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.

Monday, September 26, 2016

ChallenGen at the SIEBM 2016 in Porto

by Marta Campos

From the 5th to 9th September, several ChallenGen members attended the XIX Iberian Symposium on Marine Biology Studies (SIEBM) in Porto, Portugal, which this year was hosted by the Interdisciplinary Centre of Marine and Environmental Research (CIIMAR). Throughout the week, scientific posters and oral communications were presented and we could learn about biodiversity, conservation, ecology, invasive species and oceanography. Moreover, eight invited speakers, from different parts of Europe, explained current research on hot topics and forecasted future directions in marine biology research. One of these speakers was Xavier Turon, who presented a talk about the use of genetic tools in marine biology in the Iberian context. His talk included some of the newest results attained in the ChallenGen Project.

Aside from this plenary lecture, 8 oral communications and 3 posters were presented with ChallenGen results, so the project had a very relevant presence in this meeting.

We also participated in several social events and cultural activities. In addition, we could enjoy the opportunity to know the wonderful city of Porto and its famous wine. We also had plenty of opportunities to eat codfish, which is cooked in apparently endless ways!

We hope to meet again in the next SIEBM which will take place in two years in Algarve!

The eight members of the ChallenGen Project who attended the SIEBM 2016, at the new CIIMAR building.

Friday, August 26, 2016

ChallenGen Project and CEAB at the XIV Firamar

by Maria Casso

Last weekend, the 20th-21st July, the Centre for Advanced Studies of Blanes (CEAB - CSIC) participated at the XIV Firamar of Sant Pol de Mar. The Firamar is a fair of artisans and activities related to the sea, like many research projects developed at the CEAB. Our ChallenGen Project, which is developed partially at the CEAB, got involved in the event.

As a member of the ChallenGen Project and the CEAB, I stayed in our stand at the fair during Saturday afternoon, explaining the work researchers conduct at the CEAB about invasive species, climate change, conservation, ecology and biodiversity. It was really nice to see how interested are many people on our job!


The stand of the CEAB at the Firamar, with some visitors during Saturday afternoon. Children could paint their own real balloon fish!

Tuesday, August 16, 2016

ChallenGen project and UB at the III Posidonia Summer Festival in Colera

by Carles Carreras

The conference about how molecular tools can be used to study our marine neighbours.
The last 9th of August we participated at the III Posidonia Summer Festival in the beautiful town of Colera. This annual event, organised by the town council and the Som-hi Association, aims to approach people to the sea by organising a large variety of talks and activities, like scientific snorkel, marine biodiversity family workshops or a marine renewable energies conference.

In this context we had the opportunity to explain the ChallenGen Project to local villagers and tourists by describing them several examples of how molecular tools can be used to study our marine neighbours. The talk took place at the Colera Trull, an ancient olive oil cellar, and people from all ages had the opportunity to became scientists for an hour by investigating with genetic markers the life of some of the animals of the Mediterranean sea. We thus discovered how littoral fishes structure their populations and adapt to local environment conditions, or how marine turtles migrate and reproduce, among others interesting examples. The talk was followed by an intense debate were we could answer everybody’s questions including the importance to study and conserve our marine biodiversity.

Tuesday, July 12, 2016

The methods developed for metabarcoding of hard bottom communities explained in an international book chapter

by Xavier Turon

Owen Wangensteen and Xavier Turon have been invited to write a chapter in the book "Marine Animal Forests. The Ecology of Benthic Biodiversity Hotspots", of the Springer International Publishing Company (ISBN: 978-3-319-17001-5), which is edited by Sergio Rossi, Lorenzo Bramanti, Andrea Gori and Covadonga Orejas. In this chapter, entitled "Metabarcoding techniques for assessing biodiversity of marine animal forests", Owen and Xavier explain the methods developed for analysing hard bottom communities using metabarcoding. We believe that it is crucial to setup standardized protocols, and that this book can be an excellent platform to share and disseminate our experience with the different steps of the metabarcoding process.

This chapter is now accepted for publication, and we foresee that it will be published in the forthcoming months.

Techniques developed in METABARPARK, such as the size fractionation of the samples, can be adopted by other teams working on metabarcoding of marine benthos.


Thursday, June 30, 2016

The ChallenGen group has a new doctor!

by Alex Garcia-Cisneros

After a longer period than seems, at least to me, I defended my thesis the last 28th of June. Some members of the ChallenGen project joined the festive day together. The thesis analysed the biology, genetic structure and phylogeography of two starfish species, Coscinasterias tenuispina and Echinaster sepositus.

During these years of thesis work, we found a low genetic diversity in both asteroid species, lower than other echinoderms with the same distribution range. However, the reasons differ depending on the species. Low diversity in E. sepositus can be explained by a recent demographic expansion from few individuals with few alleles, while in C. tenuispina by the presence of asexual reproduction processes along all its distribution range, even with totally monoclonal populations. Furthermore, our results demonstrate that fissiparity in C. tenuispina increases with environmental instability. However, well-fed individuals do not lose their potential for sexual reproduction (development of gonads, only males). Finally, a last chapter in C. tenuispina presents at least one mechanism to avoid or postpone senescence and ensure persistence of clonal populations: telomere elongation.

Although there were nerves, or more precisely, I was extremely nervous, it was a really good festive day.

Me, with my son, receiving the PhD certificate from Marta Pascual, the principal investigator at the UB of the Challengen project, who was a member of the thesis tribunal.


Thursday, June 23, 2016

New paper published: Spatio-temporal patterns of genetic diversity of Styela plicata in harbour populations

by Xavier Turon

We add another paper to the Styela plicata history: “Stochasticity in space, persistence in time: genetic heterogeneity in harbour populations of the introduced ascidian Styela plicata”, by Mari-Carmen Pineda, Beatriz Lorente, Susanna López-Legentil, Creu Palacín and Xavier Turon, which has been published today (23rd June) in PeerJ.

In this study, we analysed genetic structure of the populations of Styela plicata in 9 harbours along the Iberian Mediterranean coast and adjacent Atlantic waters (>1,200 km range) at two time points 5 years apart (2009 and 2014). Using COI sequence data of ca. 400 specimens, we found strong spatial genetic structure, with significant differences among many populations, but no significant differences among years. Our results revealed spatial genetic heterogeneity and temporal homogeneity in S. plicata, suggesting a limited role of recurrent, vessel-mediated transport of organisms among small to medium-size harbours. Our study area is representative of many highly urbanized coasts with dense harbour networks. In these environments, the episodic chance arrival of colonisers appears to determine the genetic structure of populations and the genetic composition of these early colonising individuals persists in the respective harbours, at least over moderate time frames (five years) that encompass ca. 20 generations of S. plicata.

This article is yet another instance of the importance of the temporal component in studies of introduced species to unravel processes occurring during secondary dispersal of non-indigenous species.
Map of the Iberian Peninsula (NW Mediterranean) showing the sampling sites of Styela plicata. Pie charts represent haplotype frequencies for the COI gene in each population analysed in 2009 and 2014.