Browsing by Author "Arranz V"

Now showing 1 - 5 of 5
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    Genogeographic clustering to identify cross-species concordance of spatial genetic patterns
    (John Wiley and Sons, Ltd, 2022-04) Arranz V; Fewster RM; Lavery SD; Burridge C
    Aim: While in recent years, there have been considerable advances in discerning spatial genetic patterns within species, the task of identifying common patterns across species is still challenging. Approaches using new data from co-sampled species permit rigorous statistical analysis but are often limited to a small number of species. Meta-analyses of published data can encompass a much broader range of species, but are usually restricted by uneven data properties. There is a need for new approaches that bring greater statistical rigour to meta-analyses and are also able to discern more than a single spatial pattern among species. We propose a new approach for comparative multi-species meta-analyses of published population genetic data that address many existing limitations. Innovation: The proposed “genogeographic clustering” technique takes a three-stage approach: (i) use common genetic metrics to gain location-specific measures across the sampled range of each species; (ii) for each species, determine the spatial genetic pattern by fitting a smooth “genogeographic” trend curve to the genetic data; and (iii) quantitatively cluster species according to their similarity in spatial pattern. We apply this technique to 21 species of intertidal invertebrates from the New Zealand coastline, to resolve common spatial patterns from disparate profiles of genetic diversity. Main conclusions: The genogeographic curves are shown to successfully capture the known spatial patterns within each intertidal species and readily permit statistical comparison of those patterns, regardless of sampling and marker inconsistencies. The species clustering technique is shown to discern groups of species that clearly share spatial patterns within groups but differ significantly among groups. Genogeographic species clustering provides a novel approach to discerning multiple common spatial patterns of diversity among a large number of species. It will permit more rigorous comparative studies from diverse published data and can be easily extended to a wide variety of alternative measures of genetic diversity or divergence.
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    MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding
    (Springer Nature Limited, 3/07/2020) Arranz V; Pearman WS; Aguirre JD; Liggins L
    The 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.
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    Metabarcoding hyperdiverse kelp holdfast communities on temperate reefs: An experimental approach to inform future studies
    (1/05/2022) Arranz V; Liggins L; Aguirre JD
    Classical 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.
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    Morphological and genetic divergence supports peripheral endemism and a recent evolutionary history of Chrysiptera demoiselles in the subtropical South Pacific
    (1/06/2022) Liggins L; Kilduff L; Trnski T; Delrieu-Trottin E; Carvajal JI; Arranz V; Planes S; Saenz-Agudelo P; Aguirre JD
    The 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.
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    The future of molecular ecology in Aotearoa New Zealand: an early career perspective
    (Taylor and Francis Group on behalf of the Royal Society of New Zealand, 2022-07-14) Liggins L; Arranz V; Braid HE; Carmelet-Rescan D; Elleouet J; Egorova E; Gemmell MR; Hills SFK; Holland LP; Koot EM; Lischka A; Maxwell KH; McCartney LJ; Nguyen HTT; Noble C; Olmedo Rojas P; Parvizi E; Pearman WS; Sweatman JAN; Kaihoro TR; Walton K; Aguirre JD; Stewart LC; Moss S
    The skills, insights, and genetic data gathered by molecular ecologists are pivotal to addressing many contemporary biodiversity, environmental, cultural, and societal challenges. Concurrently, the field of molecular ecology is being revolutionised by rapid technological development and diversification in the scope of its applications. Hence, it is timely to review the future opportunities of molecular ecological research in Aotearoa New Zealand, and to reconcile them with philosophies of open science and the implications for Indigenous data sovereignty and benefit sharing. Future molecular ecologists need to be interdisciplinary, equipped to embrace innovation, and informed about the broader societal relevance of their research, as well as advocates of best practice. Here, we present an ideal future for molecular ecology in Aotearoa, based on the perspectives of 23 early career researchers from tertiary institutions, Crown Research Institutes, research consultancies, and government agencies. Our article provides: a guide for molecular ecologists embarking on genetic research in Aotearoa, and a primer for individuals in a position to support early career molecular ecologists in Aotearoa. We outline our goals and highlight specific considerations–for molecular ecology and the scientific community in Aotearoa–based on our own experience and aspirations, and invite other researchers to join this dialogue.