Literature DB >> 33432777

Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis.

Paula Arribas1, Carmelo Andújar1, Martin I Bidartondo2,3, Kristine Bohmann4, Éric Coissac5, Simon Creer6, Jeremy R deWaard7,8, Vasco Elbrecht9, Gentile F Ficetola5,10, Marta Goberna11, Susan Kennedy12,13, Henrik Krehenwinkel13, Florian Leese14,15, Vojtech Novotny16,17, Fredrik Ronquist18, Douglas W Yu19,20,21, Lucie Zinger22, Thomas J Creedy23, Emmanouil Meramveliotakis24, Víctor Noguerales24, Isaac Overcast22,25, Hélène Morlon22, Alfried P Vogler2,23, Anna Papadopoulou24, Brent C Emerson1.   

Abstract

High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site-based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled "Next Generation Biodiversity Monitoring" was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3-day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS-based strategy to collectively build an integrative framework for site-based biodiversity data generation.
© 2021 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

Entities:  

Keywords:  DNA metabarcoding; Genomic Observatories; biodiversity assessment; harmonized data generation; high-throughput sequencing

Mesh:

Year:  2021        PMID: 33432777      PMCID: PMC7986105          DOI: 10.1111/mec.15797

Source DB:  PubMed          Journal:  Mol Ecol        ISSN: 0962-1083            Impact factor:   6.185


  81 in total

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Journal:  Nat Genet       Date:  2012-01-27       Impact factor: 38.330

7.  Performance of two Southern California benthic community condition indices using species abundance and presence-only data: relevance to DNA barcoding.

Authors:  J Ananda Ranasinghe; Eric D Stein; Peter E Miller; Stephen B Weisberg
Journal:  PLoS One       Date:  2012-08-07       Impact factor: 3.240

8.  The founding charter of the Genomic Observatories Network.

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Journal:  Gigascience       Date:  2014-03-07       Impact factor: 6.524

9.  Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns.

Authors:  Amnon Amir; Daniel McDonald; Jose A Navas-Molina; Evguenia Kopylova; James T Morton; Zhenjiang Zech Xu; Eric P Kightley; Luke R Thompson; Embriette R Hyde; Antonio Gonzalez; Rob Knight
Journal:  mSystems       Date:  2017-03-07       Impact factor: 6.496

10.  Megascience. 'Omics data sharing.

Authors:  Dawn Field; Susanna-Assunta Sansone; Amanda Collis; Tim Booth; Peter Dukes; Susan K Gregurick; Karen Kennedy; Patrik Kolar; Eugene Kolker; Mary Maxon; Siân Millard; Alexis-Michel Mugabushaka; Nicola Perrin; Jacques E Remacle; Karin Remington; Philippe Rocca-Serra; Chris F Taylor; Mark Thorley; Bela Tiwari; John Wilbanks
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

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  5 in total

1.  Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods.

Authors:  Paula Arribas; Carmelo Andújar; Kristine Bohmann; Jeremy R deWaard; Evan P Economo; Vasco Elbrecht; Stefan Geisen; Marta Goberna; Henrik Krehenwinkel; Vojtech Novotny; Lucie Zinger; Thomas J Creedy; Emmanouil Meramveliotakis; Víctor Noguerales; Isaac Overcast; Hélène Morlon; Anna Papadopoulou; Alfried P Vogler; Brent C Emerson
Journal:  Gigascience       Date:  2022-07-19       Impact factor: 7.658

2.  Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies - An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae).

Authors:  Uda Gedara Sasanka Lakmali Ranasinghe; Jonas Eberle; Jana Thormann; Claudia Bohacz; Suresh P Benjamin; Dirk Ahrens
Journal:  Ecol Evol       Date:  2022-05-19       Impact factor: 3.167

3.  Airborne environmental DNA for terrestrial vertebrate community monitoring.

Authors:  Christina Lynggaard; Mads Frost Bertelsen; Casper V Jensen; Matthew S Johnson; Tobias Guldberg Frøslev; Morten Tange Olsen; Kristine Bohmann
Journal:  Curr Biol       Date:  2022-01-06       Impact factor: 10.834

Review 4.  Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation.

Authors:  Thomas J Creedy; Carmelo Andújar; Emmanouil Meramveliotakis; Victor Noguerales; Isaac Overcast; Anna Papadopoulou; Hélène Morlon; Alfried P Vogler; Brent C Emerson; Paula Arribas
Journal:  Mol Ecol Resour       Date:  2021-09-30       Impact factor: 8.678

5.  Community assembly and metaphylogeography of soil biodiversity: Insights from haplotype-level community DNA metabarcoding within an oceanic island.

Authors:  Carmelo Andújar; Paula Arribas; Heriberto López; Yurena Arjona; Antonio Pérez-Delgado; Pedro Oromí; Alfried P Vogler; Brent C Emerson
Journal:  Mol Ecol       Date:  2022-06-21       Impact factor: 6.622

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