@article{18630, abstract = {Markov chains are the de facto finite-state model for stochastic dynamical systems, and Markov decision processes (MDPs) extend Markov chains by incorporating non-deterministic behaviors. Given an MDP and rewards on states, a classical optimization criterion is the maximal expected total reward where the MDP stops after T steps, which can be computed by a simple dynamic programming algorithm. We consider a natural generalization of the problem where the stopping times can be chosen according to a probability distribution, such that the expected stopping time is T, to optimize the expected total reward. Quite surprisingly we establish inter-reducibility of the expected stopping-time problem for Markov chains with the Positivity problem (which is related to the well-known Skolem problem), for which establishing either decidability or undecidability would be a major breakthrough. Given the hardness of the exact problem, we consider the approximate version of the problem: we show that it can be solved in exponential time for Markov chains and in exponential space for MDPs.}, author = {Chatterjee, Krishnendu and Doyen, Laurent}, issn = {1860-5974}, journal = {Logical Methods in Computer Science}, number = {4}, pages = {11:1--11:34}, publisher = {EPI Sciences}, title = {{Stochastic processes with expected stopping time}}, doi = {10.46298/lmcs-20(4:11)2024}, volume = {20}, year = {2024}, } @article{18923, abstract = {Combinatorial optimization is a challenging problem applicable in a wide range of fields from logistics to finance. Recently, quantum computing has been used to attempt to solve these problems using a range of algorithms, including parameterized quantum circuits, adiabatic protocols, and quantum annealing. These solutions typically have several challenges: 1) there is little to no performance gain over classical methods; 2) not all constraints and objectives may be efficiently encoded in the quantum ansatz; and 3) the solution domain of the objective function may not be the same as the bit strings of measurement outcomes. This work presents “nonnative hybrid algorithms”: a framework to overcome these challenges by integrating quantum and classical resources with a hybrid approach. By designing nonnative quantum variational anosatzes that inherit some but not all problem structure, measurement outcomes from the quantum computer can act as a resource to be used by classical routines to indirectly compute optimal solutions, partially overcoming the challenges of contemporary quantum optimization approaches. These methods are demonstrated using a publicly available neutral-atom quantum computer on two simple problems of Max k-Cut and maximum independent set. We find improvements in solution quality when comparing the hybrid algorithm to its “no quantum” version, a demonstration of a “comparative advantage.”}, author = {Wurtz, Jonathan and Sack, Stefan and Wang, Sheng-Tao}, issn = {2689-1808}, journal = {IEEE Transactions on Quantum Engineering}, pages = {1--14}, publisher = {IEEE}, title = {{Solving nonnative combinatorial optimization problems using hybrid quantum–classical algorithms}}, doi = {10.1109/tqe.2024.3443660}, volume = {5}, year = {2024}, } @article{17481, abstract = {Phase-field models such as the Allen–Cahn equation may give rise to the formation and evolution of geometric shapes, a phenomenon that may be analyzed rigorously in suitable scaling regimes. In its sharp-interface limit, the vectorial Allen–Cahn equation with a potential with N≥3 distinct minima has been conjectured to describe the evolution of branched interfaces by multiphase mean curvature flow. In the present work, we give a rigorous proof for this statement in two and three ambient dimensions and for a suitable class of potentials: as long as a strong solution to multiphase mean curvature flow exists, solutions to the vectorial Allen–Cahn equation with well-prepared initial data converge towards multiphase mean curvature flow in the limit of vanishing interface width parameter ε↘0. We even establish the rate of convergence O(ε 1/2 ). Our approach is based on the gradient-flow structure of the Allen–Cahn equation and its limiting motion: building on the recent concept of “gradient-flow calibrations” for multiphase mean curvature flow, we introduce a notion of relative entropy for the vectorial Allen–Cahn equation with multi-well potential. This enables us to overcome the limitations of other approaches, e.g. avoiding the need for a stability analysis of the Allen–Cahn operator or additional convergence hypotheses for the energy at positive times.