444 research outputs found
Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes
No full textAim:Meiofaunal communities that inhabit the marine benthos offer unique opportunities to simultaneously study the macroecology of numerous phyla that exhibit different life-history strategies. Here, we ask: (1) if the macroecology of meiobenthic communities is explained mainly by dispersal constraints or by environmental conditions; and (2) if levels of meiofaunal diversity surpass existing estimates based on morphological taxonomy.Location:UK and mainland European coast.Methods:Next-generation sequencing techniques (NGS; Roche 454 FLX platform) using 18S nuclear small subunit ribosomal DNA (rDNA) gene. Pyrosequences were analysed using Amplicon Noise followed by chimera removal using Perseus.Results:Rarefaction curves revealed that sampling saturation was only reached at 15% of sites, highlighting that the bulk of meiofaunal diversity is yet to be discovered. Overall, 1353 OTUs were recovered and assigned to 23 different phyla. The majority of sampled sites had c. 60–70 unique operational taxonomic units (OTUs) per site, indicating high levels of beta diversity. The environmental parameters that best explained community structure were seawater temperature, geographical distance and sediment size, but most of the variability (R2 = 70%–80%) remains unexplained.Main conclusions:High percentages of endemic OTUs suggest that meiobenthic community composition is partly niche-driven, as observed in larger organisms, but also shares macroecological features of microorganisms by showing high levels of cosmopolitanism (albeit on a much smaller scale). Meiobenthic communities exhibited patterns of isolation by distance as well as associations between niche, latitude and temperature, indicating that meiobenthic communities result from a combination of niche assembly and dispersal processes. Conversely, isolation-by-distance patterns were not identified in the featured protists, suggesting that animals and protists adhere to radically different macroecological processes, linked to life-history strategies
Animals, protists and bacteria share marine biogeographic patterns
No full textOver millennia, ecological and evolutionary mechanisms have shaped macroecological patterns across the tree of life. Research describing these patterns at both regional and global scales has traditionally focused on the study of metazoan species. Consequently, there is a limited understanding of cross-phylum biogeographic structuring and an escalating need to understand the macroecology of both microscopic and macroscopic organisms. Here we used environmental DNA (eDNA) metabarcoding to explore the biodiversity of marine metazoans, protists and bacteria along an extensive and highly heterogeneous coastline. Our results showed remarkably consistent biogeographic structure across the kingdoms of life despite billions of years of evolution. Analyses investigating the drivers of these patterns for each taxonomic kingdom found that environmental conditions (such as temperature) and, to a lesser extent, anthropogenic stressors (such as fishing pressure and pollution) explained some of the observed variation. Additionally, metazoans displayed biogeographic patterns that suggested regional biotic homogenization. Against the backdrop of global pervasive anthropogenic environmental change, our work highlights the importance of considering multiple domains of life to understand the maintenance and drivers of biodiversity patterns across broad taxonomic, ecological and geographical scales.</p
Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water
No full textEnvironmental DNA (eDNA) surveys are increasingly being used for biodiversity monitoring, principally because they are sensitive and can provide high resolution community composition data. Despite considerable progress in recent years, eDNA studies examining how different environmental sample types can affect species detectability remain rare. Comparisons of environmental samples are especially important for providing best practice guidance on early detection and subsequent mitigation of non-indigenous species. Here we used eDNA metabarcoding of COI (cytochrome c oxidase subunit I) and 18S (nuclear small subunit ribosomal DNA) genes to compare community composition between sediment and water samples in artificial coastal sites across the United Kingdom. We first detected markedly different communities and a consistently greater number of distinct operational taxonomic units in sediment compared to water. We then compared our eDNA datasets with previously published rapid assessment biodiversity surveys and found excellent concordance among the different survey techniques. Finally, our eDNA surveys detected many non-indigenous species, including several newly introduced species, highlighting the utility of eDNA metabarcoding for both early detection and temporal / spatial monitoring of non-indigenous species. We conclude that careful consideration on environmental sample type is needed when conducting eDNA surveys, especially for studies assessing community change.</p
Second-generation environmental sequencing unmasks marine metazoan biodiversity
