PhD position (m/f/d) Evolutionary history of allotetraploid species of the Chenopodium album aggregate at Czech University of Life Sciences, Institute of Botany of the Czech Academy of Sciences, Plant Biodiversity and Evolution Research Group, in collaboration with American Brigham Young University and University of Nebraska Omaha, Praha, Czech Republic, Start: 1 October 2023 (preferably months earlier)
We are seeking a highly motivated Ph.D. student to take part in the investigation of the evolutionary history of allotetraploid species of the Chenopodium album aggregate. The main aim of the project is to elucidate the origin of four allotetraploid species with identical subgenome composition and to identify the genomic regions underlying their diversification.
The study is funded by an international collaborative project between Czech (Czech University of Life Sciences and Institute of Botany of the Czech Academy of Sciences) and American (Brigham Young University and University of Nebraska Omaha) research institutions, supported by the Inter-Excellenece program of the Czech Ministry of Education, Youth and Sport.
The origin of species is one of the key issues in biology. An equally interesting question is how species maintains their integrity. What mechanisms ensure that we can call them species? There is still a gap in our knowledge about how the coexistence of two essentially distinct subgenomes drives the speciation on one side, and what mechanisms maintain the species’ integrity on the other, in allopolyploids originating from the same parental combination.
The allotetraploid species of the Chenopodium album agg. with CCDD genomic composition (those originating from the same parental combination) are a good example of allopolyploids to study the aforementioned tasks. Traditionally four species are recognized within this group based on morphology.
These species are widespread and morphologically well differentiated indicating a low level of interspecific gene flow despite frequent sympatric occurrence. Therefore, they represent a good model group to study the diversification and adaptation of allotetraploid species with the same combination of subgenomes.
We will use the advantage of a high-quality reference genome available for this group and re-sequence the genomes of cca 200 individuals to target phylogenomic, population genomic and structural genomic analyses on the CC and DD subgenomes separately.
Specifically, we will investigate: (1) whether the recognized taxa are the result of multiple independent allopolyploidization events or diversification of a single allotetraploid ancestor; (2) if there are any subgenome-specific signatures of selection underlying both the genomic diversification and its maintenance in the recognized Chenopodium taxa.
Responsibilities and duties of the Ph.D. candidate:
- plant cultivation and morphometric analyses
- DNA extraction and library preparation
- phylogenomic and population genomic analyses based on NGS (Illumina) data
- presentation of results at international conferences and preparation of publications
- MSc (or equivalent) in Biology
- experience with basic molecular genetic techniques (DNA extraction, PCR)
- experience with genetic/genomic data analysis (phylogenetics or population genetic)
- good English communication skills (written and spoken)
- experiences with Illumina library preparation
- basic experience with bioinformatic and statistical analysis of NGS data
- basic experience with bash and R scripting
- good presentation skills
- willing to learn
- networking skills
- ability to collaborate and cooperate with other team members
- keen interest in plant evolution and speciation
- a four-year position with a tax-free Ph.D. stipend (120.000 – 192.000,- CZK/year)
- additional funding (60% employment) covered by the project (gross salary 273.000 – 298.000,- CZK, which is cca 230.000 – 250.000 CZK/year after tax)
- friendly and inspiring working environment in an international working group
- collaboration with researchers from other institutions in Czech Republic and the USA
- opportunity to master up-to-date methods (both wet lab and bioinformatic)
- possibility to attend international conferences
- flexible working hours, 25 days of paid vacation
- subsidized meals at the university canteen
The position is available from 1st of October 2023, at the latest. However, an earlier start (June/July 2023) is preferred. Please submit your full application in English by the 15th of March, 2023 by e-mail as a single pdf file to firstname.lastname@example.org .
The application should include: cover letter specifying the applicant’s motivation to apply for the position, previous research experiences and research interests (1-2 pages) CV, names and e-mail addresses of two potential academic referees, For informal queries about the position or the project, please contact Dr. Karol Krak email@example.com