PhD Fellowship in Evolutionary Biology (University of Copenhagen)

Our group and research Plant domestication and the development of agriculture were a turning point for human history. Studying plant domestication is essential to understand the origin of complex societies and to develop better crops able to adapt to today’s changing environment. In our research group, we are interested in understanding the evolutionary processes that shaped plants during domestication. Through comparative genomics and ancient DNA, we focus on characterising key aspects of plant domestication: demographic history, dispersion trajectories, selection signatures, and plant-microbiome coevolution. One aspect of plant domestication that remains mostly unexplored—and will be the focus of the PhD project—is the role of the root microbiome. Plant microbiomes have a notable impact on plant fitness and might have contributed to plant adaptation as humans dispersed plants outside of their native environment and selected for desirable traits. We will study the coevolution of legumes and their root bacteria through the domestication process using a combination of modern and ancient plant and bacterial genomes. To do so, we will work on different species of legumes (genus Phaseolus) that were domesticated in the Americas. We will generate genomic data from wild and domesticated plants and their root microbiome, as well as genomic data from ancient bean seeds at intermediate stages of domestication. Through comparative and population genomics we will characterise the demographic histories, dispersion patterns and selection signatures of the plant and its root symbionts. The PhD fellow will be part of a newly established research group led by Assistant Prof. Jazmín Ramos Madrigal, funded by the Novo Nordisk Foundation, within the Globe Institute Section for Hologenomics. PhD project description The PhD project is part of a larger initiative aimed at studying the coevolution of legumes and their root bacteria through the domestication process. Due to their ability to form symbiotic relationships with soil bacteria, legumes offer a unique opportunity to investigate the coevolution of plants and their root microbiome across different environments. Additionally, since legume seeds can be found in the archaeological record, they can be used to trace these species through time using ancient DNA. The PhD project involves sampling Phaseolus nodule data from wild and domesticated plants, generating whole-genome sequencing data from wild and domesticated legumes, as well data from ancient bean seeds, and data analysis and integration of the results. The PhD fellow will work closely with Assistant Prof. Jazmín Ramos Madrigal and a laboratory technician to perform the work. In general, this PhD project will have three components: Field work to collect plant material from Mesoamerica and South America Laboratory work aimed at generating high-throughput DNA sequencing data from modern and archaeological plant material Computational analyses of the data using population genomics and metagenomics tools Supervisors Assistant Prof. Jazmín Ramos Madrigal. Globe Institute, Section for Hologenomics. jazmin.madrigal@sund.ku.dk Profesor Tom Gilbert. Globe Institute, Section for Hologenomics. tgilbert@sund.ku.dk Start: 1 July 2025 Duration: 3 years as a PhD student Job description Your key tasks as a PhD student at Globe are: Carrying through an independent research project under supervision. Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points. Participating in active research environments including a stay at another research team. Obtaining experience with teaching or other types of dissemination related to your PhD project Teaching and disseminating your knowledge. Writing a PhD thesis on the grounds of your project Key criteria for the assessment of applicants We are looking for candidates within the fields of biology, ecology, genomics, agronomy, molecular biology, or similar with experience relevant to the project (see qualifications below). The ideal candidate will have a curious mindset with strong interest in evolutionary biology, ecology and in the subjects related to the PhD position (see project description), and experience in: Carrying out fieldwork Carrying out molecular biology laboratory work Proficiency in the English language, both written and spoken The candidate should have interest in learning or experience in: Carrying out ancient DNA laboratory work Processing and analysing high-throughput genomic sequencing data Conducting population genomics, comparative genomics or metagenomic computational analyses Working in an interdisciplinary research group Other relevant assessment criteria: Experience with engaging with diverse stakeholders the grade point average achieved Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project, e.g. biology, ecology, agronomy, environmental sciences. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years). Place of employment The place of employment is at the Globe Institute, Section for Hologenomics (Øster Voldgade 5-7, 1350, Copenhagen) Faculty of Health and Medical Sciences, University of Copenhagen. We offer creative and stimulating working conditions in a dynamic and international research environment. Our research facilities include state-of-the-art core facilities including dedicated ancient DNA clean labs, modern DNA labs, an automated pipeline for DNA extraction and sequencing, and a constantly-expanding computer cluster. About Globe Institute The Globe Institute is part of the Faculty of Health and Medical Sciences at the University of Copenhagen. The Institute’s main purpose is to address basic scientific questions through interdisciplinary approaches. The institute operates at the intersection of natural and medical sciences and the humanities. Information on the institute can be found at: https://www.globe.ku.dk/. The Globe Institute is committed to creating an inclusive and diverse environment where employees and students can belong and thrive. See https://globe.ku.dk/about/diversity-programme/ for more information. All qualified applicants will receive full consideration. Candidates who, through their research, teaching, and/or service, contribute to diversity and competencies of our Institute are encouraged to apply. The University of Copenhagen strives to offer a family friendly and flexible working environment with a sustainable balance between work- and private life, including parental leave schemes (up to 47 weeks for both parents) and up to six weeks of paid holidays per year. The university offers a variety of services for international researchers and accompanying families Terms of employment The average weekly working hours are 37 hours per week. The position is a fixed-term position limited to a period of 3 years. The start date is 1 July 2025. The employment is conditioned upon the applicant’s successful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant. The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty’s rules on achieving the degree. Salary, pension and terms of employment are in accordance with the agreement between the Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary starts at approximately 30,716.02 DKK/Roughly 4,117.65 EUR (April 2024 level) plus pension. Questions For specific information about the PhD fellowship, please contact Assistant Prof. Jazmín Ramos Madrigal. General information about PhD studies at the Faculty of Health and Medical Sciences is available at the Graduate School’s website: https://healthsciences.ku.dk/phd/guidelines/ Application procedure Your application must be submitted electronically by clicking ‘Apply now’ below. The application must include the following documents in PDF format: 1. Motivated letter of application (max. one page) 2. CV incl. education, experience, language skills and other skills relevant for the position 3. Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted. As a prerequisite for a PhD fellowship employment, your master’s degree must be equivalent to a Danish master’s degree. We encourage you to read more in the assessment database: https://ufm.dk/en/education/recognition-and-transparency/find-assessments/assessment-database Please note that we might ask you to obtain an assessment of your education performed by the Ministry of Higher Education and Science 4. Publication list (if possible) Application deadline: Sunday the 16th of March 2025, 23.59pm CET We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements. The further process After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor. The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement. Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself. You find information about the recruitment process at: https://employment.ku.dk/faculty/recruitment-process/ The applicants will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities. Interviews are expected to be held in week 14 The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background. APPLY NOW Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career. Info Application deadline: 16-03-2025 Employment start: 01-07-2025 Working hours: Full time Department/Location: Globe Institute If you apply for this position please say you saw it on Bioloxy

