We are seeking a highly motivated Ph.D. student to take part in the investigation of the phylogeography of North American desert species of the genus Chenopodium. The main aim of the project is to better understand the evolutionary history of the North American desert biota in the context of Neogene orogenic activity and the Pleistocene glacial-interglacial cycles, as well as the influence of these events on geographic patterns of genetic diversity predicted by refugia hypotheses. The study is funded by an international collaborative project between Czech (Czech University of Life Sciences) and American (Brigham Young University, Utah) research institutions, supported by the Inter-Excellenece program of the Czech Ministry of Education, Youth and Sport.
Project description:
The origin and historical dynamics of desert communities in North America have intrigued naturalists for over a century. Well-preserved macrofossils of flora and fauna in these ecoregions have allowed an understanding of the historical dynamics in desert communities. Moreover, in the last three decades extensive molecular data utilized in evolutionary studies has shed light on the timing of the origin of many of the lineages that inhabit these ecosystems. There is an emerging consensus about the timing of the interspecific and intraspecific divergence of arid-adapted biota in the deserts of North America. On one hand, pre-Quaternary interspecific divergence has been estimated for several lineages, and has been associated with the Neogene orogenic events that promoted the expansion of aridlands in western North America. On the other hand, intraspecific divergence has been associated with the late Neogene (Late Miocene/Pliocene) and Quaternary (Pleistocene/Holocene) periods. Suggesting that the Pleistocene glacial-interglacial cycles promoted intraspecific divergence and demographic changes but infrequently speciation. Evolutionary and phylogeographic studies of the North American desert biota have found evidence of Pleistocene demographic expansion, and strong phylogeographical structure linked to either late Neogene or Quaternary time periods. Nevertheless, there is still some debate when disentangling the effect of the late Neogene orogenic activity versus Pleistocene climate events on the phylogeographic and demographic history in this region. To better understand the evolutionary history of the North American desert biota in the context of Neogene orogenic activity and the Pleistocene glacial-interglacial cycles, as well as the influence of these events on geographic patterns of genetic diversity predicted by refugia hypotheses, we would like to study the phylogeographic and demographic history of two closely related annual diploid Chenopodium species. The first one is taxonomically well-defined C. fremontii while the second is the C. neomexicanum agg. which in fact contains several poorly differentiated species distributed in different deserts in the southwest of the USA. In this project we plan to test the following hypotheses: H1) Neogene orogenic activity is responsible for interspecific differentiation. H2) Pleistocene glacial-interglacial cycles had an effect on the intraspecific population divergence and demographic history of both species. To test these hypotheses, we will use coalescent statistical phylogeography approaches based on approximate Bayesian computation, comparing explicit scenarios of population divergence and demographic history considering late Neogene and Pleistocene time frames. In addition, we will carry out Ecological Niche Modelling (ENM) and perform geographical projections of niche models on different palaeo-climatic scenarios for the late Pleistocene. H3) The phylogeographic history of Chenopodium species is predicted by Pleistocene glacial-interglacial refugia. For testing this hypothesis, we will estimate habitat stability based on ENM projections in the late Pleistocene and then estimate the linear associations between habitat stability and genetic diversity estimates, as predicted by climate refugia. Alternatively, we will also test the southern refugia hypothesis by estimating the linear associations of latitude with habitat stability, and with the referred parameters of genetic diversity.
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
Requested qualification:
- MSc (or equivalent) in Biology/Botany
- experience with field work, sampling and plant determination
- 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)
Desirable qualification:
- experiences with Illumina library preparation
- basic experience with GIS analyses
- basic experience with bioinformatic and statistical analysis of NGS data
- basic experience with bash and R scripting
Personal qualities:
- good presentation skills
- willing to learn
- networking skills
- ability to collaborate and cooperate with other team members
- keen interest in plant evolution and speciation
We offer:
- a four-year position with a tax-free Ph.D. stipend (120.000 – 192.000,- CZK/year)
- additional funding (30% employment) covered by the project (gross salary 200.000,– CZK, which is cca 113.600,– 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
Application:
The position is available from 1st of October 2024, at the latest. Please submit your full application in English by the 30th of June, 2024 by e-mail as a single pdf file to mandak@fzp.czu.cz
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 prof. Bohumil Mandák mandak@fzp.czu.cz