English
norskBlar i forfatter "Turon, Xavier"
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DNA Metabarcoding of Deep-Sea Sediment Communities Using COI: Community Assessment, Spatio-Temporal Patterns and Comparison with 18S rDNA
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-03-26)Among the complex ecosystems and habitats that form the deep sea, submarine canyons and open slope systems are regarded as potential hotspots of biodiversity. We assessed the spatial and temporal patterns of biodiversity in sediment communities of a NW Mediterranean Canyon and its adjacent open slope (Blanes Canyon) with DNA metabarcoding. We sampled three layers of sediment and four different depths ... -
DNA metabarcoding of littoral hardbottom communities: high diversity and database gaps revealed by two molecular markers
(Journal article; Tidsskriftartikkel; Peer reviewed, 2018-05-04)Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular markers: the “Leray fragment” of mitochondrial <i>cytochrome c oxidase</i> (COI), for which a novel primer ... -
DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
(Journal article; Tidsskriftartikkel; Peer reviewed, 2022-01-19)DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software ... -
East is East and West is West: Population genomics and hierarchical analyses reveal genetic structure and adaptation footprints in the keystone species Paracentrotus lividus (Echinoidea)
(Journal article; Tidsskriftartikkel; Peer reviewed, 2019-12-14)<i>Aim</i> - The Atlanto‐Mediterranean edible purple sea urchin, <i>Paracentrotus lividus</i>, is a commercially exploited keystone species in benthic communities. Its browsing activity can deeply modify the littoral landscape, and changes in its abundance are of major conservation concern. This species is facing nowadays contrasting anthropogenic pressures linked to predator release, exploitation ... -
Enjoying the warming Mediterranean: Transcriptomic responses to temperature changes of a thermophilous keystone species in benthic communities
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-07-29)Information about the genomic processes underlying responses to temperature changes is still limited in non-model marine invertebrates. In this sense, transcriptomic analyses can help to identify genes potentially related to thermal responses. We here investigated, via RNA-seq, whole-transcriptomic responses to increased and decreased temperatures in a thermophilous keystone sea urchin, <i>Arbacia ... -
From metabarcoding to metaphylogeography: separating the wheat from the chaff
(Journal article; Tidsskriftartikkel; Peer reviewed, 2019-11-10)Metabarcoding is by now a well‐established method for biodiversity assessment in terrestrial, freshwater, and marine environments. Metabarcoding data sets are usually used for α‐ and β‐diversity estimates, that is, interspecies (or inter‐MOTU [molecular operational taxonomic unit]) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies ... -
Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-09-24)In the marine realm, biomonitoring using environmental DNA (eDNA) of benthic communities requires destructive direct sampling or the setting‐up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent ... -
Metabarcoding reveals high-resolution biogeographical and metaphylogeographical patterns through marine barriers
(Journal article; Tidsskriftartikkel; Peer reviewed, 2022-12-29)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 ... -
Spatio-temporal patterns of genetic variation in Arbacia lixula, a thermophilous sea urchin in expansion in the Mediterranean
(Journal article; Tidsskriftartikkel, 2018-06-14)The genetic structure of 13 populations of the amphiatlantic sea urchin <i>Arbacia lixula</i>, as well as temporal genetic changes in three of these localities, were assessed using ten hypervariable microsatellite loci. This thermophilous sea urchin is an important engineer species triggering the formation of barren grounds through its grazing activity. Its abundance seems to be increasing in most ... -
To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography
(Journal article; Tidsskriftartikkel; Peer reviewed, 2021-04-05)<i>Background</i> - 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 ... -
The Two Sides of the Mediterranean: Population Genomics of the Black Sea Urchin Arbacia lixula (Linnaeus, 1758) in a Warming Sea
(Journal article; Tidsskriftartikkel; Peer reviewed, 2021-11-10)Global environmental changes may have a profound impact on ecosystems. In this context, it is crucial to gather biological and ecological information of the main species in marine communities to predict and mitigate potential effects of shifts in their distribution, abundance, and interactions. Using genotyping by sequencing (GBS), we assessed the genetic structure of a keystone species in the ... -
Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding
(Journal article; Tidsskriftartikkel; Peer reviewed, 2018-12-21)We analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were <i>Caulerpa cylindracea</i>, <i>Lophocladia lallemandii</i> and <i>Asparagopsis armata</i>. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the ...
