Postdoc position in Amphibian Evolutionary Genomics (3 years)

We seek a postdoctoral research fellow in amphibian evolutionary genomics to work in the group of Prof. Wiesław Babik at the Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland. The position is within the recently awarded National Science Centre (NCN) grant “Do antigen-processing genes coevolve with MHC class I genes in salamanders?”

Background. Understanding the mechanisms driving evolution of the genes underlying adaptive immunity is of major scientific importance and has implications for conservation. In this project we will test whether Antigen Processing Genes (APG) coevolve with Major Histocompatibility Complex (MHC) class I  genes in salamanders. Coevolution has been suggested as the ancestral vertebrate condition, potentially limiting the efficiency and flexibility of adaptive immunity. Selection pressure to remove this constraint is therefore expected in multiple evolutionary lineages. Limited information available for salamanders reveals intriguing patterns of MHC I and APG variation, making this group ideal for testing the coevolution hypothesis and providing fundamental insights into the evolution of the adaptive immunity.

Job description. The postdoc will test predictions of the coevolution hypothesis. More specifically (s)he will: i) resequence the focal genes in multiple species from several families, ii) perform bioinformatics analysis of resequencing data, iii) test for correlation between APG and MHC variation iv) look for signatures of adaptive evolution. (S)he will work together with the PI and other team members, including a network of international collaborators.

Requirements:

  • PhD degree in biology or a related discipline obtained not earlier than 7 years prior to the employment in the project (note: this period is extended in case of paternity leave, or other circumstances described in the Polish National Science Centre OPUS project regulations), or
  • A statement that the PhD thesis has been submitted and the candidate is expected to obtain the degree before commencing the employment;
  • Documented experience in the bioinformatic analysis of DNA sequence data in evolutionary context;

Conditions of employment:

  • full-time employment for 36 months, salary ca. 7000 PLN/month gross
  • benefits of a full-time employee according to the Polish law (health insurance, social security, retirement benefits, etc.)
  • all social benefits of the University staff (www.en.uj.edu.pl/en/staff/staff-benefits/office),
  • employment start: between 01.11.2017 and 01.02.2018 (negotiable)

Deadline for applications: September 30th 2017; Interviews October 9-12 2017; Decision October 18th.

If no candidate meets the requirements, the recruitment period will be extended. If you are interested in this position but cannot apply before the deadline, let us know and we will inform you about the extension.

Detailed requirements and the recruitment procedure are given below.

Contact: Wiesław Babik (wieslaw.babik@uj.edu.pl)

 

Detailed information about the recruitment procedure and specific requirements

Specific criteria used in the selection procedure:

- experience in Linux/Unix shell and scripting (Python/Perl/R) skills

- background in population genetics and/or molecular evolution

- molecular laboratory experience

- publication record;

- experience in leading projects, working in international teams, internships;

- opinion of the recognized researchers with whom the candidate collaborated;

- communication skills, communication in English language.

The recruitment procedure:

At the first stage, the candidates should send to wieslaw.babik@uj.edu.pl (cc to   binoz@uj.edu.pl) the following documents as pdf email attachments (deadline: 30 Sept. 2017):

  1. An application expressing the interest in obtaining the position and the following statement: “I hereby give consent for my personal data included in my application to be processed for the purposes of recruitment, in accordance with the Personal Data Protection Act dated August, 29,1997 (uniform text: Journal of Laws of the Republic of Poland 2014 item 1182, with further amendments)”;
  2. CV, including also information about internships and participation in or leading of research projects;
  3. Copy of PhD diploma or a certificate with the statement that the PhD thesis has been submitted and the candidate can expect receiving the degree before commencing the employment;
  4. List of publications (for the most important papers provide doi identifiers or links to the texts, the journals’ IF, and the number of citations) and conference presentations (only as the presenting author);
  5. Pdf of up to three publications most important from the perspective of the selection criteria;
  6. Short description of the research achievements (maximum half page);
  7. A reference letter from the supervisor or the research team leader, with whom the candidate collaborated;
  8. Information about at least one additional independent researcher with whom the candidate collaborated and who agreed to prepare a confidential opinion by 8 Oct. 2017 (name, affiliation, e-mail address).

Interview: The best candidate or candidates selected based on the above information will be invited for an interview, which will take place in the Institute headquarters or, in justified cases, via Skype on 9 12 Oct. 2017. A provisional decision will be made immediately after completing the interviews.

