A role of genomic diversity and pathogen pressure in the invasion success – a case of common raccoon
A Phd position funded from National Science Centre stipend (3500 PLN/month gross) is available for 3 years, followed by 1 year of the stipend offered through the regular PhD program of Institute of the Nature Conservation, Polish Academy of Sciences
PI: dr hab. Aleksandra Biedrzycka (ORCID 0000-0001-5096-2767).
Formal conditions: Admission to the Doctoral School of Natural and Agricultural Sciences at Polish Academy of Sciences.
The candidates must follow rules and requirements of the Doctoral School and submit the required documents (https://botany.pl/index.php/en/teaching-en/doctoral-school-en/admissions-en) along with the application.
Starting date: 01.10.2021
Project description: Invasive Alien Species (IAS) are animals and plants that are introduced accidentally or deliberately into a natural environment where they are not normally found, with serious negative consequences for their new environment. Human-mediated biological invasions are a component of global change, and their impact on the communities and ecosystems they invade is substantial and complex. Understanding ecological and evolutionary processes that promote invasion is a key first step in developing long-term approaches to prevent future invasions and to manage existing ones. Genetic studies of expanding populations demonstrate that adaptation to novel environments can occur within 20 generations or less, indicating that evolutionary processes can influence invasiveness. Still, it remains largely unknown how local environments shape genomes and population genetic structure of invasive species that successfully colonise a wide range of habitats.
The ecological factor that is believed to affect invasion success profoundly is the pathogen pressure. According to the enemy release hypothesis, an alien species introduced to a new region will experience reduced impacts from natural enemies resulting in a competitive advantage over resident species.
We use native and invasive populations of common raccoon Procyon lotor to determine the genetic factors responsible for the spectacular success of the invasion of this species in Europe. Comparing genomic diversity of populations in the native and invasive range of the species we determine the mechanisms responsible for rapid local adaptation that determines the success of the invasive species. Using a number of single nucleotide polymorphisms located both in the functional and noncoding regions of the raccoon genome we are going to search for footprints of selection and determine the genomic regions that undergone selection as a result of the invasion process.
To get a comprehensive insight into the factors playing a role in successful invasion, we will use DNA metabarcoding approach to assess and compare the composition of raccoon pathogenic fauna between native and invasive populations. According to the enemy release hypothesis, raccoon pathogens from introduced populations should present lover diversity and prevalence, which facilitates the success of invader. The results from our project will give insight into the genomic basis of adaptation in successful invasive species.
Scope of work:
The PhD student will be involved in a project described above, her/his specific responsibilities will be
1. Fieldwork - The coordination of sample collection and collaboration with hunters in Poland, Czech Republic and Germany.
2. Lab work
- DNA extraction from various sample types (tissue, smears) for genomic analysis and metabarcoding
- Preparation of genomic libraries for RAD-seq experiment, sequencing of libraries
- Preparation of amplicon libraries for pathogen metabarcoding and library sequencing.
3. Data analysis (using R and Linux/Unix environment)
- Participation in sequencing data filtering and SNP calling and analysis of SNP diversity. Comparing genomic diversity of native and invasive raccoon populations and searching for genomic signatures of selection and population structure.
The aim of this task is to characterise variation in a large number of SNPs randomly scattered through the genome. Rad-seq methods have the ability to detect loci under selection in genome scans, given the density of markers and the extent of linkage disequilibrium (LD). Random location of Rad-seq SNPs both in coding and noncoding regions will also enable understanding of population structure and demography, assessing population subdivision, migration rates and routes or population size changes through time.
- Metabarcoding data analysis.
Comparing the pathogen pressure between the invasive and native populations. We will test for bacterial, micro-eukaryotic and helminth composition.
Candidates should have a background in ecology, evolution, genetics and/or bioinformatics and be an independent learner. Familiarity with R, Linux/Unix, computing clusters, and the use of bioinformatic tools would be advantageous. A driving license is also a plus.
The application should include:
1) A scan of MSc diploma in biology, biotechnology or other relevant;
2) A reference letter from recognized scientist who have a first-hand knowledge of the applicant’s skills and past research experience.
3) A Curriculum Vitae (maximum 2 pages) including information on relevant academic achievements, publications, awards, and relevant experience and training. This document should also include identification information (PESEL number for candidates from Poland, or passport number for candidates from abroad);
4) A motivation letter (maximum 2 pages), explaining how the applicant’s background and research interests make them a suitable candidate for the position;
5) A short description of studies included in the master thesis (maximum 1 page) and a thesis pdf version.
Interested applicants should contact dr Aleksandra Biedrzycka biedrzycka@iopkrakow.pl.
