PhD in Evolutionary Ecology and genomics Full-time NEW

PhD in Evolutionary Ecology and Genomics

PhD candidate position in Evolutionary Ecology and genomics with specialization in amphibian skin microbiome.

Uppsala University, Department of Ecology and Genetics

The Department of Ecology and Genetics at Uppsala University is part of the Evolutionary Biology Centre (EBC), a leading international research environment in ecology, evolution, and biodiversity science. The department brings together researchers and students from around the world and conducts research spanning evolutionary ecology and genetics to ecosystem studies.

PhD student position in Evolutionary Ecology and Genomics, focusing on biodiversity and the evolution of amphibian skin microbiomes within the Animal Ecology programme at the Department of Ecology and Genetics.

Project description

How microbes influence the ecology and evolution of host organisms is a fundamental question in biology. Microbiome can have a strong impact on behavior, health, and immune responses of the host. In response to changing temperatures, the health status of host populations can be influenced by host microbiomes. Broad-scale studies have shown that skin microbiome composition of amphibians changes along latitudinal gradients, and microbiome composition can be disrupted by temperature and infections. However, large-scale studies examining microbiome interactions in wild amphibians remain scarce at Swedish and global scales.

The PhD candidate will work on the project “Amphibian skin microbiomes and infection diseases”, within the group of Maria Cortazar Chinarro at the Department of Ecology and Genetics. The position is fully funded for four years. More information about her research can be found here: https://www.uu.se/institution/ekologi-och-genetik/forskning/zooekologi/cortazar-chinarros-grupp

This Phd project aims to explore skin microbiome diversity and composition across populations and at regional scales and broad-scale latitudinal gradients. High-quality metagenomic resources from the skin of both common and endangered amphibian species will be generated to infer phylogenetic relationships and examine how host evolutionary history, genetic variation, environmental (abiotic) factors, and infectious diseases shape host–skin microbiome interactions. To investigate these relationships, the project will characterize the skin microbiome composition—including bacteria, viruses, fungi, and protists—using an integrative approach that combines metabarcoding, metagenomics, and population genomics methods.

Throughout the doctoral programme, the student will apply a wide range of bioinformatic methods and sequencing approaches, including amplicon sequencing analyses, shotgun metagenomics, and metatranscriptomics. The project will also involve extensive fieldwork and molecular laboratory work to generate high-quality sequencing data.

Duties

At the start of the PhD project, the selected candidate will be responsible for organizing, coordinating, and conducting regional- and broad-scale fieldwork, as well as molecular laboratory work. This will include DNA and RNA extractions and the preparation of samples for sequencing, such as constructing amplicon and metagenomic libraries for short-read (Illumina) and long-read (PacBio/Nanopore) sequencing. In the later stages of the PhD, and depending on the amount of high-quality data generated, the availability of existing pathogen resources, and the student's interests, the project may expand to investigate newly emerging diseases and develop technologies to detect them in wild amphibian populations.

PhD-students at IEG are encouraged to enroll in teaching. The levels and content of teaching depend on the availability of teaching duties and the interests of the student, but will in general not exceed 20% of full-time employment and mainly consist of teaching assistant roles in different undergraduate courses offered by the biology section.

The candidate is expected to actively participate in the daily activities of the research group and in programme and departmental events, such as departmental and programme seminars, as well as internal networking meetings and conferences.

Qualifications required

To meet the entry requirements for doctoral studies, you must:

• hold a Master's (second-cycle) degree in Ecology, Evolutionary Biology, Conservation Biology or related field.
• have completed at least 240 credits in higher education with at least 60 credits at Master's level including an independent project worth at least 15 credits, or
• have acquired substantially equivalent knowledge in some other way.

The successful candidate holds a Master's degree in evolutionary ecology or a closely related field, with a strong background in host-parasite evolution and genomics. Proficiency in bioinformatic analyses, including population genomics and metagenomics, is required, as is demonstrated experience with molecular laboratory techniques and high-throughput sequencing data. A valid driving licence (type B) is mandatory, as the position involves ecological fieldwork at sites that may not be accessible by public transport.

Qualifications desired

Experience with microbiome analyses and ecological fieldwork is considered an advantage. Given the collaborative nature of the project, we place importance on strong teamwork, communication, and interpersonal skills. We also value personal qualities such as curiosity, initiative, responsibility, and the ability to work both independently and as part of a research team.

Additional skills, such experimental evolution work on infection diseases will be considered advantageous.

About the employment

The employment is a temporary position according to the Higher Education Ordinance chapter 5 §7. Scope of employment: full-time. Starting date 2026-10-01 or as agreed. Location: Uppsala.

For further information about the position, please contact Researcher, Group Leader, Maria Cortazar Chinarro, maria.cortazar@ebc.uu.se.

Application instructions

The application should include 1) a letter describing yourself, your research interests, why you want to pursue a Ph.D., and why you are suitable for the position (maximum of 2 pages), 2) your CV, 3) a brief description of your education, 4) a copy of your master's degree and your course grades, along with a copy of your master's thesis, 5) names and contact details of at least two referees (email addresses and phone numbers), and 6) any publications if applicable.

The application should be written in English.

You are welcome to submit your application no later than June 01, 2026. UFV-PA 2026/844.