Biology subjects

Turon, X.

Publications and source records attributed to Turon, X..

8 recordsLinked to original sources

bioRxiv2025

From storms to warming seas: a long-term metabarcoding survey in port communities unveils high genetic diversity and ecological resilience of non-indigenous species

Ports are key gateways for the introduction and spread of non-indigenous species (NIS), yet the ecological and genetic temporal dynamics of these introductions remain poorly understood. Long term temporal monitoring is essential to unravel invasion processes, anticipate biodiversity shifts, and inform effective management and biosecurity strategies. In this study, we conducted a five-year (2019-2024) monthly metabarcoding survey in a northwestern Mediterranean port using artificial collectors. By sequencing a fragment of the Cytochrome Oxidase I gene, we identified 2,225 Molecular Operational Taxonomic Units (MOTUs), including 93 NIS. In addition, we examined both interspecific temporal patterns and intraspecific trends of genetic diversity over time. Although NIS accounted for only 4% of total species richness, they represented over 26% of total read abundance, underscoring their strong influence on community structure. Interestingly, NIS had a significantly more homogeneous species composition through time than native species. In 2020, the passage of the Gloria storm reshaped community dynamics, triggering a temporary rise in species richness and MOTU counts, likely due to an influx of native taxa and a gradual decline and increased NIS dominance. Genetic analyses revealed that NIS exhibited higher haplotypic diversity and lower genetic differentiation than native taxa, suggesting sustained gene flow, likely facilitated by maritime transport. MOTUs with longer temporal persistence, particularly among NIS, also showed greater intraspecific diversity, supporting the "insurance hypothesis" and highlighting the role of genetic variability in resilience and invasion success. Overall, our findings showed that NIS, despite their low species richness, maintain high abundances, connectivity, and genetic diversity over time. These attributes likely enhance the NIS ability to persist in dynamic and disturbed port environments, and provide key information for understanding the invasion process. This study highlights the need to integrate genetic diversity metrics into marine biomonitoring assessments and management.

molecular biology↗

bioRxiv2025

The coloNISation: spatio-temporal metabarcoding surveys in ports reveal homogenised communities with high genetic diversity and connectivity of non-indigenous species

Large commercial ports facilitate the introduction of non-indigenous species (NIS), while smaller harbours and marinas contribute to their regional spread. Harbour networks are thus important drivers of introductions. Despite extensive research effort on NIS in recent years, no study has yet assessed genetic connectivity among harbours considering whole-community composition. Here, we analysed spatio-temporal patterns of metazoan communities over one year in four medium-size harbours along the NW Mediterranean coast sampled by deploying standardised biological collectors. Using cytochrome c oxidase subunit I (COI) metabarcoding, we identified 1,770 metazoan molecular operational taxonomic units (MOTUs), of which 82 were classified as NIS based on a custom database of Mediterranean NIS. Despite their lower species count compared to natives, NIS accounted for 34-70% of reads in harbours. The southernmost harbour had the highest NIS number of reads, likely due to its proximity to aquaculture facilities. While we observed some variation in the spatial structure of metazoan communities across harbours, NIS showed consistently low differentiation values, sharing significantly more MOTUs among sites. Seasonal patterns influenced both NIS and the rest of the community. Haplotype diversity was significantly higher in NIS, which also exhibited lower genetic differentiation across harbours compared to native species, indicating NIS spread via local boating and likely recurrent introductions. These findings highlight distinct dynamics between NIS and native species in artificial environments, emphasising the importance of continued monitoring in harbour networks to manage coastal NIS proliferation. HIGHLIGHTSCOI metabarcoding of standardised collectors detected over 1,700 MOTUs of marine metazoans in ports over a year. Less than 4% were NIS MOTUs, but they comprised 34-71 % of the reads. NIS were more homogeneously distributed among ports than other MOTUs. NIS showed higher genetic variability but lower genetic differentiation than native species. Different dynamics underpin NIS and native assemblages in port communities. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/688838v1_ufig1.gif" ALT="Figure 1000"> View larger version (32K): org.highwire.dtl.DTLVardef@fa0a5corg.highwire.dtl.DTLVardef@1be29ccorg.highwire.dtl.DTLVardef@1aa4e85org.highwire.dtl.DTLVardef@91842_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Expanding on the portuarization syndrome from an ecological perspective: eDNA reveals rich diversity, non-indigenous hotspots, and biotic homogenization in ports

Ports are well-known entry points for marine non-indigenous species (NIS), which arrive as hitchhikers on ships. Ports are also expected to be gateways for the spread of NIS in the wild and resemble each other more than communities outside due to their singular characteristics. However, the uniqueness of species assemblages in ports and how they differ from natural habitats have only been marginally investigated, notably at regional scale. Using eDNA metabarcoding, we obtained a comprehensive and standardized overview of metazoan community diversity in 12 paired ports and adjacent natural areas along the northwestern Mediterranean Sea. As expected, we found that NIS are more abundant in ports than in natural habitats, and that the species assemblages in ports differ from those in natural habitats. In addition, we observed that communities in ports are far more homogeneous than their natural counterparts. This finding supports the hypothesis of biotic homogenization in highly anthropized habitats. We also observed a pattern that had previously been documented mainly in fish, but that we identified here in every phylum studied except Arthropoda: species richness detected in ports is comparable to, and in some case even greater than, that observed in natural habitats. Overall, our findings broaden, through an ecological perspective, the "portuarization syndrome" concept, which originally defined ports as unique replicated environments that promote specific evolutionary processes.

ecology↗

bioRxiv2021

DnoisE: Distance denoising by Entropy. An open-source parallelizable alternative for denoising sequence datasets

DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons are generated during amplification and sequencing procedures and 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 currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE3 algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing run times on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.

bioinformatics↗

bioRxiv2021

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

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. Using a typical 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 COI datasets, and compared the outcome of applying these processes in different orders. Our results indicate that denoising based on the UNOISE3 algorithm preserves a higher intra-cluster variability. We suggest and test ways to improve this algorithm taking into account the natural variability of each codon position in coding genes. The order of the steps (denoising and clustering) has little influence on the final outcome. We recommend researchers to consider reporting 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.

genetics↗

bioRxiv2020

Microbiome structure of ecologically important bioeroding sponges (family Clionaidae): The role of host phylogeny and environmental plasticity.