}, author = {Fischer, Julian L and Marveggio, Alice}, issn = {1873-1430}, journal = {Annales de l'Institut Henri Poincaré C}, number = {5}, pages = {1117--1178}, publisher = {EMS Press}, title = {{Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow}}, doi = {10.4171/AIHPC/109}, volume = {41}, year = {2024}, } @misc{22234, abstract = {Lists of nontrivial integral points on some (families of) cubic surfaces. (2024-07-18)}, author = {Browning, Timothy D and Sutherland, Andrew}, publisher = {Göttingen Research Online Data}, title = {{Data and code for: Integral points on cubic surfaces: heuristics and numerics}}, doi = {10.25625/4FLFH8}, year = {2024}, } @unpublished{19063, abstract = {Instruction-tuned Large Language Models (LLMs) show impressive results in numerous practical applications, but they lack essential safety features that are common in other areas of computer science, particularly an explicit separation of instructions and data. This makes them vulnerable to manipulations such as indirect prompt injections and generally unsuitable for safety-critical tasks. Surprisingly, there is currently no established definition or benchmark to quantify this phenomenon. In this work, we close this gap by introducing a formal measure for instruction-data separation and an empirical variant that is calculable from a model's outputs. We also present a new dataset, SEP, that allows estimating the measure for real-world models. Our results on various LLMs show that the problem of instruction-data separation is real: all models fail to achieve high separation, and canonical mitigation techniques, such as prompt engineering and fine-tuning, either fail to substantially improve separation or reduce model utility. The source code and SEP dataset are openly accessible at https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed. }, author = {Zverev, Egor and Abdelnabi, Sahar and Tabesh, Soroush and Fritz, Mario and Lampert, Christoph}, booktitle = {arXiv}, title = {{Can LLMs separate instructions from data? And what do we even mean by that?}}, doi = {10.48550/arXiv.2403.06833}, year = {2024}, } @article{14826, abstract = {The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.}, author = {Kuhn, Andre and Roosjen, Mark and Mutte, Sumanth and Dubey, Shiv Mani and Carrillo Carrasco, Vanessa Polet and Boeren, Sjef and Monzer, Aline and Koehorst, Jasper and Kohchi, Takayuki and Nishihama, Ryuichi and Fendrych, Matyas and Sprakel, Joris and Friml, Jiří and Weijers, Dolf}, issn = {1097-4172}, journal = {Cell}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {1}, pages = {130--148.e17}, publisher = {Elsevier}, title = {{RAF-like protein kinases mediate a deeply conserved, rapid auxin response}}, doi = {10.1016/j.cell.2023.11.021}, volume = {187}, year = {2024}, } @article{17373, abstract = {Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating the electrostatic properties of material surfaces, enabling the imaging of variations in work function, topology, surface charge density, or combinations thereof. Regardless of the underlying signal source, SKPM results in a voltage image, which is spatially distorted due to the finite size of the probe, long-range electrostatic interactions, mechanical and electrical noise, and the finite response time of the electronics. In order to recover the underlying signal, it is necessary to deconvolve the measurement with an appropriate point spread function (PSF) that accounts the aforementioned distortions, but determining this PSF is difficult. Here, we describe how such PSFs can be determined experimentally and show how they can be used to recover the underlying information of interest. We first consider the physical principles that enable SKPM and discuss how these affect the system PSF. We then show how one can experimentally measure PSFs by looking at well-defined features, and that these compare well to simulated PSFs, provided scans are performed extremely slowly and carefully. Next, we work at realistic scan speeds and show that the idealized PSFs fail to capture temporal distortions in the scan direction. While simulating PSFs for these situations would be quite challenging, we show that measuring PSFs with similar scan conditions works well. Our approach clarifies the basic principles and inherent challenges to SKPM measurements and gives practical methods to improve results.