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.

Tuesday, June 21, 2016

Another ChallenGen meeting

by Marta Campos

On the 20th June, the members of ChallenGen Project held a general meeting at the Biology Department of the University of Barcelona.

It was our pleasure to learn about ongoing work of the MarSymbiomics project, with which several collaborative papers have been prepared.
This encounter gave us the opportunity to interact with each other, and to present the latest news and updates on howour research and work is going on . During the last trimester, for example, Maria was in Venezia doing a research stay, Alex and Carles worked with informatics analysis and Clara and Marc prepared two oral communications for the XVI day of evolutionary biology, organizated by the Institute of Catalan Studies. We also learnt about the last results published or submitted within the framework of ChallenGen.

Moreover, the CEAB-CSIC researcher Iosune Uriz was our invited speaker and explained us the main results until now of her project MarSymbiomics.

It was a great week start!

Monday, April 18, 2016

Measuring settlement rates of sea urchins. New paper out!

by Owen Wangensteen

Team members of the ChallenGen Project at the University of Barcelona, in collaboration with scientists from the University of La Laguna (Canary Islands) have just published a new paper on Scientia Marina journal, describing and testing new designs of artificial collectors for quantitative assessment of settlement rates in sea urchins.

The study of population dynamics of sea urchins is crucial for understanding the ecology of Mediterranean and temperate Atlantic rocky shores, since these echinoderms are often the main herbivore species in shallow benthic ecosystems and they are responsible of linking the primary production from seaweeds to other higher levels of the trophic chains. Many sea urchin populations may be limited by the settlement rates (the process by which the planktonic sea urchin larvae settle and become juvenile sea urchins). Methods for measuring these settlement rates were not standardized and yielded non-comparable results. The work presented in this paper, carried out in parallel at Canary Islands and Costa Brava (Spain) shows that three-dimensional collectors made from “bioballs” (a biofilm-friendly, high surface material often used as filters in aquaria) are the most suitable device for this assessment, allowing for an accurate and repeatable measurement of this elusive, yet important, ecological process.

The best part is that these bioballs collectors are useful not only for sea urchins settlers. They could be suitable for assessing settlement and colonization rates for a wide-range of marine invertebrates and can help marine biologists to get a more accurate view of the population dynamics of many species present in benthic ecosystems.

The three types of collector tested in this work: plastic biofilter ball (A, C), vertical brush (B, D) and horizontal triangular mat of coconut fibre (B, E).

Thursday, April 14, 2016

Monitoring ascidians in the Venetian Lagoon

by Maria Casso

A wood pile dolphin, full of benthic organisms, and half eaten by wood-boring species.
Marco and the fog during the sampling.
The Benthic Ecology research group from the Istituto di Scienze Marina, ISMAR (Consiglio Nazionale delle Ricerche, CNR), placed in the Venetian Lagoon, is hosting me for a 3 months research stay. They focuses on ecology of coastal transitional ecosystems, specially benthic communities. More recently, they are interested on wood-boring marine organisms (shipworms and gribbles). This is very important in a place like the Venetian Lagoon as it has a large wooden maritime cultural heritage.

The aim of my stay in Venice is to study the invasive ascidians, which grow on top of those wooden marine structures. To do this, yesterday we went to a field trip around the Venetian Lagoon with Davide Tagliapietra, Marco Sigovini and Irene Guarneri. It was foggy in the beginning but more sunny at the end of the sampling. The objective of the field trip was to determine the distribution of some invasive ascidians and to collect samples for aquaria experiments.

Monday, April 11, 2016

ChallenGen at the workshop “Application of genomic tools for benthic monitoring”

by Xavier Turon

The 4-5 April 2016, the Natural History Museum of Geneva (Switzerland) hosted the workshop “Application of genomic tools for benthic monitoring of marine environment: from technology to legal and socio-economic aspects”, organised by Prof. Jan Pawlowski of the University of Geneva.

