Browsing by Author "Arranz V"
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- ItemMARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding(Springer Nature Limited, 2020-07-03) Arranz V; Pearman WS; Aguirre JD; Liggins LThe use of DNA metabarcoding to characterise the biodiversity of environmental and community samples has exploded in recent years. However, taxonomic inferences from these studies are contingent on the quality and completeness of the sequence reference database used to characterise sample species-composition. In response, studies often develop custom reference databases to improve species assignment. The disadvantage of this approach is that it limits the potential for database re-use, and the transferability of inferences across studies. Here, we present the MARine Eukaryote Species (MARES) reference database for use in marine metabarcoding studies, created using a transparent and reproducible pipeline. MARES includes all COI sequences available in GenBank and BOLD for marine taxa, unified into a single taxonomy. Our pipeline facilitates the curation of sequences, synonymization of taxonomic identifiers used by different repositories, and formatting these data for use in taxonomic assignment tools. Overall, MARES provides a benchmark COI reference database for marine eukaryotes, and a standardised pipeline for (re)producing reference databases enabling integration and fair comparison of marine DNA metabarcoding results.
- ItemMetabarcoding hyperdiverse kelp holdfast communities on temperate reefs: An experimental approach to inform future studies(2022-05-01) Arranz V; Liggins L; Aguirre JDClassical taxonomic approaches to quantifying biodiversity can be notoriously laborious and restrictive. Instead, molecular metabarcoding is emerging as a rapid, high-throughput, and cost-effective tool to catalog biodiversity. Despite the appeal of metabarcoding, methodological and procedural biases must be understood before robust biodiversity inferences can be made. Here, we use CO1 metabarcoding to characterize marine eukaryote communities associated with Ecklonia radiata, the dominant eco-engineering kelp of temperate Australasia. To establish a standardized and reproducible community metabarcoding protocol, we examined the influence of different sample preparation, laboratory, and bioinformatic steps on inferences of species richness and composition of communities associated with E. radiata holdfasts (the root-like structure anchoring the kelp to the substratum) sampled from northeastern New Zealand. Specifically, we examined the effect of sieving the community into different size fractions and the replicability of results across DNA extractions, polymerase chain reactions and sequencing. Overall, we found that sieving the community into two size fractions before DNA extraction enabled detection of a greater diversity of taxa than not sieving samples. When compared with traditional morphology-based inventories of kelp holdfast biodiversity, we found that although the taxonomic precision of our metabarcoding approach at the species and genus level was limited by the availability of reference sequences in public repositories, we recovered ~40% more taxa and a greater taxonomic breadth of organisms than morphological surveys (e.g., 18 phyla as compared with 14 phyla). On the basis of our findings, we provide methodological guidelines for the use of metabarcoding as a tool for surveying and monitoring the hyperdiverse species assemblages associated with kelp holdfasts.
- ItemMorphological and genetic divergence supports peripheral endemism and a recent evolutionary history of Chrysiptera demoiselles in the subtropical South Pacific(2022-06-01) Liggins L; Kilduff L; Trnski T; Delrieu-Trottin E; Carvajal JI; Arranz V; Planes S; Saenz-Agudelo P; Aguirre JDThe delineation of species and their evolutionary relationships informs our understanding of biogeography and how regional faunas are assembled. The peripheral geography and local environment of reefs in the subtropical South Pacific likely promotes the allopatric and adaptive divergence of taxa colonising from the tropics; however, the fauna of this region has been relatively understudied. Here, we address the taxonomic and evolutionary relationships among Chrysiptera taxa of the subtropical South Pacific. We use meristic counts, morphometrics and genetic markers to characterise the similarities and differences among four taxa restricted to the South Pacific region that have strikingly different colouration: C. notialis, a taxon restricted to eastern Australia, New Caledonia, Lord Howe Island and Norfolk Island; C. galba, found in the Cook Islands, southern French Polynesia and Pitcairn Islands; and the two disjunct populations of C. rapanui, found in the eastern Pacific around Rapa Nui (Isla de Pascua or Easter Island) and Motu Motiro Hiva (Salas y Gómez) and in the South-western Pacific around Rangitāhua (Kermadec Islands). Our morphometric analysis confirmed that these four taxa, including the two disjunct populations of C. rapanui, are morphologically distinct. However, our genetic analysis revealed that only C. rapanui from Rapa Nui was genetically differentiated, whereas C. rapanui of Rangitāhua, C. galba and C. notialis all shared a common haplotype. Furthermore, none of the taxa could be consistently differentiated based on individual meristic features. Our study reconciles a formerly perplexing and disjunct distribution for C. rapanui, to reveal that C. rapanui is an endemic of Rapa Nui and that the Chrysiptera of French Polynesia, Rangitāhua, and the South-western Pacific have only a very recent history of divergence. Our analyses suggest these subtropical taxa have diverged from a predominantly tropical Chrysiptera genus in morphological features important in determining colonisation success, locomotion and feeding ecology.