Thursday, 8 April 2021

New Paper Published!

 By Adrià Antich

Antich, A., Palacin, C., Wangensteen, O.S. & Turon, X.To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography. BMC Bioinformatics 22, 177 (2021).

In this paper, we address a methodological question concerning metabarcoding pipelines: What is best, to denoise or to cluster sequences? These are two crucial steps when analysing metabarcoding data. However, pipelines depend on the barcode analysed. For COI, we concluded that both steps are necessary and that there is little effect of the order in which they are performed. We also developed our own software to denoise sequences considering the entropy values of the different codon positions for coding barcodes such as COI. Here is the abstract:

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 different 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 influence on the final 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.

Wednesday, 24 March 2021

New PopCOmics paper published!


Posted by Hector Torrado


Impact of individual early life traits in larval dispersal: A multispecies approach using backtracking models

By Torrado, H., Mourre, B., Raventos, N., Carreras, C., Tintoré, J., Pascual, M., & Macpherson, E. (2021).Progress in Oceanography, 192, 102518. DOI: 10.1016/j.pocean.2021.102518


In this paper we use individual-based early life trait data, in combination with backtracking Lagrangian particle dispersion simulations, to design more precise larval dispersal models for nine common coastal fish species along the western Mediterranean Sea. Our results show that having good individually otolith-inferred information about these parameters helps to a better definition of recruit’s origin area and in defining hydrodynamic units.


Here is the abstract:


Dispersal is a key process shaping species population structure. In demersal marine fishes, which usually have sedentary adult phases, dispersion relies on drifting larval stages. However, the dynamics and seasonal variability of seawater masses can greatly determine the connectivity patterns of these species along the same geographic gradient. For this reason, detailed information on the release moment of larvae is needed to obtain accurate patterns of connectivity. In this study, we performed backtracking Lagrangian particle dispersion simulations, with individual-based early life traits data, obtained from otolith reading for 1,413 juveniles of nine fish species belonging to three families (Sparidae, Pomacentridae and Labridae). For each species, individuals had been sampled from four to seven localities in the western Mediterranean Sea between the Gulf of Lion to the Gibraltar Strait. These nine species reproduce in different seasons of the year and their pelagic larval duration (PLD) range from 7 to 43 days. We identified three hydrodynamic units separated by oceanographic discontinuities (Balearic Sea, West Algerian Basin and Alboran Sea) with low settler’s exchange according to our simulations, independently of the PLD and reproductive season of the species. Hatching date and PLD showed significant effects on larval dispersal distance and orientation, both at the intraspecific and interspecific levels, highlighting the importance of these variables in determining the geographic origin of individuals. Our multispecies modelling approach adds a step forward for an accurate description of larval dispersion and recruitment, key to understand population resilience and define management strategies.

 Keywords: Fish larvae, Oceanographic models, Lagrangian particle dispersion, Individual-based model, Early life traits, Otolith reading.


With this paper PopCOmics contributes to the identification of natural management units that can be useful for conservation strategies.






Tuesday, 23 March 2021

New paper on early life in fishes and climate change

Posted by Enrique Macpherson


Núria Raventós, Héctor Torrado, Rohan Arthur, Teresa Alcoverro & Enrique Macpherson (2021) Temperature reduces fish dispersal as larvae grow faster to their settlement size. Journal of Animal Ecology DOI: 10.1111/1365-2656.13435


Global climate change has profound implications for benthic fish communities as it mediates critical early-in-life processes during their planktonic phase. We assess how increasing temperatures can influence the potential dispersal and early-life traits of temperate larval fish communities.

We show that increasing temperature (ca. 4ºC) results in considerable reduction (10-25%) in the dispersal potential. Temperature was the strongest driver of larval growth and pelagic larval duration (PLD) – productivity only marginally influencing these trends. This was because, with increasing temperature, larvae grew quicker to their settlement size.


Here is the abstract:


As species struggle to cope with rising ocean temperatures, temperate marine assemblages are facing major reorganisation. Temperature mediates critical early-in-life processes, when many benthic species with a dual life history disperse through the plankton. Impacts of rising temperatures can thus ripple through the population with community-wide consequences. However, responses are highly species-specific, making it difficult to discern assemblage-wide patterns. We show that increasing temperature results in considerable reduction in the dispersal potential of temperate fish. Examining the otolith microstructure of 9 common species across a temperature gradient in the Mediterranean Sea, we find a nearly universal, assemblage-wide decline in pelagic larval duration (PLD) of between 10-25%. This was because, with increasing temperature, larvae grew quicker to their settlement size. Settlement size itself was largely invariant, an apparently ontogenetically fixed, size-dependent process. Declining PLD did not, however, affect post-settlement growth, which was uncoupled from larval growth. These results suggest that evolutionary hard wiring places strong limits to species’ adaptive capacities, resulting in reduced connectivity and population isolation as waters warm.





Monday, 22 March 2021

Congratulations Dr. Torrado!



Posted by Enrique Macpherson


On February, the 3rd, our team member Héctor Torrado defended his PhD “From genomics to models: Population studies at individual level in littoral fishes from the Western Mediterranean”. He was supervised by Marta Pascual and Enrique Macpherson.


Dr. Torrado obtained the congratulations and highest marks from the jury. We join these congratulations and celebrate having a new doctor in the group.


This is the abstract of his dissertation:


Connectivity and local adaptation are two contrasting evolutionary forces influencing population structure. Due to their complex life cycle, marine fish species tend to be structured in metapopulations, connected almost exclusively by movements in the larval phase. In this thesis, we study the population genomic structure of several Mediterranean littoral fishes and the potential factors affecting their distribution. To asses this goal, we combine a set of different methodologies including population genomics, otolith reading, oceanographical dispersion models and graph theory.


We show a negative effect of temperature on pelagic larval duration but no effect on settlement size and thus raising temperatures would reduce dispersal capabilities of fishes. With an individual-based oceanographic dispersal model, we observed an effect of both hatching date and pelagic larval duration in the dispersal distances and orientations, but variable among species. Furthermore, we found a clear effect of the oceanographic fronts in dispersal capabilities of our species, allowing us to identify three hydrodynamic units in the Western Mediterranean delimited by these fronts.


We found different genomic structuring between sympatric species of Symphodus despite their similar early life traits. Nonetheless, we identified in both species candidate regions for local adaptation by combining outlier analysis with environmental and phenotypic association analyses. We provided tools and guidelines for laboratory and bioinformatics analyses to optimise studies using 2b-RAD sequencing on different non-model organisms with different genome sizes. Additionally, we found in three different localities clear trends of selective mortality for hatch date and lower for growth rate and pelagic larval duration in a common littoral fish. We confirmed these results with a phenotype-genotype association study, finding loci related with these traits, suggesting a genetic basis of differential mortality between settlers and survivors. Finally, we defined the main clusters and the main nodes of connectivity in three fish species in the Western Mediterranean. With this information, we evaluated the protection state of the areas with high importance for connectivity maintenance, finding a small proportion of them protected. All together, these results provide new valuable information about connectivity, population structure and adaptation in littoral fishes of the Mediterranean Sea.



Congratulations, Héctor!