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Using genomic data of sponges to reveal patterns of genetic diversity and connectivity in the Mediterranean Sea


Ocean and Earth Science

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Dr A Riesgo , Dr M Rius No more applications being accepted Competition Funded PhD Project (European/UK Students Only)

About the Project

Project Rationale:

Understanding the genetic diversity and connectivity patterns of marine invertebrates and how they adapt to their local environments is vital to design conservation strategies. Sponges are crucial components of the benthic ecosystems both because of their abundance and the services they provide [1]. Sponges are among the most threatened species to global warming, especially in seas like the Mediterranean [2], where massive decimations of sponges have recently been reported in correlation with increments in seawater temperature [2]. Given the important ecological role of sponges, such vast losses can have remarkable cascading effects on entire ecosystems [2]. In addition, given that all organisms rely on their genetic diversity to cope with changing environments, if that is reduced, the species’ adaptive potential is compromised, which could result in extinction.

Our aim with the present project is to evaluate the effects of both biological and environmental factors on the geographic distribution of genetic variation of Atlanto-Mediterranean sponges. We aim to understand whether gene flow exists across basins and how it varies depending on the reproductive strategy of the species (brooding vs. oviparous). Also, we will assess the adaptation patterns at the genomic level (using SNP datasets) across the entire distribution of the species.

Methodology:

• 1: Structure and connectivity: The student will use sample collections stored at NHM for two brooding species (Ircinia variabilis and I. fasciculata) and one oviparous species (Petrosia ficiformis), plus collect more samples. 10 populations per species (8 existing and 2 to be collected) will cover their entire distribution. Genome-reduced representation markers will be used to measure genetic diversity and structure using bioinformatic pipelines.
• 2: Local adaptation: The student will identify loci under selection, and test the correlation between their allele frequencies and matrices of environmental parameters (temperature, salinity, chlorophyll A), focusing on differences between Atlantic vs. Mediterranean locations, which have the most divergent conditions.
• 3: Hybridization in Ircinia spp.: The student will assess the frequency of hybridization to assess whether it increases genetic diversity, and whether it is behind specific adaptation patterns where it occurs.
• 4: Microbiomes and disease decimations in I. fasciculata: In a population collected before and after a massive death in Granada (Spain), the student will study pre-disease and surviving genotypes and their microbiomes, doing Amplicon sequencing of the 16S using MiSeq, to understand whether specific microbiome communities linked to certain genotypes are responsible of their resilience.

Training:

The INSPIRE DTP programme provides comprehensive personal and professional development training alongside extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial/policy partners. The student will be registered at the University of Southampton and hosted at the Natural History Museum.
Specific training will include: (i) field-based surveys of subtidal invertebrates; (ii) extensive training in genomic laboratory techniques.; (iii) Bioinformatic and statistical analysis of genomic data.

The successful candidate will write scientific papers for highly ranked international journals and present research in international conferences/workshops. They will directly interface with policymakers like IUCN-Mediterranean, Biodiversity Foundation, and the Spanish Marine Protected Areas Network (RAMPE and MAGRAMA), via long-standing funding and science-policy projects.

Funding Notes

You can apply for fully-funded studentships (stipend and fees) from INSPIRE if you:
Are a UK or EU national.
Have no restrictions on how long you can stay in the UK.
Have been 'ordinarily resident' in the UK for 3 years prior to the start of the project.

Please click http://inspire-dtp.ac.uk/how-apply for more information on eligibility and how to apply

References

[1] Bell, JJ et al. 2015. Conserv Biol 29, 42-53. [2] Garrabou, J et al. 2009. Glob Change Biol 15, 1090-103.
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