Our group and research
Plant domestication and the development of agriculture were a turning point for human history. Studying plant domestication is essential to understand the origin of complex societies and to develop better crops able to adapt to today’s changing environment. In our research group, we are interested in understanding the evolutionary processes that shaped plants during domestication. Through comparative genomics and ancient DNA, we focus on characterising key aspects of plant domestication: demographic history, dispersion trajectories, selection signatures, and plant-microbiome coevolution.

One aspect of plant domestication that remains mostly unexplored—and will be the focus of the PhD project—is the role of the root microbiome. Plant microbiomes have a notable impact on plant fitness and might have contributed to plant adaptation as humans dispersed plants outside of their native environment and selected for desirable traits.

We will study the coevolution of legumes and their root bacteria through the domestication process using a combination of modern and ancient plant and bacterial genomes. To do so, we will work on different species of legumes (genus Phaseolus) that were domesticated in the Americas. We will generate genomic data from wild and domesticated plants and their root microbiome, as well as genomic data from ancient bean seeds at intermediate stages of domestication. Through comparative and population genomics we will characterise the demographic histories, dispersion patterns and selection signatures of the plant and its root symbionts.

The PhD fellow will be part of a newly established research group led by Assistant Prof. Jazmín Ramos Madrigal, funded by the Novo Nordisk Foundation, within the Globe Institute Section for Hologenomics.

PhD project description
The PhD project is part of a larger initiative aimed at studying the coevolution of legumes and their root bacteria through the domestication process. Due to their ability to form symbiotic relationships with soil bacteria, legumes offer a unique opportunity to investigate the coevolution of plants and their root microbiome across different environments. Additionally, since legume seeds can be found in the archaeological record, they can be used to trace these species through time using ancient DNA.

The PhD project involves sampling Phaseolus nodule data from wild and domesticated plants, generating whole-genome sequencing data from wild and domesticated legumes, as well data from ancient bean seeds, and data analysis and integration of the results. The PhD fellow will work closely with Assistant Prof. Jazmín Ramos Madrigal and a laboratory technician to perform the work.