No full textBiodiversity is of crucial importance for ecosystem functioning, sustainability and resilience, but the magnitude and organization of marine diversity at a range of spatial and taxonomic scales are undefined. In this paper, we use second-generation sequencing to unmask putatively diverse marine metazoan biodiversity in a Scottish temperate benthic ecosystem. We show that remarkable differences in diversity occurred at microgeographical scales and refute currently accepted ecological and taxonomic paradigms of meiofaunal identity, rank abundance and concomitant understanding of trophic dynamics. Richness estimates from the current benchmarked Operational Clustering of Taxonomic Units from Parallel UltraSequencing analyses are broadly aligned with those derived from morphological assessments. However, the slope of taxon rarefaction curves for many phyla remains incomplete, suggesting that the true alpha diversity is likely to exceed current perceptions. The approaches provide a rapid, objective and cost-effective taxonomic framework for exploring links between ecosystem structure and function of all hitherto intractable, but ecologically important, communities
Publisher correction: Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water
No full textCorrection to: Scientific Reports https://doi.org/10.1038/s41598-019-47899-7, published online 09 August 201
Michel de Certeau: recorridos por el "creer" y sus constelaciones contemporáneas
No full textFrench historian Michel De Certeau has been committed to reflection on “believing” from different points of view. The author of this article focuses on De Certeau’s studies on belief and contemporary constellations. He provides an introductory set of texts in order to aid his reception in Latin American context.El historiador francés Michel de Certeau se ha dedicado mucho a reflexionar acerca del “creer” desde áreas y acontecimientos muy diversos. En este artículo, el autor se concentra en sus análisis del creer y sus constelaciones contemporáneas, ofreciendo un panorama introductorio de textos y tramas para impulsar la recepción, todavía incipiente, de su pensamiento en el contexto latinoamericano
Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity
No full textThe use of environmental DNA (eDNA) in biodiversity assessments offers a step-change in sensitivity, throughput and simultaneous measures of ecosystem diversity and function. There remains, however, a need to examine eDNA persistence in the wild through simultaneous temporal measures of eDNA and biota. Here, we use metabarcoding of two markers of different lengths, derived from an annual time series of aqueous lake eDNA to examine temporal shifts in ecosystem biodiversity and in an ecologically important group of macro-invertebrates (Diptera: Chironomidae). The analyses allow different levels of detection and validation of taxon richness and community composition (beta-diversity) through time, with shorter eDNA fragments dominating the eDNA community. Comparisons between eDNA, community DNA, taxonomy and UK species abundance data further show significant relationships between diversity estimates derived across the disparate methodologies. Our results reveal the temporal dynamics of eDNA and validate the utility of eDNA metabarcoding for tracking seasonal diversity at the ecosystem scale
Voyage de M. E. Simon dans l\u27Afrique australe
No full textSur quarante-deux espèces que M. E. Simon m\u27a données provenant de son voyage au Transvaal et dans la colonie du Cap, vingt-deux se trouvent inédites. Je suis heureux de donner a plusieurs de ces dernières le nom de Ieur aimable detecter. En outre, je me trouve obligé de creer deux nouveaux genres pour classer des individus qui ne peuvent rentrer dans les coupes déjà établies. Le genre Sulydus, pour un petit Braconide, voisin mais bien distinct des Hedylus Marsh. Le genre Menius, ponr un insecte des plus curieux, rappelant les Myzine Latr., mais d\u27un ensemble de formes tout différent. Le Menius aspericornis vient constituer un nonveau chainon a ce groupe peu homogène d\u27Hyménoptères bizarres et peu connus
Choosing and Using Introns in Molecular Phylogenetics
No full text Introns are now commonly used in molecular phylogenetics in an attempt to recover gene trees that are concordant with species trees, but there are a range of genomic, logistical and analytical considerations that are infrequently discussed in empirical studies that utilize intron data. This review outlines expedient approaches for locus selection, overcoming paralogy problems, recombination detection methods and the identification and incorporation of LVHs in molecular systematics. A range of parsimony and Bayesian analytical approaches are also described in order to highlight the methods that can currently be employed to align sequences and treat indels in subsequent analyses. By covering the main points associated with the generation and analysis of intron data, this review aims to provide a comprehensive introduction to using introns (or any non-coding nuclear data partition) in contemporary phylogenetics. </jats:p
Second-generation sequencing derived insights into the temporal biodiversity dynamics of freshwater protists
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