********************GradStudentPositions******************** PhD Project Proposal: From root to field: unraveling the ecological and genetic bases of genotype interactions to design resilient durum wheat variety mixtures Keywords: Durum wheat, variety mixtures, root architecture, plant-plant interactions, functional ecology, quantitative genetics, QTL, climate resilience, drought stress Abstract: Durum wheat is a key crop in Mediterranean regions, increasingly affected by drought stress due to climate change. This PhD project aims to understand how root system architecture, particularly root branching intensity, shapes interactions between genotypes and determines the performance of durum wheat variety mixtures. By combining functional ecology and quantitative genetics, the project will identify the genetic basis of root traits and develop predictive tools to design more resilient and productive varietal mixtures. Context: Durum wheat plays a critical role in global agricultural systems, particularly in semi-arid regions, due to its adaptability, economic significance, and contribution to food security (Sissons 2016). Like other crops from these regions, durum wheat is already experiencing yield reductions caused by increased temperatures and reduced water availability (Rao 2011). Diversifying durum wheat fields by introducing mixtures of varieties instead of mono-genotypic stands could be a solution to improve resource use efficiency through positive interactions between varieties (Barot et al. 2017). Our group has identified several Quantitative Trait Loci (QTLs) associated with Root Branching Intensity (RBI) in durum wheat (Triticum turgidum ssp. durum). Our preliminary data indicate that these candidate QTLs associate with varietal mixture performance under contrasted environmental conditions, suggesting that RBI genes could be involved in plant-plant interactions and could thus be used as a predictive tool to design varietal mixtures. However, optimizing varietal mixture composition remains a major scientific challenge (Borg et al. 2018; Wuest et al. 2021), primarily because the mechanisms underlying varietal interactions are poorly known. Objective: The overarching objective of this thesis is to use plant-plant interactions to enhance the resilience of durum wheat to adverse abiotic conditions, especially drought. More specifically, we aim to develop a better understanding of how plants interact belowground to design assembly rules for varietal mixtures with optimal composition to face water limitations. Methods: In this PhD project, we will combine functional ecology and quantitative genetics to uncover the genetic determinants of root architectural traits and assess their effect on mixture performance. In contrast to previous trait-based approach, our interdisciplinary approach will allow scale down to the genetic levels, potentially leading to a better understanding of the mechanisms underlying varietal interactions under contrasted resource conditions, and providing direct outputs for plant breeding such as molecular markers that could be used to design climate-resilient and genetically diverse durum wheat varieties. This work will be organized in three major tasks: - Detailed root phenotyping on a panel of 180 durum wheat genotypes, conducted under both controlled conditions and in the field, with a specific focus on root branching. - Genetic analyses (GWAS) to identify the QTLs involved in root system architecture and their interaction with water availability. - Variety mixture experiments under different water availability scenarios to assess agronomic performance and decipher the ecological mechanisms (complementarity, competition) related to root traits. To conduct the experiment, the partners will benefit from the collaboration and the expertise of the "Terrain d'Expérience" experimental platform from UMR CEFE for the greenhouse and the "UE DIASCOPE" form the INRAE for the field experiment. Expected results: The first expected result is a dataset of root traits and root trait plasticity in response to water stress, measured using standardized protocols in a wide range of durum wheat varieties. Such high-quality dataset will fill the gap in the low representation of root traits in currently available crop trait databases (e.g., CropTraits). This dataset will be used to study root trait diversity and trait covariations between the above and belowground compartments, and how these are affected by resource availability, which will be published in the first scientific article. The second result will be a characterization of the genetic architecture of architectural root traits in durum wheat and an exploration of the interaction between these genetic factors and durum wheat growth environment, notably through water availability management. The last result will be the experimental assessment of the benefits of varietal mixtures, especially under low water availability conditions. This work will also validate the effect of RBI QTLs on mixture performance and uncover the ecological mechanisms that underly this effect. In addition to this fundamental knowledge, it will help develop predictive models of mixture performance based on root functional traits and genetic markers, fostering plant breeding innovations for the design of resource-efficient varietal mixtures. References: Barot S, Allard V, Cantarel A, et al (2017) Designing mixtures of varieties for multifunctional agriculture with the help of ecology. A review. Agronomy for Sustainable Development 37:13. https://doi.org/10.1007/s13593-017-0418-x Borg J, Kiær LP, Lecarpentier C, et al (2018) Unfolding the potential of wheat cultivar mixtures: A meta-analysis perspective and identification of knowledge gaps. Field Crops Research 221:298-313. https://doi.org/10.1016/j.fcr.2017.09.006 Rao SC (2011) Challenges and strategies of dryland agriculture. Scientific Publishers Sissons M (2016) Durum wheat chemistry and technology. Academic Press Wuest SE, Peter R, Niklaus PA (2021) Ecological and