CZ.1.07/2.3./20.0303

Zpráva z pracovní cesty - Antverpy (Belgie)

26.-28.6.2014 uskutečnila Joelle Gouy de Bellocq, PhD. (post-doc, člen NextGen Teamu) pracovní cestu do Belgii. 

The goal of my visit to Antwerp, Belgium, (26-28 June 2014) was to meet with Prof. Herwig Leirs and Sophie Gryseels from the Evolutionary Ecology group of the University of Antwerp to discuss and plan a project on Next-Generation sequencing of 5 new strains of arenaviruses and 1 new hantavirus we discovered during our previous project on RNA viruses in Africa. We also meet with collaborators from the Clinical and Epidemiological Virology group of the Rega Institute from the KU Leuven to discuss preliminary results and plan the next steps on the genetic analyses of Hepaciviruses in African small mammals samples.

Zpráva z pracovní cesty - Uganda + Kongo

21.5.-14.6.2014 se Mgr. Václav Gvoždík, PhD. zúčastnil zahraniční cesty v Ugandě a Kongu.

Zahraniční pracovní cesta byla realizována s cílem aktivně se zúčastnit dvou mezinárodních vědeckých konferencí: African Amphibian Working Group Meeting v Ruhija, Bwindi NP, Uganda & 1st International Conference on Biodiversity in the Congo Basin, Kisangani, Konžská demokratická republika (DRC). Na konferencích jsem prezentoval výsledky svých výzkumů biodiverzity rovníkové Afriky, kterými se intenzivně zabývám v posledních letech. Celkově jsem byl spoluautor na 7 odborných příspěvcích, z toho u tří jako první autor. V Ugandě jsem prezentoval přednášku na téma „Evolutionary history of Leptopelis tree frogs across the sky island system of Tanzania“, v Kisangani v Konžské demokratické republice pak jako první autor např.: „Sympatry of two species of dwarf crocodile (Osteolaemus tetraspis and O. osborni) in the Republic of the Congo confirmed by the multilocus genetic approach and morphology“. V rámci prezentovaných výzkumů byly aplikovány moderní multigenové přístupy.

Abstrakty všech příspěvků byly publikovány v konferenčních sbornících. Pracovní cesta byla velice přínosná pro networking, navazování nových odborných kontaktů, které jsou v tomto komplikovaném regionu střední Afriky funkční zejména při osobních setkáních, které pak umožní další fungující spolupráci do budoucích výzkumů. Odborné kontakty se podařilo navázat zvláště s výzkumnými pracovníky ‘Centre de Surveillance de la Biodiversité’, Univerzita v Kisangani, DRC a Wildlife Conservation Society – programy Uganda a DRC.

 

Zpráva z pracovní cesty - San Juan, Puerto Rico (USA)

Oleksiy Yanchukov:

From 29.05.14 to 15.06.14, I traveled to USA for a working visit.

For the first week of the visit, I went to the laboratory of Prof. Stephen Proulx in the University of Santa Barbara, to discuss (i) the theoretical models of spatial population structure and the evolution of gene duplications, and (ii) the modelling of the transposon-mediated expansion of gene families in the house mouse. The first project is a continuation of our previous work in the UC Santa Barbara and the second relates to my current collaboration with Vaclav Janousek from IVB and Dr. Robert Karn and Dr. Christina Laukaitis in the University of Arizona.

From 7-13 June 2014, I traveled to San Juan, Puerto Rico to take part in the annual international meeting of the Society for Molecular Biology and Evolution (SMBE). There I presented a poster about the spatial population genetics models of gene duplication evolution and discussed my research with colleagues.

Zpráva z workshopu - Ploen (Německo)

23.-25.5.2014 se v německém Ploenu konal workshop Wild House Mouse Meeting, kterého se zúčastnili 3 členové NextGen týmu a prezentovali zde své vědecké výsledky:  

Václav Janoušek:

Genomics features associated with regions of high and low introgression in the house mouse hybrid zone

Oleksiy Yanchukov:

On May 23-25, I attended the international workshop on the evolutionary biology of the house mouse (Mus musculus), held in the Max-Plank Institute of Evolutionary Biology (MPI) in Ploen, Germany. I used this opportunity to learn about the current state of the research of the wild house mouse model system, but also to meet with collaborators Robert Karn and Christina Laukaitis and discuss the progress of our joint project on gene family size expansion in the mouse genome. I also established many contacts in the house mouse research community, and discussed, with director of the MPI Dr. Diethart Tautz, the possibility of collaboration in the laboratory of the MPI in Ploen to genotype the house mouse samples from the hybrid zone for the variants in gene copy number. The MPI in Ploen will welcome, in the near future, the researchers in mouse research team from Studenec for a working visit and will provide them with the use of necessary equipment and laboratory space to obtain the data on the gene copy number variants in their samples.

Stuart J. E. Baird:

Genome wide multilocus analysis of a hybrid zone

Stuart J.E. Baird, Alexey Yanchukov, Milos Macholan, Pavel Munclinger, Jaroslav Pialek

We use a hybrid zone with well-developed genomic resources to highlight what may soon be possible for non-model systems. The European House Mouse hybrid zone (HMHZ) is well studied, and the mouse and human genomes were completed in parallel due to the pivotal role of laboratory mice in medical research. This means mouse genome functional annotation is dense and cheap methods exist to recovery SNP variation at the population genomic scale. We combine 1400 SNPs for 1400 mice near the HMHZ and 0.5 million SNPs for 250 mice at a wider geographic scale to assess variation in gene flow permeability of the HMHZ species barrier along the mouse genome. As genome sampling and computational resources are no longer bottlenecked the challenge becomes making sound (model based) inference about the evolutionary process. Comparison with analyses using traditional datasets shows that the existing modelling framework of multilocus hybrid zone population genetics predicts genome wide patterns extremely well, providing a logical starting point for extensions that take advantage of higher resolution data. Dense SNPs allow co-estimation of source taxon and phase of DNA strands along chromosome pairs ie reconstruction of recombinant haplotypes as interdigitated blocks labelled by source. We illustrate how applying Fisher’s model of genome admixture can then distinguish ancestral polymorphism from introgressive, and allow us to move away from simplistic genome-outlier analyses and towards a model based understanding of the dynamics of introgression across a species barrier.