The workshop was intended as a forum for the exchange of ideas about the potential of eDNA- related techniques for assessing biodiversity and the impact of human activities on it. It was attended by environmental professionals, members of regulating bodies, and scientists. The presentations and discussion were very lively, and the overarching idea is that DNA-derived indicators may be effectively used in the field of environmental monitoring (as they are in other applied sciences). However, more development and standardization is necessary before they can be integrated with- or substitute altogether- current techniques using morphology-based indicators, which are slow, time-consuming, and reliant on a worlwide dwindling taxonomic expertise.

Xavier Turon and Owen Wangensteen contributed to the workshop with the talk “Issues in metabarcoding of marine benthos”, where they pinpointed some conflicting issues, such as the use of DNA vs RNA, the choice between 18S rDNA or COI markers, or the use of a fixed vs a variable threshold for clustering sequences into MOTUs. The talk was illustrated with results obtained in the projects CHALLENGEN and METABARPARK.

Xavier Turon and Tom Wilding, of the Scottish Association for Marine Science, at the entrance of the Natural History Museum, with a lovely pet!

Wednesday, March 9, 2016

Temporal genetic structure in the introduced ascidian Styela plicata

by M.Carmen Pineda

It’s been almost three years since the last paper on Styela plicata was published by our group, but the saga is not over yet!! The article entitled “Stable populations in unstable habitats: temporal genetic structure of the introduced ascidian Styela plicata in North Carolina”, by M.Carmen Pineda, Xavier Turon, Rocio Perez-Portela and Susanna Lopez-Legentil, has been just published online in the journal Marine Biology.

The solitary ascidian Styela plicata.
Styela plicata is a solitary ascidian, which has been introduced by ship fouling to harbours and marinas around the globe. This species has been extensively studied during the last years, based on its potential to become a plague. However, this is the first time that its genetic composition is studied on a temporal scale. On this recent study, a combination of nuclear and mitochondrial markers (7 microsatellites and a fragment of the gene Cytochrome Oxidase subunit I, COI) were used to analyse the genetic composition of one population subjected to environmental fluctuations and periodical die-offs, every 2 months and over 2.5 years. Overall, our results indicate that the investigated population is stable over time and relies on a periodic arrival of larvae from other populations, maintaining high genetic diversity and a complex interplay of allele gains and losses.

Temporal analyses exploring genetic trends over time are a great tool to predict the likelihood of long time survival of an introduced population in a new habitat and its invasive potential. This kind of information is particularly relevant when deciding which introduced species are more detrimental, and should help resource managers to focus their control and eradication efforts.

Thursday, February 11, 2016

New paper published: Clavelina oblonga in the Ebro Delta

by Xavier Turon

The article “When invasion biology meets taxonomy: Clavelina oblonga (Ascidiacea) is an old invader in the Mediterranean Sea” by Víctor Ordóñez, Marta Pascual, Margarita Fernández and Xavier Turon is now published online in Biological Invasions.

An oyster culture rope totally covered by colonies of Clavelina oblonga.
In this paper we report the taxonomic status of a marine pest that has recently proliferated in bivalve cultures of the Ebro Delta, smothering mussel spat and causing concern among fishermen. The species was initially identified as Clavelina phlegraea, described in 1929 in Italy and endemic of the Mediterranean. Further morphological and genetic studies, however, have concluded that C. phlegraea is a synonym of the Atlantic species C. oblonga, which has been introduced into the Mediterranean at least 80 years ago, but was known under a different name there. This study illustrates the problems of traditional taxonomy to cope with the global-scale distribution of introduced species.

We have also monitored growth and reproductive cycles of C. oblonga in the Ebro Delta, which were markedly seasonal, with peak abundance and reproduction in summertime, followed by regression in winter. Avoidance of mussel and oyster seeding during late summer and early autumn can readily reduce the damage caused by this species.

Tuesday, January 26, 2016

New paper published

by Xavier Turon

New paper published in Frontiers in Zoology: “Feeding cessation alters host morphology and bacterial communities in the ascidian Pseudodistoma crucigaster”, by Susanna López-Legentil, Xavier Turon and Patrick M. Erwin.

