Saturday, October 27, 2018

CHALLENGEN comes to an end

By Xavier Turon and Marta Pascual

Dear followers of the ChallenGen project, we must announce that the project ended officially the 31st December 2017.
We have waited to make this post so that some papers with results could appear and a new project is up and running.
We are very happy about the success of the ChallenGen project and the advances made in the three main objectives, along with our participation in dissemination and outreach activities and student formation.
We have an impressive list of ca. 50 papers, which is on a par with other projects with much (and we mean real much) more budget available.
These results are level with the output in form of meeting presentations, divulgation activities and media appearance. The team has been keen in reaching both the specialized audiences and the general public.
We also emphasize that 5 PhD theses have been completed or initiated within the project, and 18 MSc theses and 12 Bachelor theses have been presented, always with the highest marks.
We want to congratulate the team of the project for the important results obtained. We are happy to announce that our activity will continue in the framework of a new project funded by the Ministry of Science, the PopCOmics project. In this new project, we seek to continue the development of molecular tools as applied to ecological and conservation issues. Please bookmark the webpage of PopCOmics and watch out for interesting news.

ChallenGen is over, long live PopCOmics!

Thursday, January 4, 2018

Results of the study of invasive algae in National Parks published in Marine Pollution Bulletin

by Xavier Turon

We are happy to report that the results concerning the invaded vs non-invaded communities sampled in 2015 have now been published in the international journal Marine Pollution Bulletin: Wangensteen OS, Cebrian E, Palacín C, Turon X. 2018. Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding. Marine Pollution Bulletin, 127:54-66.

Elsevier kindly provides a 50 days free access (starting 21 Dec) to this article at,ashmKxI. After this period you will need a subscription to be able to download it

In this paper we report on the effect that invasive algae have at the community level, targeting mainly the smaller size components (small macrofauna and meiofauna), using the 18S and the COI genes and the fractionation procedure and bioinformatic pipeline developed in our project. Here goes the abstract:

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 Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds.

Images of the communities analysed, with (left) and without (right) invasive algae. A,B: Cc (Caulerpa cylindracea) communities. C,D: Ll (Lophocladia lallemandii) communities. E,F: Aa (Asparagopsis armata) communities. Pictures: (A) from Eneko Aspillaga; (B,F) from the authors; (C,D) from Pol Capdevila; (E) from Enric Ballesteros.

Results from metabarcoding communities from the National Parks published in PeerJ Preprints

by Xavier Turon

While the article is being peer-reviewed, we have published the manuscript in Pre-print format in the repository PeerJ Preprints, where it is freely available at Wangensteen OS, Palacín C, Guardiola M, Turon X. 2017. Metabarcoding litoral hard-bottom communities: unexpected diversity and database gaps revealed by two molecular markers. PeerJ Preprints 5:e3429v1.

We report in this manuscript the astonishing diversity found in communities from Islas Cies and Cabrera. We address several technical aspects, compare the two genes studied (18S and COI), and perform ecological analyses. Here goes the abstract:

We developed a metabarcoding method for biodiversity characterization of structurally complex natural marine hard-bottom communities. Novel primer sets for two different molecular markers: the “Leray fragment” of mitochondrial cytochrome c oxidase, COI, and the V7 region of ribosomal RNA 18S were used to analyse eight different marine shallow benthic communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea). Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. We found unexpectedly high values for MOTU richness, suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignation of the detected sequences. Nevertheless, over 90% (in abundance) of the sequenced reads could be successfully assigned to phylum or lower taxonomical level. This identification rate might be significantly improved in the future, as reference databases are updated. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples, and emerges as a robust, fast, objective and affordable method for comprehensively characterizing the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans, allowing for standardized biomonitoring of these ecologically important communities. The new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities.

Percent of MOTUs found for the main categories of organisms in the three fractions studied with 18S (left) and COI (right) in all communities.

Monday, November 20, 2017

ChallenGen last meeting

by Maria Casso

The 17th November, in Barcelona, we had the (most probably) last meeting of the ChallenGen Project. Anna and Héctor talked about DNA libraries preparation for GBS-like methods. At the end of the meeting we put in common all the publications, conferences and other outputs the group published thanks to the ChallenGen Project. You can check out our publications here.

We will have news soon about the next project!

