the Pacific Ocean. Results are discussed in terms of endemism, diversification processes, and conservation implications for the Indo-West Pacific marine biodiversity. We emphasize the need to further our knowledge on biodiversity of invertebrate groups in peripheral areas.
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http://dx.doi.org/10.1002/ece3.3554 | DOI Listing |
Nucleic Acids Res
December 2024
Malaria Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
The malaria parasite needs nearly half of its genes to propagate normally within red blood cells. Inducible ways to interfere with gene expression like the DiCre-lox system are necessary to study the function of these essential genes. However, existing DiCre-lox strategies are not well-suited to be deployed at scale to study several genes simultaneously.
View Article and Find Full Text PDFPLoS One
December 2024
Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.
As the technology for mass identification of species is advancing rapidly, we developed a field sampling method that takes advantage of the emerging possibilities of combining sensor-based data with automated high-throughput data processing. This article describes the five field sampling methods used by the LIFEPLAN project to collect biodiversity data in a systematic manner, all over the world. These methods are designed for use by anyone with basic biology or ecology knowledge from the higher education or university level.
View Article and Find Full Text PDFMol Ecol Resour
December 2024
Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
Relatively little is known of the host associations and compatibility of fungal plant pathogens and endophytes. Publicly available plant genomic DNA can be mined to detect incidental fungal DNA, but taxonomic assignment can be challenging due to short lengths and variable discriminative power among different genomic regions and taxa. Here, we introduce a computationally lightweight and accessible Snakemake pipeline for rapid detection and classification (identification and assignment to taxonomic rank) of pathogenic and endophytic fungi (and other fungi associated with plants) that targets the internal transcribed spacer (ITS) region, a fungal barcode standard.
View Article and Find Full Text PDFSci Rep
December 2024
Food System Integrity, AgResearch Limited, Hopkirk Research Institute, Massey University, Cnr University Avenue and Library Road, Private Bag 11008, Palmerston North, 4442, New Zealand.
Understanding the composition of complex Escherichia coli populations from the environment is necessary for identifying strategies to reduce the impacts of fecal contamination and protect public health. Metabarcoding targeting the hypervariable gene gnd was used to reveal the complex population diversity of E. coli and phenotypically indistinct Escherichia species in water, soil, sediment, aquatic biofilm, and fecal samples from native forest and pastoral sites.
View Article and Find Full Text PDFData Brief
December 2024
Thai Nguyen University of Education, Thai Nguyen City, 24000, Viet Nam.
Species of the genus have the potential to be natural medicines and have industrial fibre production uses. Many species of this genus are morphologically similar and are difficult to distinguish, especially when their morphology is distorted. This dataset includes sequence information of several DNA regions isolated from the genome of , namely ITS (from the nuclear genome), , trnL-trnF, trnH-psbA, and (from the chloroplast genome) and phylogenetic analysis results based on the isolated sequences.
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