Completing the documents needed for signing the contract: The candidate for whom the position has been provisionally granted is required to submit the following documents in printed and signed form to the Institute office (by mail or in person) within 5 working days:

1) all the documents required for the first stage of the competition,

2) a personal questionnaire required by the Jagiellonian University office,

3) a statement stating that the JU will be the primary and sole place of work for the time of the employment,

4) declaration under art. 109 sec. 1 Law on Higher Education (of not being charged for criminal offenses),

5) declaration of knowledge and acceptance of intellectual property and intellectual property law.

Failure to provide these documents or not obtaining the doctorate degree before the agreed date of employment results in cancellation of the decision and reopening the recruitment procedure.

The questionnaire form and required statements forms can be downloaded at: www.dso.uj.edu.pl/druki-do-pobrania/dokumenty-dla-kandydatow-pracownikow. The forms are offered in Polish; if you do not read Polish or need help: please contact wieslaw.babik@uj.edu.pl. If none of the candidates meets the expected requirements, the University reserves the right to extend or cancel the competition.

 

SUMMARY OF THE PROJECT

Research project objectives/Research hypothesis

The adaptive immunity is a major vertebrate innovation essential for fighting the pathogen challenge. Understanding the mechanisms driving evolution of the genes underlying adaptive immunity is of major importance and has implications for designing conservation strategies. In this project we propose to test whether the Antigen Processing Genes (APG) coevolve with the MHC class I (MHC I) genes in salamanders. Proteins encoded by the APG process antigens for presentation by MHC I. The coevolution hypothesis posits that an MHC I allele presents most efficiently antigens processed the APG alleles co-occurring on the same haplotype. Coevolution between APG and MHC I, enabled by their tight linkage, has been proposed as the ancestral gnathostome condition that occurs in most non-mammalian taxa. Coevolution could impose constraints on the MHC class I variation potentially limiting the efficiency of adaptive immunity. Coevolution would generate high APG polymorphism, maintained by balancing selection as observed in several species. The coevolution hypothesis assumes that each MHC haplotype has only a single highly expressed class I gene, which coevolves with tightly linked APG. The presence of multiple highly expressed MHC I genes in several taxa appears incompatible with that view, because it is unclear whether or how coevolution between MHC and APG could occur in such situations. It is possible that in these taxa, similarly as in mammals, MHC class I genes do not coevolve with APG. If coevolution indeed limits flexibility of the adaptive immunity, this constraint may have been removed independently in various evolutionary lineages. It is also possible that coevolution is more complex than currently thought and can occur even if multiple MHC class I genes are highly expressed. However almost nothing is known about evolutionary mechanisms affecting the APG in most non-mammalian vertebrates. Limited information available for salamanders reveals intriguing patterns of MHC I and APG variation, making this group ideal for testing the coevolution hypothesis.

Research project methodology

The coevolution hypothesis generates several predictions:

  • APG should be tightly linked to the MHC class I gene(s).
  • APG should be highly polymorphic.
  • Transspecies polymorphism should be observed in APG.
  • The level of nonsynonymous APG polymorphism should correlate with that of MHC I genes.
  • APG allelic lineages should define stable MHC haplotypes.
  • Widespread signal of positive selection should be detected in APG at a large phylogenetic scale.

We will evaluate these predictions using population-level DNA sequence data from 25 salamander species representing five families. Polymorphism of MHC I, APG and control genes will be assessed. The strength of linkage between MHC I and APG will be determined in a large recombinant population of Lissotriton newts. Correlation between MHC and APG variation will be estimated controlling for phylogenetic relationships. Coding sequence of APG identified in transcriptome assemblies will be used to test for positive selection across the salamander phylogeny.

Expected impact of the research project on the development of science, civilization and society

If coevolution is indeed the ancestral vertebrate condition limiting the potential of the adaptive immunity, then selection to remove this constraint has likely operated in multiple evolutionary lineages. Alternatively, it is possible that coevolution can occur without impairing efficiency and flexibility of adaptive immunity. Addressing these issues will provide fundamental insights into our understanding of mechanisms driving the evolution of the adaptive immune system. The results of the proposed project will thus be of broad interest and of relevance for the fields of molecular evolution, adaptation genetics and comparative immunology.

Published Date: 31.08.2017
Published by: Małgorzata Biel