Monday, June 26, 2017

ChallenGen at the 2017 mid-year meeting of The Crustacean Society (TCS)

by Enrique Macpherson

Enrique Macpherson, Marta Pascual and Ferran Palero were members of the Organising Committee of the 2017 mid-year meeting of The Crustacean Society (TCS), of which EM was also the chair.

The meeting was organized by the Spanish Research Council (CSIC) and University of Barcelona (UB) and took place in Cosmocaixa, Barcelona, Spain, from 19th to 22nd June 2017. A total of 211 scientists from 34 countries attended the meeting. This symposium, with already some decades of existence, has given particular emphasis to the areas historically covered by the TCS meetings (ecology, fisheries, larvae, taxonomy, among many others topics). The meeting also included the “11th Colloquium Crustacea Decapoda Mediterranea” and the “5th Crustacean Larval Conference”.

The congress has been organized with parallel oral sessions and poster exhibitions, and included several invited plenary lectures made by world renowned crustacean researchers. Members of ChallenGen contributed with two oral presentations and ten posters (see Publications and Outreach: Conferences).

Thursday, May 18, 2017

ChallenGen at the Pint of Science festival in Blanes

by Xavier Turon

The Pint of Science festival aims to deliver interesting talks on the latest science research in an accessible format to the public – mainly across bars and pubs (preferably with a pint of beer in hands). It is an International festival being held annually over three days at the same time in hundreds of cities across the world. Blanes, the host city of the CEAB, has participated for the first time in this year’s Pint of Science festival. The scientists of the CEAB gave nine talks three evenings (15-17 May 2017).

Xavier Turon participated in the first day of the festival, presenting the opening talk at a nice bar (Casal la Cooperativa) on the topic: Biodiversity 2.0: genetics and computers to study the living organisms. Needless to say, his talk capitalized on results obtained during the ChallenGen project, particularly those related to biodiversity assessment via metabarcoding.

It was an enjoyable and challenging experience to try to explain in lay terms some complex analysis we do in our research. The audience was very interested and asked many questions after the talk.

Wednesday, March 15, 2017

ChallenGen at the meeting "Developing new genetic tools for bioassessment of aquatic ecosystems in Europe"

by Xavier Turon

ChallenGen was present at the meeting on metabarcoding held in Essen (Germany) in March 7th-9th 2017. This was the kick-off conference of the European Union COST action DNAqua-Net.

This project aims at integrating a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel eco-genomic indices and metrics for routine application for biodiversity assessments and biomonitoring of European water bodies. It also envisages training and dissemination activities. The objectives of ChallenGen are fully compatible with the goals of DNAqua-Net and we wanted to be counted in and contribute.

Xavier Turon is one of the Spanish members of DNAqua-Net and attended this conference, where ca. 200 researchers gathered together to present results, discuss hot topics, and delineate the way forward for achieving a wide acceptance by management bodies of genetic methods for biodiversity assessment in the European context.

Xavier presented the communication "Under the canopy: community-wide effects of invasive algae in marine protected areas revealed by metabarcoding", by Xavier Turon, Owen Wangensteen, Emma Cebrian and Creu Palacín. In this contribution the main results concerning the effects of three invasive algae (Caulerpa cylindracea and Lophocladia lallemandii in Cabrera, and Asparagopsis armata in the Atlantic) on the benthic communities were exposed. We have also drafted and sent a manuscript for publication with these results. This contribution is also a result of the collaboration between ChallenGen and the National Park projects Metabarpark and Corclim.

A heatmap representation of the samples of communities with and without Asparagopsis armata from Cíes Islands, separated by invasion status (green: non-invaded, red: invaded) and fraction (blue: macrobenthos; turquoise: meiobenthos).

Tuesday, October 18, 2016

New paper published: Genetic diversity and demography of the red starfish

A beautiful specimen of the red starfish Echinaster sepositus.
by Alex Garcia-Cisneros

One of the most wonderful starfish of the Mediterranean suffered a large demographic expansion since the last maximum glacial period. However, its demographic expansion does not prevent it to have a weakness point: a low genetic diversity that might indicate the vulnerability of the species. These and more results were recently published by the ChallenGen team in a manuscript entitled “Low genetic diversity and demographic expansion in the red starfish Echinaster sepositus (Retzius 1816)” at the Scientific Reports.

