PhD Position in Speciation Genomics We invite applications for a PhD position within the project "Divergence and gene flow along giant newt genomes", funded by the Polish National Science Centre (NCN) OPUS grant. About the project Genomic gigantism has evolved independently in several eukaryotic lineages. While we understand the mechanistic basis of genome size increase, i.e. the proliferation and retention of repetitive sequences, the evolutionary mechanisms driving genome expansion have been debated for decades but are not fully understood. What remains almost completely unknown is how the sequence and structure of giant genomes evolve and what the evolutionary genomic consequences of genome gigantism are. A major gap in our knowledge is how divergence accumulates along giant genomes as populations differentiate into species, and its corollary - how introgression occurs during this process. There are at least three main reasons why divergence may accumulate qualitatively differently in giant genomes. First, the recombination rate per base par is often low, which can reduce the effectiveness of positive selection, and increase the role of linked selection over large parts of the genome. Second, due to the high proportion of repetitive sequences, a large fraction of divergence is expected to occur in repetitive parts of the genome, which can translate into presence/absence differences of many Gb even between closely related taxa. Third, giant genomes appear to be a permissive environment for transposable elements, allowing their long-term retention and providing an abundant source of variation potentially relevant to adaptation. With advances in technology, now is an opportune time to delve into these questions, particularly by comparing giant genomes with what is known about their smaller counterparts. Salamanders (Urodela) are an ancient clade characterised by genome gigantism, as the haploid genome size of all species exceeds 10 Gb. In this project, we propose to study divergence and introgression along the giant genomes in newts of the Lissotriton vulgaris species complex. The nine lineages that make up the complex form a speciation continuum that has been extensively studied at the genetic and genome-size levels, laying the foundation for the genomic work. We will integrate information on structural differences, divergence in single-copy and repetitive parts of the genome across a speciation continuum with direct assessment of introgression in replicated natural hybrid zones. We will combine the analysis of several chromosome-scale genome assemblies, obtained through a strategic partnership with the Tree of Life (ToL) programme at Wellcome Trust Sanger Institute with low coverage whole genome sequencing of hundreds of samples from our extensive DNA collection. The successful candidate will quantify divergence and introgression in single-copy genomic regions and identify the determinants of divergence and introgression. The project will integrate genomic data from core populations of different lineages with samples from replicated transects across two natural hybrid zones. The research will involve bioinformatic, statistical, and population-genomic analyses of low-coverage whole-genome sequencing data, leveraging chromosome-scale reference genome assemblies. The PhD student will gain extensive experience in handling and interpreting large-scale genomic datasets, developing a strong skill set in bioinformatics and computational biology. Host Institution & Location The PhD student will be based at the Institute of Environmental Sciences, Jagiellonian University in Kraków, Poland one of the leading research institutes in Ecology and Evolution in Central Europe (www.eko.uj.edu.pl/en_GB). Kraków is a vibrant city with a rich cultural scene (European City of Culture 2000), hosting over 100 festivals and numerous cultural events annually. The city offers modern museums, theaters, cinemas, restaurants, and excellent access to outdoor activities such as hiking and biking. It is also well-connected to other European cities. Funding & Salary The position is funded for 48 months, offering a tax-free stipend of approximately 8,000 PLN (~1,900 EUR, around 130% of the average net salary in Poland). The stipend will increase by about 40% after a successful mid-term evaluation (after the second year). To estimate living costs in Kraków, applicants can use tools such as Numbeo (www.numbeo.com). Requirements The successful candidate must hold (or expect to obtain by July 2025) an M.Sc. degree in a relevant field. We seek applicants with: - A strong interest in Evolution, Population Genetics, and/or Genomics. - Experience with, or a keen interest in learning, Bioinformatics and Computational Biology. - Strong English language, communication, and organizational skills. Previous experience in population genetics, evolutionary biology, genomics is an advantage but not required. Application Process To apply, please send: - A cover letter explaining your background, skills, and motivation for this position. - A CV. - Contact details of at least one academic reference willing to provide a recommendation. Applications and informal inquiries should be sent to Prof. Wies³aw Babik (wieslaw.babik@uj.edu.pl, https://molecol.eko.uj.edu.pl/en_GB/zespol/pracownicy/wieslaw-babik). Deadline & Selection Process Review of applications is ongoing. To ensure full consideration, please apply by 30th April 2025. The selected candidate will receive assistance with the formal application to the PhD school at Jagiellonian University, with entrance exams scheduled for early July 2025. The PhD position starts on 1st October 2025. We look forward to receiving your application! Wieslaw Babik Institute of Environmental Sciences Jagiellonian University Gronostajowa 7 30-387 Kraków Poland tel. +48 12 664 51 71 fax. +48 12 664 69 12 www: http://www.molecol.eko.uj.edu.pl/en_GB/zespol/pracownicy/wieslaw-babik Wies³aw Babik (to subscribe/unsubscribe the EvolDir send mail to golding@mcmaster.ca)