News & jobs

Here you can read news, announcements and job positions related to our group.

PhD position starting 1st October 2018

posted May 22, 2018, 4:00 AM by Jacek Radwan   [ updated May 22, 2018, 4:01 AM ]

PhD position in evolutionary biology is available for four years starting from 1st October 2018 in NCN-funded project aiming to investigate the effect of sexual selection on genome-wide genetic variation using a powerful approach of experimental evolution coupled with genome re-sequencing.  The student will receive stipend of 4500 PLN/month and, in addition to carrying our research, will have opportunity to attend specialized courses for PhD students in English. The candidate should hold MSc degree in biological sciences or bioinformatics.

Further information about the project and application procedure can be obtained from the project leader via email: jradwan@amu.edu.pl

 

Brief summary of the project:

Genetic variation is a fuel of evolution, therefore assessing the role of sexual selection in maintaining this variation is fundamental to our understanding of evolutionary processes occurring in sexual species.  The rate and extent of adaptation depend on available genetic variation, which sexual selection has long been thought to deplete. However, recent theory predicts that, contrary to the traditional view, sexual selection may actually increase genetic variation due to sexual antagonism and other trade-offs associated with evolution of costly sexually-selected traits. Yet, the effect of sexual selection on the amount of genetic variation segregating in populations has not been investigated empirically. The aim of the proposed project is to investigate effect of sexual selection on genome-wide genetic variation using a powerful approach of experimental evolution coupled with genome re-sequencing.

The project will use a species very well suited for this purpose, the bulb mite Rhizoglyphus robini, a well-established model in sexual selection research. The project will benefit from the fact that the genome of this species has recently been assembled and annotated.

Replicate populations will be allowed to evolve for about 20 generations under treatments differing in (i) sex ratio, and thus intensity of sexual selection and (ii) the frequency of males bearing an elaborated sexually-selected trait: thickened legs used for intrasexual contests. Previous research demonstrated that the trait is associated with increased ontogenetic  intersexual conflict and life history trade-offs. Genomes of mites from replicated experimental evolution lines will then be sequenced and used for testing whether evolution of costly, condition-dependent sexually selected traits depletes (as predicted by traditional theory) or helps to maintain genetic polymorphism in functional parts of the genome (amino-acid substitutions in protein coding genes, and nucleotide substitutions in cis-regulatory sequences). The results will be interpreted in the context of intragenomic variation in recombination rate, a major determinant of genetic variation. The variation in recombination rate will be estimated in the proposed project.

Novel MHC alleles give their guppy hosts advantage in dealing with ectoparasites

posted Jan 18, 2018, 2:36 AM by Jacek Radwan   [ updated Jun 15, 2018, 5:33 AM ]

In our recent article "Immunogenetic novelty confers a selective advantage in host–pathogen coevolution" published in PNAS (read informal story behind the paper here), we demonstrate that MHC alleles to which Gyrodactylus flukes had no opportunity to adapt are associated with less severe infection in hosts. The major histocompatibility complex (MHC) is one of the most polymorphic gene families in the vertebrate genome, with natural selection actively promoting and maintaining variability. The exact mechanism/mechanisms responsible for these characteristics remain unclear, but identifying them is fundamental to our understanding of host–pathogen dynamics. Using targeted crosses of the model Trinidadian guppy, a tractable parasite, and exposure-controlled infection trials, we show that novel MHC variants are associated with less severe infections. Uniquely, our experimental design separates novel variant advantage from other modes of selection and confounding variables, such as individual MHC variability and genomic background. We thus demonstrated a fundamental process driving evolution of the vertebrate immune system, which helps explain the unique features of MHC genes. Reprints available on request from jraadwan[at]amu.edu.pl

New grants and stipends for our team members!

posted May 16, 2017, 6:40 AM by Mateusz Konczal   [ updated May 16, 2017, 7:06 AM by Piotr Bentkowski ]

Recently we received some grants and stipends!

PRELUDIUM is a National Science Center’s opportunity intended for pre-doctoral researchers about to embark on their scientific career. We are happy to announce that Aleksandra Łukasiewicz from our team received this grant for the project entitled Environmental quality and intensity of sexual conflict. The project aim to test the assumption that the low-quality food during development should reduce intensity of sexual conflict. Ola with her project was first in the ranking in the environmental biology & evolution panel (NZ8)! Congratulations Ola! Here you can find out more about the project.

