PhD student in Evolution of Indo-Pacific birds
The Department of Bioinformatics and Genetics is offering a four-year PhD position focused on analyzing population-level genomic data from museum bird samples. The project will employ cutting-edge genomic techniques and involve the development of new bioinformatic tools for understanding the evolution of genetic diversity. This PhD position is part of a five-year research program funded by the Wallenberg Foundation, aimed at developing and applying computational tools to understand the evolution of biodiversity (see https://islandevolution.github.io/ ). The candidate will use whole genomic data to answer questions pertaining to the ecology, evolution, demographics, adaptation and hybridisation of Indo-Pacific passerine birds. The Indo-Pacific represents the largest island world on the planet and is well-suited for testing major ecological and evolutionary questions. The candidate is expected to take part in developing specific projects based on interest and experience. The PhD student will be supervised by José Cerca (DDLS Fellow), and collaborate closely with Knud A. Jønsson (Head of Bioinformatics and Genetics), and Martin Irestedt (Researcher) at the Swedish Museum of Natural History. Other potential collaborators at the department include Tom van der Valk and his research group as well as Johan Nylander and Per Ericson.
Application deadline: 21 February 2025
Anställningstyp: Temporary employment
PhD student in evolution of Diplotaxis in Cape Verde
The Department of Bioinformatics and Genetics is offering a four-year PhD position focused on analyzing population- and species-level genomic data from museum plant samples. The project will employ cutting-edge genomic techniques and involve the development of new bioinformatic tools for understanding the evolution of genetic diversity. This PhD position is part of a five-year research program funded by the Wallenberg Foundation, aimed at developing and applying computational tools to understand the evolution of biodiversity (see https://islandevolution.github.io/ ). The candidate will use whole genomic data to answer questions pertaining to the ecology, evolution, demographics, adaptation and hybridisation of Cape Verdean Diplotaxis, a radiation encompassing multiple environments. The candidate is expected to take part in developing specific projects based on interest and experience. The PhD student will supervised by José Cerca (DDLS Fellow), and collaborate closely with colleagues at the Swedish Museum of Natural History and colleagues in Oslo (Christian Brochmann), Prague (Filip Kolá) and Munich (Mathieu Gardère) as well as several institutions in Cabo Verde.
Application deadline: 21 February 2025
Anställningstyp: Temporary employment
Researcher to Department of Population Analysis and Monitoring
The main task of the project is to process and analyze ~300 historical (i.e. 150-1000 years old) and about 4,000 published modern herring genomes to assess their adaptive responses to sea warming in the North and Baltic Seas (https://www.vr.se/swecris#/project/2023-00588_Formas) The data processing will include the use of bioinformatic tools and pipelines developped for ancient DNA data, allowing to examine or correct for DNA damage (e.g. PMDtools, Generode), as well as the use of probabilistic methods (e.g. ANGSD) to call SNP from low coverage data. The data analyzes will include analyses of genetic differentiation among historical and modern populations using factor analyzes (FA) for neutral and non-neural markers. The successful candidate will also investigate temporal shifts in known alleles underlying ecological adaptations (Han et al. 2020; Elife) using genome scans of selection and outlier loci (e.g. FST). Finally, the project will Species Distribution Modelling (e.g. Maxent) using current and future environmental variables and current herring occurrence data to assess herring future distribution. The project will also rely on genomic simulations (e.g. SLIM) to examine genomic responses to ocean warming and related changes in environmental conditions. The candidate is expected to prepare manuscripts for publication in high-impact international journals. Although all laboratory work will be performed and completed by a laboratory technician by the start of employment, there will be opportunities to gain experience in ancient/historical DNA laboratory work, including DNA extractions from historical/past herring material (e.g. fin clippings, bones) and preparation of WGS libraries using appropriate protocols for degraded DNA. The successful candidate will be encouraged to develop their own research ideas and to apply for their own funding (e.g. EMBO, Marie Curie actions, the Swedish Research Council, Formas) to build on this project or their own projects, with the help of the principal investigator (Dr .Nicolas Dussex).
Application deadline: 28 February 2025
Anställningstyp: Temporary employment
PhD student (4 years) in Evolution of toxicity in birds and frogs
The Department of Bioinformatics and Genetics at the Swedish Museum of Natural History is offering a four-year PhD position focused on exploring the convergent evolution of toxicity in New Guinean passerine birds and Neotropical poison dart frogs. The project will combine field and manipulation experiments with comparative genomics, transcriptomics and chemical analyses to broaden our understanding of convergent evolution of toxic lifestyles in two distinct vertebrate clades. The student is expected to work on one or more of the following aspects: i) determine the source of BTX and its adaptive significance in toxic birds, ii) pinpoint the underlying genomic adaptations allowing for storage and transportation of toxins in both birds and frogs, and iii) evaluate the roles that gut microbial symbionts play in toxin uptake, and in facilitating the hosts adaptations to be toxic. The candidate will use whole genomic data, meta-barcoding data and transcriptomics data to answer the above questions and is expected to take part in developing specific projects based on interest and experience. There is also the possibility (albeit not mandatory) to participate in fieldwork at the Copenhagen Zoo or in Papua New Guinea. The PhD student will be supervised by Knud Jønsson, NRM and Kasun Bodawatta (University of Copenhagen, Denmark) and will have close collaboration with Christine Beemelmanns at the Hans Knöll Institute in Leipzig, Germany. Other potential collaborators at the Department include Martin Irestedt, Johan Nylander, Tom van der Valk and José Cerca. More broadly, the museum is home to a collection of highly skilled entomologists including Niklas Apelqvist and Kjell Arne Johansson who may facilitate the entomological work related to diet analyses.
Application deadline: 3 March 2025
Anställningstyp: Temporary employment