Congratularions Dr. Barbanti!

A new PopCOmics Doctor

by Xavier Turon

On October, the 9th, our team member Ana Barbanti defended her PhD “Sea turtle conservation: genetics and genomics for a better management” at the University of Barcelona. She was supervised by Marta Pascual and Carles Carreras.

The defence was a success, combining presential and virtual attendees. Dr. Barbanti got the highest marks and congratulations from all members of the jury.

Here goes the abstract:

Conservation actions aim to preserve and recover animal and plant species using in-situ or exsitu strategies. The first, aims to protect and sustain populations in their natural habitat, the second are implemented when local populations are extinct or are about to be. Conservation genetics can provide important insights into the dynamics of endangered populations facilitating their management. This thesis uses traditional markers and new generation sequencing to improve conservation management of the loggerhead (Caretta caretta) and the green turtle (Chelonia mydas). In the first 2 chapters we used microsatellites and mtDNA to assess the outcome of a reintroduction program of green turtles in the Cayman Islands and the status of the reintroduced wild population. We found that 90% of adult wild females and 80% of wild F1 hatchlings were related to the captive population, proving the program successful. This relatedness did affect negatively the fitness of the wild population. Moreover, we found that after only one generation, genetic differentiation between the populations was significant. Our results suggest that assisted colonisation is a viable solution to the global decline of biodiversity. The third chapter explores the potential of 2b-RAD methodology in the field of non-model species population genomics and provides guidelines to optimise protocol and decision making using 2b-RAD. We discovered that, given the big genome size of the loggerhead turtle, a selective-base ligation should be used to obtain an overall depth of coverage of 20x and make the study cost-effective. The fourth chapter studies the population structure and local adaptation of 9 Eastern Mediterranean loggerhead turtle rookeries using 2b-RAD genomic sequencing. We found a high level of population structure and no overlapping among rookeries. Bayesian clustering indicated our individuals to be grouped in nine genetic clusters, which correspond to the distribution found in the PCoA. We found that atmospheric temperature and geographic location of the rookery have a significant impact on population structure, as outlier loci were found associated with these predictors. These results aim to use fine scale genetic information of the Eastern Mediterranean Sea to inform and improve conservation management of loggerhead turtle rookeries.

Congratulations from the team, Dr. Barbanti!

Deep-Sea Metabarcoding

New Paper On Deep-Sea Metabarcoding

By Xavier Turon

DNA Metabarcoding of Deep-Sea Sediment Communities Using COI: Community Assessment, Spatio-Temporal Patterns and Comparison with 18S rDNA

By Atienza S, Guardiola M, Præbel K, Antich A, Turon X, Wangensteen OS

Diversity 2020, 12:123 DOI 10.3390/d12040123

Our paper on COI metabarcoding of sediment communities in deep-sea canyons in NW Mediterranean has been published in the special issue Molecular Biodiversity Assessment in the Deep Sea of the Diversity Journal.

Metabarcoding highlights our current deep ignorance on deep-sea communities. We know just 2,805 morphological species from deep Mediterranean. But we detected > 15,000 MOTUs in our very local study! COI Leray-XT recovers the same ecological patterns than 18S, but with enhanced potential for development of novel taxonomy-free ecological bioindicators.

Here is the abstract:

Among the complex ecosystems and habitats that form the deep sea, submarine canyons and open slope systems are regarded as potential hotspots of biodiversity. We assessed the spatial and temporal patterns of biodiversity in sediment communities of a NW Mediterranean Canyon and its adjacent open slope (Blanes Canyon) with DNA metabarcoding. We sampled three layers of sediment and four different depths (900–1750 m) at two seasons, and used a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) as a metabarcoding marker. The final dataset contained a total of 15,318 molecular operational taxonomic units (MOTUs). Metazoa, Stramenopiles and Archaeplastida were the dominant taxa and, within metazoans, Arthropoda, Nematoda and Cnidaria were the most diverse. There was a trend towards decreasing MOTU richness and diversity in the first few cm (1 to 5) of the sediment, with only 26.3% of the MOTUs shared across sediment layers. Our results show the presence of heterogeneous communities in the studied area, which was significantly different between zones, depths and seasons. We compared our results with the ones presented in a previous study, obtained using the v7 region of the 18S rRNA gene in the same samples. There were remarkable differences in the total number of MOTUs and in the most diverse taxa. COI recovered a higher number of MOTUs, but more remained unassigned taxonomically. However, the broad spatio-temporal patterns elucidated from both datasets coincided, with both markers retrieving the same ecological information. Our results showed that COI can be used to accurately characterize the studied communities and constitute a high-resolution method to detect ecological shifts. We also highlight that COI reference databases for deep-sea organisms have important gaps, and their completeness is essential in order to successfully apply metabarcoding techniques.

Keywords: DNA metabarcoding; COI; 18S rRNA gene; deep-sea; submarine canyons; meiofauna

With this paper PopCOmics contributes to further the development of genetic tools applied to α- and β-diversity studies in marine communities… more to come soon!