START is a stipend from Foundation for Polish Sciences that is dedicated to young researchers, at the outset of their career, who have already achieved some success in their field.  This year foundation awarded 100 young researchers; 3 people with most highly rated research accomplishments received distinctions. One of them is Mateusz Konczal. Mateusz received this award for his work in evolve & resequence research. More about his work is published byPolish Press Agency (in polish).

Kin selection promotes female productivity and cooperation between the sexes

posted Mar 16, 2017, 12:32 AM by Jacek Radwan   [ updated May 16, 2017, 7:05 AM by Piotr Bentkowski ]

Hamilton’s theory of kin selection explains the evolution of costly traits that benefit other individuals by highlighting the fact that passing genes to offspring is not the only way of increasing the representation of those genes in subsequent generations: Genes are also shared with other classes of relatives. Consequently, any heritable trait that affects fitness of relatives should respond to kin selection. In the article just published in Science Advances we tested this core prediction of kin selection theory by letting bulb mites (Rhizoglyphus robini) evolve in populations structured into groups of relatives or nonrelatives during the reproductive phase of the life cycle. In accordance with predictions derived from kin selection theory, we found that evolution in groups of relatives resulted in increased female reproductive output. This increase at least partly results from the evolution of male traits that elevate their partners’ fecundity. Thus, our results demonstrate that kin selection can mediate sexual conflict and, more generally, highlight the power and universality of kin selection. Press release (in Polish)

Transcriptome-based primer design: bank vole MHC class I

posted Nov 4, 2016, 4:33 AM by Magdalena Migalska

Although high-throughput sequencing has increasingly been used for genotyping families of co-amplifying genes, its potential to facilitate the initial characterisation of such genes in non-model species has not been explored. In our recent article in Heredity we found that, while de novo transcriptome assembly of major histocompatibility complex (MHC) class I genes does not reconstruct sequences of individual alleles, it allows the identification of conserved regions for PCR primer design.

Using the newly designed primers, we characterised for the first time MHC class I sequences in an Arvicolinae rodent, the bank vole (Myodes glareolus). We showed high allelic diversity and inter-individual variation in the number of expressed loci. Phylogenetic analysis revealed a lack of orthology to MHC I of other Cricetidae, which is consistent with the high gene turnover of this region. Strong signatures of positive selection were found for eight amino acid sites, most of which are inferred to bind antigens in human MHC, indicating conservation of structure despite rapid sequence evolution.

Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in the sedge warbler

posted Oct 26, 2016, 7:01 AM by Magdalena Migalska   [ updated Oct 26, 2016, 9:58 AM ]

Characterisation of highly duplicated genes, such as those of the major histocompatibility complex (MHC), remains a challenging task. In a recent article in Molecular Ecology Resources we demonstrated that the high throughput sequencing enables accurate genotyping of large sets of co-amplifying loci given the sufficient coverage per amplicon is reached.

With ultra-deep Illumina sequencing of replicated samples and a simulated dataset we tested the effect of amplicon coverage (range: 500-20 000 reads) on the repeatability of genotyping using four different protocols:
- AVT: Allele Validation Threshold (Radwan et al. 2012)  
- RA: Replicated Amplicon (Sommer et al. 2013)
- DOC: Degree Of Change (Lighten et al. 2014)
- AC: Adjustable Clustering with AmpliSAS (Sebastian et al. 2016)

The within-method repeatability of allele calling increased with coverage and approached or exceeded 90% at ≥ 5 000 reads per amplicon. The agreement between methods was also high, especially at high coverages, which adds confidence in the reliability of genotyping and affirms comparability of results between research groups. The findings were further supported by the analysis of the simulated dataset.

The AC method (developed by our team, see Sebastian et al. 2016) proved to be the most effective. Moreover, the AC can easily be implemented with existing on-line software AmpliSAS.

Red Queen drives positive selection on MHC genes

posted Nov 25, 2015, 5:25 AM by Jacek Radwan

MHC genes are the paradigm for the positive selection whereby novel MHC alleles are strongly favored by natural selection. Our simulations (Ejsmond and Radwan 2015; PLOS Computational Biology)  showed that novel mutations in MHC are strongly favored by frequency-dependent selection arising from host-pathogen coevolution (the Red Queen process), but not by heterozygote advantage. Our results challenge the predominating view on the processes driving the evolution of MHC genes.