evolutionary approaches to improving crop variety mixtures. Nature Ecology & Evolution 5:1068-1077. https://doi.org/10.1038/s41559-021-01497-x Funding and Practical Information: Fully funded 3-year doctoral contract, covering salary, experimental costs, travel, and conference participation. Candidate Profile: Required: Master's or Engineering degree in plant sciences, agronomy, ecology, or genetics. Desired Skills: Greenhouse and field experimentation, functional ecology, statistical analysis, plant genetics. Essential Qualities: Autonomy, rigor, and teamwork abilities. Language Requirements: French B2 minimum, English B2 minimum. Application: Application deadline: July 31, 2025 Contract Start Date: Between October 1 and December 1, 2025 Applications (CV, motivation letter, preferred start date, recommendation letter) to be sent to: Florian Fort - florian.fort@cefe.cnrs.fr Germain Montazeaud - germain.montazeaud@inrae.fr Germain Montazeaud (to subscribe/unsubscribe the EvolDir send mail to golding@mcmaster.ca) ********************GradStudentPositions******************** PhD Position in Evolutionary and Molecular Ecology Link to apply: https://www.kuleuven.be/personeel/jobsite/jobs/60500112 Project Overview We are excited to offer a fully funded PhD position focused on the ecology, evolution, and molecular mechanisms of plasticity and adaptation in Daphnia, with a particular emphasis on melanistic Daphnia zschokkei from alpine lakes. The project combines fieldwork, genomics, transcriptomics, and functional experiments to answer fundamental questions in evolutionary biology. Suggested research questions (RQs): * RQ1: Evolution and taxonomic status of Daphnia zschokkei Several Daphnia species and ecotypes display melanization, yet the evolutionary history of this adaptive phenotype remains largely unresolved. Daphnia zschokkei, a melanized taxon inhabiting alpine lakes, was originally described as a distinct species but is currently treated as an ecotype of D. longispina, based on single-locus and microsatellite data. However, preliminary whole-genome analyses suggest that these melanized populations may form a distinct genetic cluster. This project aims to determine whether melanization evolved once and spread across the Alps, or arose repeatedly from local D. longispina populations. Whole-genome sequencing of melanized "zschokkei" and non-melanized D. longispina across a wide geographic range will be used to resolve phylogenetic relationships, clarify taxonomic status, and reconstruct the evolutionary origins of this trait. Including other melanized populations from the D. longispina complex will allow broader inferences about the evolution of melanization. * RQ2: Quantifying variation in melanization Melanization can be constitutively expressed or environmentally induced. To better understand variation in this trait, we will collect clonal lineages from multiple D. zschokkei populations (as part of RQ1), measure melanization levels in the field, and rear the clones under standardized lab conditions for several generations. This will allow us to determine baseline levels of constitutive expression. After baseline quantification, clones will be exposed to UV treatments to assess plastic responses. Environmental data from each site (UV exposure, turbidity, depth, nutrient levels, predator abundance) will be integrated to assess which factors best explain phenotypic variation. * RQ3: Genetic basis and regulatory architecture of melanin expression Initial findings suggest that melanization in D. zschokkei is largely plastic, implicating regulatory mechanisms. By integrating whole-genome data (RQ1) and phenotypic data (RQ2), we will perform genome-wide association studies, outlier detection, and selection scans to identify candidate genes and regulatory elements involved in melanization. In selected populations, we will conduct controlled induction experiments and collect samples for RNA-seq and ATAC-seq to identify expression patterns and accessible chromatin regions linked to regulatory variation. This integrative approach will help distinguish between constitutive and inducible components of melanization and test whether adaptation occurred through parallel evolution or a shared genetic innovation. Promising regulatory elements will be functionally validated using CRISPR/Cas9 in collaboration with partner labs. * RQ4: Comparative genomics of melanin regulation in Daphnia Melanized forms are also found in several species within the D. pulex complex, such as D. melanica, D. tenebrosa, and D. middendorfiana. Using the approaches developed in RQ3, we will identify candidate genes and regulatory elements in these taxa and compare them to findings from the D. longispina complex. This comparative framework will illuminate whether similar genetic mechanisms underlie melanization across Daphnia lineages. Candidate Profile We are looking for a highly motivated PhD candidate with: * A strong academic track record * Enthusiasm for evolutionary ecology, population genetics and functional genomics * Bioinformatics skills * Excellent command of written and spoken English This is a full-time position initially offered for one year, with the possibility of extension up to four years. Research Environment You will be jointly supervised by Prof. Steven Van Belleghem at KU Leuven (Belgium) and Prof. Markus Moest at the Research Institute for Limnology, University of Innsbruck (Austria), located on the shores of Lake Mondsee. * The research group of Steven Van Belleghem (KU Leuven) focuses on eco-evolutionary and functional genomics in a variety of systems. Website: https://bio.kuleuven.be/eeb/sv * The research group of Markus Moest (Mondsee) specializes in the ecology and evolution of the D. longispina group. The institute provides state-of-the-art infrastructure for Daphnia fieldwork, culturing, and experimental biology. Markus Moest's extensive network across the Alps will facilitate a wide-reaching and efficient sampling campaign. Website: https://www.uibk.ac.at/limno/personnel/moest/index.html.en