From Metabarcoding to Metaphylogeography

Post by Xavier Turon:

New PopCOmics paper:

From metabarcoding to metaphylogeography: separating the wheat from the chaff, by Turon, Antich, Palacin, Præbel and Wangensteen.

We are pleased to announce that our seminal paper on metaphylogeography has been published in ESA’s journal Ecological Applications, here is the link

https://esajournals.onlinelibrary.wiley.com/doi/10.1002/eap.2036

In this paper we set the foundations for the use of intra-motu variability in the assessment of phylogeography and population genetics patterns of many species at a time using databases intended for biodiversity studies with COI metabarcoding.

And here is the abstract:

Metabarcoding is by now a well‐established method for biodiversity assessment in terrestrial, freshwater and marine environments. Metabarcoding data sets are usually used for α‐ and β‐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 data sets 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 data set 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 data set. 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.

We hope this paper will have a strong impact, we will follow this lead to study metaphylogeographic patterns in the framework of the PopCOmics project!

III PopCOMics General Assembly

by Xavier Turon

On November the 12th, 2019, we held in Barcelona the third General Assembly of the PopCOmics project. 16 people attended the meeting, comprising most of the research teams at the University of Barcelona and at the Centre for Advanced Studies at Blanes.

Marta Pascual and Xavier Turon gave an overview of the mid-term report that was presented to the Spanish Ministry in September. In short, all tasks are already ongoing, some already finished, and some still in the first phases. Several new species have been added to the initial workplan.

We were lucky in having already 21 papers with the direct results of the project (and 18 more with related side results related), 3 invited keynotes, 58 meeting presentations, 2 doctoral theses already deposited, 3 Master Theses, and 3 Degree Theses presented. All this speaks of excellent achievements at this stage of the project.

We then had interesting presentations and discussions about the ongoing research. Francesc Mestres gave a talk about the results of five years of genetic monitoring of populations of Liocarcinus depurator in the Atlanto-Mediterranean transition. Oriol Sacristan introduced us to his studies on Cliona sponge symbionts in his Marie Curie SCOOBA project. The doctoral students of the project, Marta Turon, Adrià Antich, Anna Barbanti, Hector Torrado, and Carles Galià updated us on their research. Finally, Núria Marco presented results of her Master Thesis on Didemnum vexillum symbionts.

We concluded with an open round of discussion in which aspects of the dissemination activities and plans for future research projects were commented. We ended up chatting over beer and lunch at the University’s cafeteria.

It was an enjoyable and profitable day and we hope to repeat it next year.

New paper on ascidian chimerism published

by Xavier Turon

We are happy to announce that a new paper has been published with the results of a study of the chimerism in Didemnum vexillum:

M. Casso, D. Tagliapietra, X. Turon, M. Pascual. « High fusibility and chimera prevalence in an invasive colonial ascidian » Scientific Reports, octubre del 2019. Doi: 10.1038/s41598-019-51950-y

In this study, which is part of Maria Casso’s PhD on the global invader Didemnum vexillum, we applied whole genome amplification protocols (WGA) and genotyping-by-sequencing techniques (GBS) to genotype individual zooids of the colonies. With this method we could investigate if the colonies were genetically homogeneous or were chimeric, that is, comprise zooids with different genotypes.

The results reveal that 44% of the colonies of D. vexillum in a natural population in the Ebro Delta (NE Iberian Peninsula) are chimeric. According to the study, this ability to create chimeras could be a determining factor to promote genetic diversity and the colonizing success of this exotic species in natural ecosystems worldwide.

Chimera formation in colonial forms proceeds through fusion of neighbouring colonies. Another objective of the article was to determine whether the ascidian colonies that merged were genetically more similar than those showing rejection. With this goal, we analysed the merging process in ascidian colonies in the Venetian Lagoon through an experimental protocol that put in contact samples from the same colony and fragments from different ones.

The colonies that merged in the experiments carried out in the Institute of Marine Sciences in Venice (Italy) did not share more genomic similarities than those that did not merge. Therefore, there were not genetic differences globally between both analysed groups, except for some loci or genomic regions –with an unknown biological function due the lack of reference genomes- where there was a major similarity regarding genetics. These loci deserve further investigation to determine their role in the fusion/rejection reaction.

This article has been also featured in the University of Barcelona News.

PopCOmics in the 20th Iberian Marine Biology Symposium

 

by Xavier Turon

PopCOmics in the 20^th Iberian Marine Biology Symposium

 In September 9-12, 2019, the XX SIEBM was held in Braga (Portugal). PopCOmics had a nice representation there.

Marta Pascual gave a keynote speech “Population structure in marine organisms: from genetics to genomics”, and four oral presentations and six posters dealt with results of the project, no less!