Male display reveals mutational load in guppy fish.

posted Nov 25, 2015, 5:13 AM by Jacek Radwan   [ updated Nov 25, 2015, 8:34 AM by Magdalena Herdegen ]

Why do females of many species show preferences for elaborated male behavioural displays or morphological ornaments continues to puzzle evolutionary biologists. One hypothesis poses that these traits reflect the load of deleterious mutations carried by males: males with heavy loads are thought to be unable to invest in costly displays. In a recent article (Herdegen and Radwan, 2015, Animal Behaviour 110: 105–111) we show that in guppy fish, induced mutations indeed negatively affected the courtship display rate, but not sexually selected orange spots. Thus our results demonstrate that energetically costly courtship display, but not orange coloration, is a reliable indicator of mutation load.  

3rd Polish Evolutionary Conference - Summary

posted Oct 2, 2015, 4:20 AM by Magdalena Migalska   [ updated Oct 2, 2015, 4:31 AM ]

Polish Evolutionary Conference in Poznań (2015)
Between 24th and 26th September 2015 we participated in organization of the 3rd Polish Evolutionary Conference (PEC) at the Biology Department of Adam Mickiewicz University in Poznan. PEC is an annual event co-organized by the Committee for Evolutionary and Theoretical Biology, Polish Academy of Science together with different scientific centers in Poland.

The conference has been a success, more than 100 students and researchers from Poland and Europe attended the event.

On 24th September the official opening had place at the Biology Department, followed by two days of informative, cross-section evolutionary lectures and a poster session hosting more than 50 posters. Participants had also a chance to attend outstanding plenary talks by Grażyna Jasieńska, Eva Jablonka, Jochen Wolf and Ryszard Korona. The conference dinner with a jazz concert in the Blue Note Jazz Club ended the second day of the conference, providing an excellent opportunity for discussion, relax and networking.

We hope that the attendees had fully enjoyed the scientific level of the conference, the venue and the friendly atmosphere. It was a great pleasure for us to co-organize and host PEC III 2015 here in Poznan, and we all look forward for the 4th PEC edition in Bialystok, next year! 

3rd PEC Abstract Book available here!



AmpliSAS: a web server for multilocus genotyping using next-generation amplicon sequencing data

posted Sep 3, 2015, 8:37 AM by Alvaro Sebastian

We want to introduce the new published tool 'AmpliSAS' developed in our lab for analyzing amplicon sequencing data. This will be specially useful in the genotyping task for complex gene families, such as MHC, with multiple loci and copy number variation among individuals (Babik et al. 2010; Lighten et al. 2014). Amplicon sequencing is also a widely used technique for taxonomic classification amplifying a variety of genes: cytochrome c oxidase subunit 1 (CO1), rRNA genes (16S/18S/28S), plant specific genes (rbcL, matK, and trnH-psbA) and nuclear internal transcribed spacers (ITSs) (Sogin et al. 2006; Kress et al. 2014; Joly et al. 2014).

You can use AmpliSAS online at: https://sites.google.com/site/evobiolab/software/amplisas

And here the link to the original article:

AmpliSAS: a web server for multilocus genotyping using next-generation amplicon sequencing data. Sebastian, A., Herdegen, M., Migalska, M. & Radwan, J. Mol. Ecol. Resour. (2015). doi:10.1111/1755-0998.12453

If you don't have access you can read the submitted (preprint) version.


Amplicon Sequencing Workflow:
Amplicon Sequencing Workflow

Abstract:

Next-generation sequencing (NGS) technologies are revolutionizing the fields of biology and medicine as powerful tools for amplicon sequencing (AS). Using combinations of primers and barcodes, it is possible to sequence targeted genomic regions with deep coverage for hundreds, even thousands, of individuals in a single experiment. This is extremely valuable for the genotyping of gene families in which locus-specific primers are often difficult to design, such as the major histocompatibility complex (MHC). The utility of AS is, however, limited by the high intrinsic sequencing error rates of NGS technologies and other sources of error such as polymerase amplification or chimera formation. Correcting these errors requires extensive bioinformatic post-processing of NGS data. Amplicon Sequence Assignment (amplisas) is a tool that performs analysis of AS results in a simple and efficient way, while offering customization options for advanced users. amplisas is designed as a three-step pipeline consisting of (i) read demultiplexing, (ii) unique sequence clustering and (iii) erroneous sequence filtering. Allele sequences and frequencies are retrieved in excel spreadsheet format, making them easy to interpret. amplisas performance has been successfully benchmarked against previously published genotyped MHC data sets obtained with various NGS technologies.

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