Life in Leuven and Mondsee Leuven is a vibrant, historic university city offering a high standard of living, excellent public transport, and a strong international community. It's only 15 minutes from Brussels Airport and under two hours by train from Paris, Amsterdam, and London. KU Leuven, founded in 1425, ranks consistently among Europe's top research universities. Mondsee is a picturesque lakeside town in the Salzkammergut region of Austria, surrounded by the Alps. The Research Institute for Limnology provides a stunning research setting with a strong focus on freshwater ecology and evolutionary biology. Application Process Please send your application as a single PDF file including: * A CV * A 1-page motivation letter (including relevant research experience) * Transcripts of your bachelor's and master's degrees * Contact details of two academic references Submit your application via the KU Leuven online platform and send it by email to both: * Steven Van Belleghem: Steven.VanBelleghem@kuleuven.be * Markus Moest: Markus.Moest@uibk.ac.at Subject line: PhD_Application_YOURNAME Deadline: 31 July 2025 Start date: 1 October 2025 (negotiable) Commitment to Diversity KU Leuven is committed to creating an inclusive environment where all talents can thrive, regardless of gender, age, cultural background, nationality, or disability. For questions about accessibility or support, contact: diversiteit.HR@kuleuven.be Steven Van Belleghem (to subscribe/unsubscribe the EvolDir send mail to golding@mcmaster.ca) ********************Jobs******************** Dear colleagues, The Institute of Biosciences of the University of São Paulo (IB-USP) invites applications for one full-time faculty position at the rank of Professor Doutor (equivalent to Tenure TRack Assistant Professor) in the Department of Zoology (DZ). Bioinformatics and Phylogenomics are fundamental to advancing scientific research by integrating genomic data and computational tools to address complex scientific questions. This interdisciplinary field is essential for unraveling evolutionary relationships, understanding biodiversity, and exploring biological processes at a molecular level. In this context, the Department of Zoology (DZ) is seeking a highly qualified candidate with demonstrated expertise in this area. The selected candidate will be expected to contribute to original research, teaching, and outreach activities. This includes working collaboratively, fostering interdisciplinary initiatives within and outside the department, and actively pursuing research funding. The candidate is expected to strengthen current research lines, ensure the consistent quality of core undergraduate and graduate courses, propose new curricular offerings, and contribute to the formation of highly qualified human resources. This strategic hire aims to address a critical departmental need, reinforce the Institute's leadership, and strengthen the long-term commitment to academic excellence in the life sciences, particularly given the department's foundational role in systematics and phylogenetics. Further information can be found at the website: https://academica.ib.usp.br/concursos/zoologia/edital-19-2025 Please contact Prof. Dr. Daniel J. G. Lahr, Department Head, with further inquiries. Daniel J. G. Lahr PhD habil., Associate Prof. Department Head, Zoology Inst of Biological Sciences, Univ. of Sao Paulo, Brazil Office number: + 55 (11) 3091 0948 http://lahr.ib.usp.br Dan Lahr (to subscribe/unsubscribe the EvolDir send mail to golding@mcmaster.ca) ********************PostDocs******************** Postdoctoral Position(s) in Genomic Analyses of Free-Breeding Dog Populations: Chornobyl, Pacific Islands, Atomic Bomb Test Sites and Other Hot Areas Hi Folks! We are looking for postdoctoral research scientists to help with projects using WGS data to address questions related to evolution in free-breeding dog populations around the world. Of particular interest are evolutionary responses to radiation exposure to dog populations in Ukraine (especially Chernobyl), atomic bomb test areas (e.g. Kazakhstan, the Marshall Islands), and other Pacific Islands. Many other exciting questions related to evolutionary history, effects of selection (natural and otherwise), disease, and development are also being addressed. The ideal candidate(s) will be smart, hard-working and have some experience doing analyses with genomic and/or population genetic data. The goal will be to use modern bioinformatic approaches for analysis of WGS and related data to address fundamental evolutionary and population genetics questions related to mutation-selection balance, the relationship between genotype and phenotype, epigenetic influences on evolution, bridging genomic and quantitative genetics and other related topics. A passion for dogs and genetics would be an asset. These projects represent an ongoing collaboration between research teams led by Tim Mousseau at the University of South Carolina and Elaine Ostrander at the NIH. See the following links for more info about the PI's: https://irp.nih.gov/pi/elaine-ostrander https://sc.edu/study/colleges_schools/artsandsciences/biological_sciences/our_people/directory/mousseau_timothy.php Successful applicants will be housed at the NIH in Bethesda, MD, and could have opportunities to engage in field work in addition to genomic and bioinformatics research if so desired. Compensation is generous. This is a unique opportunity for anyone wishing to gain experience using the latest genetic tools to address fundamental evolutionary questions as a member of one of the most productive labs in this field in the world. Interested? Please contact mousseau@sc.edu for more information. Tim Mousseau, PhD, FRGS, FACLS, FAAAS Professor of Biological Sciences University of South Carolina Columbia, SC 29208 USA +1-803-920-7704 mousseau@sc.edu http://cricket.biol.sc.edu/Mousseau/Mousseau.html Google ScholarResearchGate "Mousseau, Timothy" (to subscribe/unsubscribe the EvolDir send mail to golding@mcmaster.ca)