In general, this PhD project will have three components:

Field work to collect plant material from Mesoamerica and South America
Laboratory work aimed at generating high-throughput DNA sequencing data from modern and archaeological plant material
Computational analyses of the data using population genomics and metagenomics tools

Supervisors
Assistant Prof. Jazmín Ramos Madrigal.

Globe Institute, Section for Hologenomics.

jazmin.madrigal@sund.ku.dk

Profesor Tom Gilbert.

Globe Institute, Section for Hologenomics.

tgilbert@sund.ku.dk

Start: 1 July 2025

Duration: 3 years as a PhD student

Job description
Your key tasks as a PhD student at Globe are:

Carrying through an independent research project under supervision.
Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.
Participating in active research environments including a stay at another research team.
Obtaining experience with teaching or other types of dissemination related to your PhD project
Teaching and disseminating your knowledge.
Writing a PhD thesis on the grounds of your project

Key criteria for the assessment of applicants
We are looking for candidates within the fields of biology, ecology, genomics, agronomy, molecular biology, or similar with experience relevant to the project (see qualifications below).
The ideal candidate will have a curious mindset with strong interest in evolutionary biology, ecology and in the subjects related to the PhD position (see project description), and experience in:

Carrying out fieldwork
Carrying out molecular biology laboratory work
Proficiency in the English language, both written and spoken

The candidate should have interest in learning or experience in:

Carrying out ancient DNA laboratory work
Processing and analysing high-throughput genomic sequencing data
Conducting population genomics, comparative genomics or metagenomic computational analyses
Working in an interdisciplinary research group

Other relevant assessment criteria:

Experience with engaging with diverse stakeholders
the grade point average achieved

Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project, e.g. biology, ecology, agronomy, environmental sciences. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years).

Place of employment
The place of employment is at the Globe Institute, Section for Hologenomics (Øster Voldgade 5-7, 1350, Copenhagen) Faculty of Health and Medical Sciences, University of Copenhagen. We offer creative and stimulating working conditions in a dynamic and international research environment. Our research facilities include state-of-the-art core facilities including dedicated ancient DNA clean labs, modern DNA labs, an automated pipeline for DNA extraction and sequencing, and a constantly-expanding computer cluster.

About Globe Institute
The Globe Institute is part of the Faculty of Health and Medical Sciences at the University of Copenhagen. The Institute’s main purpose is to address basic scientific questions through interdisciplinary approaches. The institute operates at the intersection of natural and medical sciences and the humanities. Information on the institute can be found at: https://www.globe.ku.dk/.

The Globe Institute is committed to creating an inclusive and diverse environment where employees and students can belong and thrive. See https://globe.ku.dk/about/diversity-programme/ for more information. All qualified applicants will receive full consideration. Candidates who, through their research, teaching, and/or service, contribute to diversity and competencies of our Institute are encouraged to apply. The University of Copenhagen strives to offer a family friendly and flexible working environment with a sustainable balance between work- and private life, including parental leave schemes (up to 47 weeks for both parents) and up to six weeks of paid holidays per year. The university offers a variety of services for international researchers and accompanying families

Terms of employment
The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 3 years. The start date is 1 July 2025.

The employment is conditioned upon the applicant’s successful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty’s rules on achieving the degree.

Salary, pension and terms of employment are in accordance with the agreement between the Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary starts at approximately 30,716.02 DKK/Roughly 4,117.65 EUR (April 2024 level) plus pension.

Questions
For specific information about the PhD fellowship, please contact Assistant Prof. Jazmín Ramos Madrigal.

General information about PhD studies at the Faculty of Health and Medical Sciences is available at the Graduate School’s website: https://healthsciences.ku.dk/phd/guidelines/

Application procedure
Your application must be submitted electronically by clicking ‘Apply now’ below. The application must include the following documents in PDF format:

1. Motivated letter of application (max. one page)

2. CV incl. education, experience, language skills and other skills relevant for the position

3. Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted. As a prerequisite for a PhD fellowship employment, your master’s degree must be equivalent to a Danish master’s degree. We encourage you to read more in the assessment database: https://ufm.dk/en/education/recognition-and-transparency/find-assessments/assessment-database Please note that we might ask you to obtain an assessment of your education performed by the Ministry of Higher Education and Science

4. Publication list (if possible)

Application deadline: Sunday the 16th of March 2025, 23.59pm CET

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor.

The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement.

Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You find information about the recruitment process at: https://employment.ku.dk/faculty/recruitment-process/

The applicants will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

Interviews are expected to be held in week 14

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.

APPLY NOW

Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.