Browsing by Author "Aguirre JD"

Now showing 1 - 6 of 6
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    Biodiversity of the Kermadec Islands and offshore waters of the Kermadec Ridge: report of a coastal, marine mammal and deep-sea survey (TAN1612)
    (Ministry for Primary Industries, 2017-01-30) Clark MR; Trnski T; Constantine R; Aguirre JD; Barker J; Betty E; Bowden DA; Connell A; Duffy C; George S; Hannam S; Liggins LJ; Middleton C; Mills S; Pallentin A; Reikkola L; Sampey A; Sewell M; Spong K; Stewart A; Stewart R; Struthers C; van Oosterom L
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    Introduced alien, range extension or just visiting? Combining citizen science observations and expert knowledge to classify range dynamics of marine fishes
    (1/07/2021) Middleton I; Aguirre JD; Trnski T; Francis M; Duffy C; Liggins L
    Aim: Despite the unprecedented rate of species redistribution during the Anthropocene, there are few monitoring programmes at the appropriate spatial and temporal scale to detect distributional change of marine species and to infer climate- versus human-mediated drivers of change. Here, we present an approach that combines citizen science with expert knowledge to classify out-of-range occurrences for marine fishes as potential range extensions or human-mediated dispersal events. Innovation: Our stepwise approach includes decision trees, scoring and matrices to classify citizen science observations of species occurrences and to provide a measure of confidence and validation using expert knowledge. Our method draws on peer-reviewed literature, knowledge of the species (e.g. contributing to its detectability, and potential to raft with, or foul, man-made structures or debris) and information obtained from citizen science observations (e.g. life stage, number of individuals). Using a case study of suspected out-of-range marine fishes in Aotearoa New Zealand, we demonstrate our approach to defining species’ ranges, assigning confidence to these definitions and considering the species detectability to overcome the data deficiencies that currently hinder monitoring the range dynamics of these species. Our classification of citizen science observations revealed that six of ten species had out-of-range occurrences; one of these was classified as an extralimital vagrant, four species had potentially extended their ranges and one species occurrence was likely due to human-mediated dispersal. Conclusion: The case study of marine fishes in New Zealand validates our approach combining citizen science observations with expert knowledge to infer species range dynamics in real time. Our stepwise approach helps to identify data deficiencies important in informing scientific inferences and management actions and can be refined to suit other data sources, taxonomic groups, geographic settings or extended with new steps and existing tools.
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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.