This article is the result of yet another collaboration between the projects ChallenGen and MarSymbiOmics. We have coupled electron microscopy and 16S rRNA gene tag pyrosequencing to investigate the bacterial communities associated with the colonial ascidian Pseudodistoma crucigaster, a species endemic to the Mediterranean Sea that has a life cycle with two phases: actively-filtering (active) and non-filtering (resting) forms.

Active (A) and resting (B) colonies of Pseudodistoma crucigaster. The active form has functional siphonal apertures for filtering water, while the resistance form has all apertures sealed by a glassy cuticle.
Resting colonies exhibited a reduced branchial sac (feeding apparatus) and a thickened cuticle. Electron microscope images also suggested higher abundance of colonizing microorganisms on surfaces of resting colonies. Accordingly, bacterial sequences associated with environmental sources (sediment and biofilms, >99 % similarity) were detected exclusively in resting colonies. Bacterial communities of P. crucigaster colonies (active and resting) were dominated by 3 core taxa affiliated (>94 % similarity) with previously described symbiotic Alphaproteobacteria in marine invertebrates. Shifts in rare bacteria were detected when ascidians entered the resting phase, including the appearance of strictly anaerobic lineages and nitrifying bacterial guilds.

These findings suggest that physical (thickened cuticle) and metabolic (feeding cessation) changes in host ascidians have cascading effects on associated bacteria, where modified oxygen concentrations and chemical substrates for microbial metabolism may create anaerobic microhabitats and promote colonization by environmental microorganisms.

Network of bacterial OTUs in three active and three resting samples of Pseudodistoma crucigaster, with edges coded by specificity.

Thursday, January 21, 2016

Master Thesis of Manuel Orobitg presented!

by Xavier Turon

In November, 2015, Manuel Orobitg, student of the Master of Ocenagropahy and Management of the Marine Environment at the University of Barcelona, presented his MSc Thesis “Morphology vs metabarcoding. A comparison of techniques for biodiversity assessment in Maërl beds”, supervised by Xavier Turon, Creu Palacin and Owen Wangensteen. This Thesis reported results from the Metabarpark project, with which the ChallenGen project is closely collaborating.

Sampling of the Maërl community in Islas Cíes.
Assortment of crustaceans from the 1 mm fraction.
In this study, Manuel analysed morphologically samples collected at the same time as the ones for the genetic studies in the detritic bottoms of Islas Cies and Cabrera Archipelago. He focused his analyses on three major groups: polychaetes, crustaceans, and molluscs. He identified at the lowest level possible, with the help of taxonomists (a big thanks goes to Daniel Martin and Lídia Delgado) the species present in the 10 mm and 1 mm filtrates, and obtained biomass values by weight. The morphological analyses found 77, 45, and 44 morphospecies of polychaetes, crustaceans, and molluscs, respectively, while the genetic analyses yielded 182, 245, and 70 MOTUs, respectively, for the same size fractions. Thus, metabarcoding allowed the determination of a higher diversity, but the taxonomic precision attained was higher with morphology. On the other hand, all structural parameters (biomass dominance curves, alpha- and beta-diversity patterns) were markedly different between the metabarcoding and the morphology datasets, indicating that both methods capture different aspects of the biodiversity structure present. The morphological datasets tended to be quantitatively dominated by a few species, while metabarcoding found a more even distribution of biomass of the dominant MOTUs.

Thursday, January 14, 2016

Starfish telomeres on a radio interview

by Alex Garcia

The starfish Coscinasterias tenuispina has the ability to reproduce sexually and asexually by fission, and many populations are even maintained by only asexual reproduction. One of our issues was to investigate if asexual populations can be maintained indefinitely. Our findings revealed that the starfish elongates their telomeres after fission, regenerating their DNA. Telomeres are repetitive sequences at the caps of chromosomes and are correlated with the age of individuals, therefore, in some point of view; the starfish have a mechanism to rejuvenate themselves.

Different media has been interested in this finding after its publication in Heredity. Among them, the radio program “Al otro lado del espejo” in which I participated last week.