}, author = {Lenton, Isaac C and Pertl, Felix and Shafeek, Lubuna B and Waitukaitis, Scott R}, issn = {1089-7550}, journal = {Journal of Applied Physics}, number = {4}, publisher = {AIP Publishing}, title = {{Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging}}, doi = {10.1063/5.0215151}, volume = {136}, year = {2024}, } @inproceedings{18155, abstract = {We study the classical problem of verifying programs with respect to formal specifications given in the linear temporal logic (LTL). We first present novel sound and complete witnesses for LTL verification over imperative programs. Our witnesses are applicable to both verification (proving) and refutation (finding bugs) settings. We then consider LTL formulas in which atomic propositions can be polynomial constraints and turn our focus to polynomial arithmetic programs, i.e. programs in which every assignment and guard consists only of polynomial expressions. For this setting, we provide an efficient algorithm to automatically synthesize such LTL witnesses. Our synthesis procedure is both sound and semi-complete. Finally, we present experimental results demonstrating the effectiveness of our approach and that it can handle programs which were beyond the reach of previous state-of-the-art tools.}, author = {Chatterjee, Krishnendu and Goharshady, Amir Kafshdar and Goharshady, Ehsan and Karrabi, Mehrdad and Zikelic, Dorde}, booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)}, isbn = {9783031711619}, issn = {1611-3349}, location = {Milan, Italy}, pages = {600--619}, publisher = {Springer Nature}, title = {{Sound and complete witnesses for template-based verification of LTL properties on polynomial programs}}, doi = {10.1007/978-3-031-71162-6_31}, volume = {14933}, year = {2024}, } @misc{22798, abstract = {This repository contains the artifact of the paper titled "Sound and Complete Witnesses for Template-based Verification of LTL Properties on Polynomial Programs" accepted at FM 2024. The task of verifying an LTL formula on a program can be reduced to verifying a Büchi specification on the product transition system. This tool takes a non-deterministic transition system together with a Büchi specification as input and based on user preferences tries to either (i) prove the existence of a run in the program that satisfies the Büchi condition or (ii) demonstrate that every run of the program satisfies the Büchi condition. The tool is written in Java and works well with openjdk 11 on Ubuntu 22.04. Running all the experiments can take weeks to finish. We have provided a script for running the strongest configuration of our tool which solves most of the benchmarks and takes less than 48 hours. Detailed guidance is given in the readme file.}, author = {Chatterjee, Krishnendu and Kafshdar Goharshady, Amir and Kafshdar Goharshady, Ehsan and Karrabi, Mehrdad and Žikelić, Ðorđe}, publisher = {Repository}, title = {{Data for Sound and Complete Witnesses for Template-based Verification of LTL Properties on Polynomial Programs}}, doi = {10.5281/zenodo.12518216}, year = {2024}, } @article{18528, abstract = {The recent measurement of magnetic field strength inside the radiative interior of red giant stars has opened the way toward full 3D characterization of the geometry of stable large-scale magnetic fields. However, current measurements, which are limited to dipolar (ℓ = 1) mixed modes, do not properly constrain the topology of magnetic fields due to degeneracies on the observed magnetic field signature on such ℓ = 1 mode frequencies. Efforts focused toward unambiguous detections of magnetic field configurations are now key to better understand angular momentum transport in stars. We investigated the detectability of complex magnetic field topologies (such as the ones observed at the surface of stars with a radiative envelope with spectropolarimetry) inside the radiative interior of red giants. We focused on a field composed of a combination of a dipole and a quadrupole (quadrudipole) and on an offset field. We explored the potential of probing such magnetic field topologies from a combined measurement of magnetic signatures on ℓ = 1 and quadrupolar (ℓ = 2) mixed mode oscillation frequencies. We first derived the asymptotic theoretical formalism for computing the asymmetric signature in the frequency pattern for ℓ = 2 modes due to a quadrudipole magnetic field. To access asymmetry parameters for more complex magnetic field topologies, we numerically performed a grid search over the parameter space to map the degeneracy of the signatures of given topologies. We demonstrate the crucial role played by ℓ = 2 mixed modes in accessing internal magnetic fields with a quadrupolar component. The degeneracy of the quadrudipole compared to pure dipolar fields is lifted when considering magnetic asymmetries in both ℓ = 1 and ℓ = 2 mode frequencies. In addition to the analytical derivation for the quadrudipole, we present the prospect for complex magnetic field inversions using magnetic sensitivity kernels from standard perturbation analysis for forward modeling. Using this method, we explored the detectability of offset magnetic fields from ℓ = 1 and ℓ = 2 frequencies and demonstrate that offset fields may be mistaken for weak and centered magnetic fields, resulting in underestimating the magnetic field strength in stellar cores. We emphasize the need to characterize ℓ = 2 mixed-mode frequencies, (along with the currently characterized ℓ = 1 mixed modes), to unveil the higher-order components of the geometry of buried magnetic fields and to better constrain angular momentum transport inside stars.