The titles of the talks were:

-Antich A, Palacín C, San Román D, Wangensteen OS, Turon X. Metabarcoding the benthic boundary layer: the role of sampling method and marker characteristics in the DNA signatures obtained at the interface between benthos and plankton.

-Turon X, Casso M, Pascual M. Population genomics revealed independent colonisation events of a global ascidian invader.

-Carreras C, García-Cisneros A, Wangensteen OS, Ordóñez V, Palacin C, Turon X, Pascual M (2019) East to West: Population genomics and hierarchical analyses reveal differential adaptation footprints in the edible sea urchin Paracentrotus lividus.

-Torrado H, Carreras C, Raventós N, Pascual P, Macpherson E(2019) Environmental and phenotypic drivers affect differential genomic responses in two sympatric congeneric fish.

And the posters were:

-Turon X, Casso M, Turon M, Marco N, Pascual M. Tunic microbiome of a global ascidian invader.

-Pascual M, Casso M, Tagliapietra D, Turon X. High fusibility and chimera prevalence in a worldwide invasive colonial ascidian.

-Pérez-Portela R, Riesgo A, Wangensteen OS, Palacín C, Turon X. Loving the warming: transcriptomic responses to acute thermal shifts in a recent colonizer in the Mediterranean, the sea urchin Arbacia lixula.

-Barbanti A, Turmo M, Blumenthal JM, Boyle J, Broderick AC, Collyer L, Ebanks-Petrie G, Godley BJ, Mustin W, Pascual M, Carreras C. Founding in action: genetic assessment of new populations from the same reintroduction program.

-Carreras C, Pous S, Vega M, Macpherson E, Pascual M. Genotyping impact of mixing samples from multiple non-model species in population genomic analyses

-Torrado H, Mourre B, Raventós N, Carreras C, Tintoré J, Pascual M, Macpherson E. Use of individual early life traits in larval dispersal models: a multispecies approach. 

The meeting was an enjoyable experience. We could meet and discuss with colleagues from the Iberian Peninsula and beyond. The presentations of the PopCOmics project were very well received and we got valuable inputs for our research.

 

Learn more about the meeting at http://20thsiebm.org/

and browse the abstracts in Frontiers Events

https://www.frontiersin.org/events/XX_Iberian_Symposium_on_Marine_Biology_Studies_(SIEBM_XX)_/6597/topic

Enjoy!

IBOL Conference

by Xavier Turon

PopCOmics in the 8th International Barcode of Life Conference

In June 17-20, 2019, the IBOL Conference was held in Trondheim, Norway. 461 participants from 61 nations gathered there and discussed about ongoing developments in barcoding and metabarcoding.

PopCOmics was represented there by Owen Wangensteen, who delivered a talk about the novel concept of metaphylogeography developed within PopCOmics… it enjoyed great acceptance, and Twitter certifies the success of his presentation!

The abstract (published in Genome dx.doi.org/10.1139/gen-2019-0097) follows:

From COI metabarcoding to metaphylogeography: finding the optimal way to get robust haplotype information from raw HTS data 

Owen S. Wangensteen, Adrià Antich, Creu Palacin, Kim Præbel, and Xavier Turon

Background: The natural variability of COI makes it the marker of choice in population genetics and phylogeography studies. The exploitation of COI metabarcoding datasets for intraspecies patterns of genetic variation makes it possible to analyse phylogeographic features for hundreds of species at one time—a field which we name metaphylogeography. The key to implement this approach is to separate erroneous sequences from real intra-MOTU variation. This requires a fine-tuned denoising algorithm to be able to distinguish low-frequency naturally existing haplotypes from artefacts generated by sequencing errors.  
Results: We calculated the changes in entropy at the different codon positions and the changes in the residual variance of AMOVA models to find optimal filtering parameters in COI metabarcoding datasets. These two independent criteria, coupled with co-occurrence patterns of sequences, can meaningfully guide the cleaning of metabarcoding datasets for metaphylogeography. Using a dataset of community DNA from benthic littoral communities from the Mediterranean and Atlantic seas, we developed a two-step cleaning procedure consisting of a denoising within MOTUs followed by a minimal abundance filtering. Reassuringly, these two independent information-content criteria provided similar optimal parameter values for the denoising and abundance filtering steps, suggesting that the natural haplotype sets can be retrieved. When we compared haplotype networks of two species inferred independently by metaphylogeography and classical phylogeography, the results were also reassuringly similar. 
Significance: Our study shows that COI metabarcoding data can be used to infer intra- and interpopulation variability of hundreds of species at one time, providing a new tool with great potential for biogeography, conservation genetics, and invasion genetics.

Group-photo of the participants at the iBOL 2019 conference

Owen delivering his talk in the Conference (note beard-less Owen!)