The authors used both mitochondrial and nuclear markers to resolve the phylogeography and population genetics of the commonly named “red starfish” (Echinaster sepositus). The authors analysed samples from most of the distribution range of the species, with 15 localities distributed between both Mediterranean basins and the Atlantic Ocean.

Besides to demonstrate the low genetic diversity of the species compared with other echinoderms, the species showed a weak genetic structure within marine basins despite the a priori low dispersal potential of its lecithotrophic larva. The lecithotrophic larva in this species does not live more than few days before the settlement and therefore, it makes it difficult to connect distant or isolated populations. Furthermore, we found sharp differences in two Mediterranean localities, Cartagena and Livorno, that are located close to large marine harbours and coastal areas affected by industry, although our experimental design does not allow us to assess the effects of pollutants on the genetic structure.

Bar plots of the Bayesian clustering analysis obtained using STRUCTURE for different K values and based on the combination of both mitochondrial sequences (COI) and microsatellite loci.

Monday, October 10, 2016

Crossing Borders: Temporal genetic differentiation over oceanographic fronts

by Ferran Palero

A new paper from the CHALLENGEN team entitled “Temporal and spatial genetic differentiation in the crab Liocarcinus depurator across the Atlantic-Mediterranean transition” has been recently published in the JCR journal Scientific Reports.

Median joining haplotype network. Each circle represents a haplotype and its size is proportional to its frequency. Location acronyms are DELT (Delta de l’Ebre), VALE (València), ALAC (Alacant), WALB (Málaga) CADI (Cádiz).

Proportion of individuals assigned to the MED haplogroup in each location and sampled year from 1000 pseudoreplicates.
Spatial genetic studies often require sampling broadly separated areas, difficult to access simultaneously. Although comparing localities surveyed at different time periods might result in spurious genetic differentiation, there is a general believe on the stability of genetic structure through time, particularly if sampled localities are isolated or very distant. However, should we really expect stable genetic patterns in marine species? To test this important question, Marta Pascual and collaborators have assessed the time-variation of phylogeography patterns of the portunid crab Liocarcinus depurator across the Atlantic-Mediterranean transition. A partial fragment of the cytochrome oxidase I gene was sequenced in 366 individuals collected during three time periods from localities at both sides of each of the three main oceanographic discontinuities in the area: Gibraltar Strait, Almeria-Oran Front and Ibiza Channel. Although localities showed genetic fluctuations through time, a significant gradient was detected along the coast for all sampling periods. Significant inter-annual differences identified within the Alicante area, north of the Almeria-Oran Front, were associated with shifts in the relative contribution of Atlantic and Mediterranean water masses. The authors conclude that the persistence of a clinal pattern in the Atlantic-Mediterranean transition area despite local fluctuations suggests a complex balance of dispersal and selection.

Despite the Alicante population from 2007 had a larger proportion of Atlantic haplotypes, an overall genetic cline remains stable across the 3-year sampling period.

Friday, September 30, 2016

DNA barcoding the phyllosoma of Scyllarides squammosus: New paper out!

by Ferran Palero

A new paper from the ChallenGen team entitled “DNA barcoding the phyllosoma of Scyllarides squammosus (H. Milne Edwards, 1837) (Decapoda: Achelata: Scyllaridae)” has been recently published in the JCR journal Zootaxa.

As shown by their fierce-looking mouthparts, phyllosoma larvae rank high on the planktonic food-chain as specialized predators. Luckily for us, they generally do not grow above a few centimeters in total length!
Despite being the slipper lobster genera with the largest number of species with commercial importance, little is known of the unique long-lived planktonic phyllosoma stages of Scyllarides. Recently, a large and diverse collection of Scyllaridae phyllosoma from the Coral Sea was analysed by members of our team. DNA-barcoding and phylogenetic analyses allowed Ferran Palero and colleagues to identify several S. squammosus phyllosoma larvae, including stages that were previously undescribed or poorly known. From a combination of adult and larval morphology with molecular data, we could reveal inconsistencies with regard to the affinities among species assigned to Scyllarides. This new evidence will contribute to future studies addressing the phylogenetic relationships within the genus.

Furthermore, this new paper represents the first contribution of Rebeca Genis-Armero, a MSc. student recently graduated from the University of Valencia and a name to keep in mind for the future of scientific drawing and phyllosoma larvae.