Hallazgo de Eastonia rugosa (Chemnitz) en el Pleistoceno de Mallorca

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El Pleistoceno del Torrente Son Granada (Baleares)

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La secuencia pleistocénica dunar de Son Mosón (Mallorca) y sus correlaciones faunísticas y estratigráficas

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Nuevos yacimientos del Pleistoceno marino de Mallorca

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To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography

Background: The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies. We argue here that methods developed and tested for ribosomal markers have been uncritically applied to highly variable markers such as cytochrome oxidase I (COI) without conceptual or operational (e.g., parameter setting) adjustment. COI has a naturally high intraspecies variability that should be assessed and reported, as it is a source of highly valuable information. We contend that denoising and clustering are not alternatives. Rather, they are complementary and both should be used together in COI metabarcoding pipelines. Results: Using a COI dataset from benthic marine communities, we compared two denoising procedures (based on the UNOISE3 and the DADA2 algorithms), set suitable parameters for denoising and clustering, and applied these steps in diferent orders. Our results indicated that the UNOISE3 algorithm preserved a higher intra-cluster variability. We introduce the program DnoisE to implement the UNOISE3 algorithm taking into account the natural variability (measured as entropy) of each codon position in protein-coding genes. This correction increased the number of sequences retained by 88%. The order of the steps (denoising and clustering) had little infuence on the fnal outcome. Conclusions: We highlight the need for combining denoising and clustering, with adequate choice of stringency parameters, in COI metabarcoding. We present a program that uses the coding properties of this marker to improve the denoising step. We recommend researchers to report their results in terms of both denoised sequences (a proxy for haplotypes) and clusters formed (a proxy for species), and to avoid collapsing the sequences of the latter into a single representative. This will allow studies at the cluster (ideally equating species-level diversity) and at the intra-cluster level, and will ease additivity and comparability between studies

Metabarcoding reveals high-resolution biogeographical and metaphylogeographical patterns through marine barriers

Aim: It has been predicted that there should be concordance between biogeographical and phylogeographical processes structuring multi-species regional assemblages. We hypothesise that oceanographic barriers in the marine environment affect concomitantly the distribution and the connectivity of the marine biota, thus producing congruent biogeographical and phylogeographical structures. We also predict that macro- and meio-eukaryotes will be differentially affected by hydrological features. Location: The Atlanto-Mediterranean transition along the E Iberian coast marked by the Almeria-Oran Front (AOF) and the Ibiza Channel hydrological discontinuities. Taxon: Eukaryotes. Methods: A new analytical framework based in the metabarcoding of community DNA and a hypervariable marker is presented. This framework allows the simultaneous detection of multispecies biogeographical and phylogeographical structures. Shallow hard-bottom communities were sampled at 12 sites over the littoral zone and community-DNA metabarcoding was performed using the cytochrome c oxidase I marker. The resulting dataset was analysed at several levels: beta diversity of Molecular Operational Taxonomic Units (MOTUs) as surrogate for species, and Exact Sequence Variants as surrogate for haplotypes. We also assessed genetic differentiation within MOTUs (metaphylogeography). Analyses were performed for the combined dataset and separately for macro- and meio-eukaryotes. Results: Both hydrological discontinuities had a detectable effect, more marked at all levels for the AOF than for the Ibiza Channel. The MOTU dataset provided more clear-cut patterns than the ESVs. The metaphylogeographical approach provided the highest resolution in terms of differentiating localities and identifying geographical barriers. The separate analyses of macro- and meio-eukaryotes showed a higher differentiation of the latter, both in terms of beta diversity and genetic differentiation. Main Conclusions: Metabarcoding coupled with metaphylogeography allowed the characterisation of the heterogeneity in community composition and population genetic structure along the Atlanto-Mediterranean transition, coherent with known hydrological discontinuities. This methodology unlocks a vast amount of information on the geographical distribution of different components of biodiversity for basic and applied research