RESUMO
The deep seafloor is teeming with life, most of which remains poorly known to science. It also constitutes an important reserve of natural resources, particularly minerals, that mining companies will start harvesting in the next few years (Nat Rev Earth Environ, 1, 2020, 158). In this context, broad biodiversity assessments of deep-sea ecosystems are urgently needed to establish a baseline prior to mining. However, significant gaps in our taxonomic knowledge and the high cost of sampling in the deep sea limit the effectiveness of conventional morphology-based surveys. In this issue of Molecular Ecology, Laroche et al. (Mol Ecol, 2020) capitalize on high throughput molecular methods to conduct one of the most detailed and rigorous surveys of the composition and biogeography of deep-seafloor metazoan communities to date. The authors show that deep seamounts in the Clarion Clipperton Zone are inhabited by rich metazoan communities that are distinct from those of the surrounding abyssal plains. These results have important conservation implications: if communities on deep seamounts were to persist after large-scale industrial mining operations on the surrounding plains, the seamounts would not serve as appropriate reservoirs to repopulate impacted areas.
Assuntos
DNA Ambiental , Ecossistema , Animais , Biodiversidade , Mineração , Inquéritos e QuestionáriosRESUMO
Traditional methods of characterizing biodiversity are increasingly being supplemented and replaced by approaches based on DNA sequencing alone. These approaches commonly involve extraction and high-throughput sequencing of bulk samples from biologically complex communities or samples of environmental DNA (eDNA). In such cases, vouchers for individual organisms are rarely obtained, often unidentifiable, or unavailable. Thus, identifying these sequences typically relies on comparisons with sequences from genetic databases, particularly GenBank. While concerns have been raised about biases and inaccuracies in laboratory and analytical methods, comparatively little attention has been paid to the taxonomic reliability of GenBank itself. Here we analyze the metazoan mitochondrial sequences of GenBank using a combination of distance-based clustering and phylogenetic analysis. Because of their comparatively rapid evolutionary rates and consequent high taxonomic resolution, mitochondrial sequences represent an invaluable resource for the detection of the many small and often undescribed organisms that represent the bulk of animal diversity. We show that metazoan identifications in GenBank are surprisingly accurate, even at low taxonomic levels (likely <1% error rate at the genus level). This stands in contrast to previously voiced concerns based on limited analyses of particular groups and the fact that individual researchers currently submit annotated sequences to GenBank without significant external taxonomic validation. Our encouraging results suggest that the rapid uptake of DNA-based approaches is supported by a bioinformatic infrastructure capable of assessing both the losses to biodiversity caused by global change and the effectiveness of conservation efforts aimed at slowing or reversing these losses.
Assuntos
Biodiversidade , Bases de Dados Genéticas , Pesquisa , Animais , Código de Barras de DNA Taxonômico/métodos , História do Século XXIRESUMO
Summary: We present MIDORI server, a user-friendly web platform that uses a curated reference dataset, MIDORI, for high throughput taxonomic classification of unknown metazoan mitochondrial-encoded gene sequences. Currently three methods of taxonomic assignments: RDP Classifier, SPINGO and SINTAX, are implemented. Availability and implementation: The web server is freely available at {http://reference-midori.info/server.php}.