The potential of increased bioerosion by excavating sponges in future environmental scenarios represents a potential threat to coral reef structure and function. If we are to predict changes to coral reef habitats, it is important to understand the biology of these sponges. Little is known about prokaryotic associations in excavating sponges despite the fact that evidence indicates they contribute to the sponge growth through their heterotrophic metabolism and may even act as microborers. Here, we provide the first detailed description of the microbial community of multiple bioeroding sponges from the Clionaidae family (Cliona varians, C. tumula, C. delitrix, Spheciospongia vesparium, Cervicornia cuspidifera) collected in inshore and offshore coral reefs in the Florida Keys. A total of 6,811 prokaryote OTUs identified using 16S rRNA gene sequencing was detected in the samples studied, including ambient water, belonging to 39 bacterial phyla and 3 archaeal phyla. The microbiomes of species harboring Symbiodinium (Cliona varians, C. tumula, Cervicornia cuspidifera) and the azooxanthellate S. vesparium were dominated by Alphaproteobacteria that represented from 83 to 96% of total sequences. These clionaid sponges presented species-specific core microbiomes, with 4 OTUs being shared by all sponge samples, albeit with species-specific enrichments. The microbiomes of C. varians and S. vesparium were stable but showed certain plasticity between offshore and inshore reefs. The distantly related Cliona delitrix does not harbor Symbiodinium, and had a microbiome dominated by Gammaproteobacteria, which represented 82% of all sequences. Most of the sponge-exclusive OTUs are found in low abundance and belong to the "rare biosphere" category, highlighting the potential importance of these microbes in the ecology of the holobiont. Sponge microbiomes may enhance functional redundancy for the sponge holobiont and allow it to respond to shifting environments over much short time scales than evolutionary change would permit. This work establishes the basis for future research to explore how microbial shifts in bioeroding sponges contribute to bioerosion in the face of a changing environment.

ecology↗

bioRxiv2019

From metabarcoding to metaphylogeography: separating the wheat from the chaff

Metabarcoding is by now a well-established method for biodiversity assessment in terrestrial, freshwater and marine environments. Metabarcoding datasets are usually used for - and {beta}-diversity estimates, that is, interspecies (or inter-MOTU) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra-MOTU) information - mostly untapped so far. The use of cytochrome oxidase (COI) amplicons is gaining momentum in metabarcoding studies targeting eukaryote richness. COI has been for a long time the marker of choice in population genetics and phylogeographic studies. Therefore, COI metabarcoding datasets may be used to study intraspecies patterns and phylogeographic features for hundreds of species simultaneously, opening a new field which we suggest to name metaphylogeography. The main challenge for the implementation of this approach is the separation of erroneous sequences from true intra-MOTU variation. Here, we develop a cleaning protocol based on changes in entropy of the different codon positions of the COI sequence, together with co-occurrence patterns of sequences. Using a dataset of community DNA from several benthic littoral communities in the Mediterranean and Atlantic seas, we first tested by simulation on a subset of sequences a two-step cleaning approach consisting of a denoising step followed by a minimal abundance filtering. The procedure was then applied to the whole dataset. We obtained a total of 563 MOTUs that were usable for phylogeographic inference. We used semiquantitative rank data instead of read abundances to perform AMOVAs and haplotype networks. Genetic variability was mainly concentrated within samples, but with an important between-seas component as well. There were inter-group differences in the amount of variability between and within communities in each sea. For two species the results could be compared with traditional Sanger sequence data available for the same zones, giving similar patterns. Our study shows that metabarcoding data can be used to infer intra- and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.

ecology↗

bioRxiv2017

A phylogenomic framework and timescale for comparative genomics and evolutionary developmental biology of tunicates

BackgroundTunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates. Their phylogeny, however, remains poorly understood and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. To resolve their evolutionary relationships and provide a first estimate of their divergence times, we used a transcriptomic approach to build a phylogenomic dataset including all major tunicate lineages, consisting of 258 evolutionarily conserved orthologous genes from representative species.\n\nResultsPhylogenetic analyses using site-heterogeneous CAT mixture models of amino acid sequence evolution resulted in a strongly supported tree topology resolving the relationships among four major tunicate clades: 1) Appendicularia, 2) Thaliacea + Phlebobranchia + Aplousobranchia, 3) Molgulidae, and 4) Styelidae + Pyuridae. Notably, the morphologically derived Thaliacea are confirmed as the sister-group of the clade uniting Phlebobranchia + Aplousobranchia within which the precise position of the model ascidian genus Ciona remains uncertain. Relaxed molecular clock analyses accommodating the accelerated evolutionary rate of tunicates reveal ancient diversification (~450-350 million years ago) among the major groups and allow comparing their evolutionary age with respect to the major vertebrate model lineages.\n\nConclusionsOur study represents the most comprehensive phylogenomic dataset for the main tunicate lineages. It offers a reference phylogenetic framework and first tentative timescale for tunicates, allowing the direct comparison with vertebrate model species in comparative genomics and evolutionary developmental biology studies.

evolutionary biology↗