BSc and MSc Potential Research Topics

Under the supervision of Dr Luis Cunha (with the co-supervision of several collaborators)

I limit my supervision to topics related to my academic or professional experience, or those I intend to initiate. Most of these topics may use molecular approaches, such as the use of several strategies long used in conservation biology, however with the recent advances in sequencing technologies, genome-wide data become available, allowing an unprecedented scale of useful information and some of these projects will fall within the scope of “Conservation genomics”. This englobes the assumption that genome-scale data allow us to protect any given species with an inherent conservation value.

These projects are well-fitted for someone with a profound interest in contributing to the conservation of a species/population but also keen in learning wet-lab techniques and bioinformatic approaches. The same techniques can be applied to other contexts, and there is also an interest in understanding the colonisation patterns of invasive species (see below a range of titles for different possible projects) or the underlying mechanisms of the stress response (some in extreme environments). Additionally, several of these projects can use previously generated genomic data for a pure in silico approach (bioinformatics-based), which might become an option under a COVID-restricted scenario. I will be happy to discuss a range of project possibilities, and you can always reach me by email.

These may include “umbrella” topics such as:

• Soil biodiversity and function;
• Functional genomics;
• Metabarcoding techniques (and methodological tweaking);
• Microbiomes (of soil and invertebrates);
• Genome sequencing;
• Eukaryotic genomes and mitogenomes;
• Biological invasion;
• Phylogenetics/omics (annelids mostly, but we can discuss other organisms);
• Response to environmental stress and xenobiotics.

 Potential Subtopics

1. Soil Biodiversity:
   • Harnessing genomic tools and building a reference genetic database for belowground fauna in the Gorongosa National Parque (Mozambique);
   • Assessing efficiency and completeness of metabarcoding methods for biodiversity mapping;
   • Mapping the Oligochaeta biodiversity of Portugal: an integrated approach using genetics and classical classification tools;
   • The earthworm diversity of Guyana: using DNA barcodes to reveal a hugely neglected diversity;
   • Evaluation of different preservatives for DNA and RNA recovery from pitfall trapping: the utility of highly saline solutions;
2. Phylogenetics/omics:
   • Hooking a worm, to catch a man: Island phylogeography and colonisation patterns of a pantropical peregrine species;
   • Unwrap my map: revealing the highly complex evolutionary history of South America biogeography through earthworm phylogenomics;
3. Microbiomes (of soil and invertebrates):
   • The effect of pesticides (and mixtures) on microbial communities of soil and gut of edaphic organisms;
   • The holobiont microbiomes of soil fauna (woodlice and earthworms);
4. Eukaryotic genomes and mitogenomes:
   • What makes a giant: Unlocking the genomics signature underlying gigantic earthworms;
   • Assessing ploidy changes in Earthworms and the role of asexual reproduction;
   • Generating genomic markers for species with particular conservation interest (e.g., SSRs, mitogenomes);
5. Biological Invasion:

• The role of non-native soil fauna in seed dispersion and plant invasiveness;
• Do edaphic peregrine species alter the microbial diversity during the invasion?
• Modelling potential distribution of pantropical invasive species around the world (and consequences of different climate change scenarios);

6. Functional Genomics:
   • Hot, but not too hot handle: the functional landscape and underlying molecular mechanisms of stress response in organisms living in an extreme environment;
   • Exploring the functional landscape of microbiomes in terrestrial hydrothermal vents;
   • Functional genomics as a tool for evaluating pesticides impacts on organisms;
7. Biocultural Diversity:
   • Farmer’s perceptions on diversity and function of the soil fauna;

I am also currently developing low cost and robust eukaryotic metabarcoding and DNA enrichment approaches to help with biodiversity mapping using a range of different sources (including non-invasive) and I would be interested in supporting a PhD Project under that scope.

In collaboration with Isa Russo (Cardiff University), two PhD topics are under focus for a joint partnership with possibility of funding:

• Heavy metal pollution impacts on freshwater biodiversity in Kruger National Park, South Africa;
• A ‘tail’ of mice and humans: Signatures of commensalism in Mastomys natalensis in sub-Saharan Africa.