}, author = {Das, Srijan B and Einramhof, Lukas and Bugnet, Lisa Annabelle}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, title = {{Unveiling complex magnetic field configurations in red giant stars}}, doi = {10.1051/0004-6361/202450918}, volume = {690}, year = {2024}, } @misc{22802, abstract = {MESA inlist file for the paper "Unveiling complex magnetic field configurations in red giant stars" (10.1051/0004-6361/202450918)}, author = {Das, Srijan B and Einramhof, Lukas and Bugnet, Lisa}, publisher = {Institute of Science and Technology Austria}, title = {{MESA inlist file}}, doi = {10.5281/zenodo.12804810}, year = {2024}, } @inproceedings{18702, abstract = {In this work we prove lower bounds on the (communication) cost of maintaining a shared key among a dynamic group of users. Being “dynamic” means one can add and remove users from the group. This captures important protocols like multicast encryption (ME) and continuous group-key agreement (CGKA), which is the primitive underlying many group messaging applications. We prove our bounds in a combinatorial setting where the state of the protocol progresses in rounds. The state of the protocol in each round is captured by a set system, with each of its elements specifying a set of users who share a secret key. We show this combinatorial model implies bounds in symbolic models for ME and CGKA that capture, as building blocks, PRGs, PRFs, dual PRFs, secret sharing, and symmetric encryption in the setting of ME, and PRGs, PRFs, dual PRFs, secret sharing, public-key encryption, and key-updatable public-key encryption in the setting of CGKA. The models are related to the ones used by Micciancio and Panjwani (Eurocrypt’04) and Bienstock et al. (TCC’20) to analyze ME and CGKA, respectively. We prove – using the Bollobás’ Set Pairs Inequality – that the cost (number of uploaded ciphertexts) for replacing a set of d users in a group of size n is Ω(dln(n/d)). Our lower bound is asymptotically tight and both improves on a bound of Ω(d) by Bienstock et al. (TCC’20), and generalizes a result by Micciancio and Panjwani (Eurocrypt’04), who proved a lower bound of Ω(log(n)) for d=1. }, author = {Anastos, Michael and Auerbach, Benedikt and Baig, Mirza Ahad and Cueto Noval, Miguel and Kwan, Matthew Alan and Pascual Perez, Guillermo and Pietrzak, Krzysztof Z}, booktitle = {22nd International Conference on Theory of Cryptography}, isbn = {9783031780103}, issn = {1611-3349}, location = {Milan, Italy}, pages = {413--443}, publisher = {Springer Nature}, title = {{The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging}}, doi = {10.1007/978-3-031-78011-0_14}, volume = {15364}, year = {2024}, } @article{18480, abstract = {Caloric restriction (CR) can extend the organism life- and health-span by improving glucose homeostasis. How CR affects the structure-function of pancreatic beta cells remains unknown. We used single nucleus transcriptomics to show that CR increases the expression of genes for beta cell identity, protein processing, and organelle homeostasis. Gene regulatory network analysis reveal that CR activates transcription factors important for beta cell identity and homeostasis, while imaging metabolomics demonstrates that beta cells upon CR are more energetically competent. In fact, high-resolution microscopy show that CR reduces beta cell mitophagy to increase mitochondria mass and the potential for ATP generation. However, CR beta cells have impaired adaptive proliferation in response to high fat diet feeding. Finally, we show that long-term CR delays the onset of beta cell aging hallmarks and promotes cell longevity by reducing beta cell turnover. Therefore, CR could be a feasible approach to preserve compromised beta cell structure-function during aging and diabetes.}, author = {Dos Santos, Cristiane and Cambraia, Amanda and Shrestha, Shristi and Cutler, Melanie and Cottam, Matthew and Perkins, Guy and Lev-Ram, Varda and Roy, Birbickram and Acree, Christopher and Kim, Keun Young and Deerinck, Thomas and Dean, Danielle and Cartailler, Jean Philippe and Macdonald, Patrick E. and Hetzer, Martin W and Ellisman, Mark and Arrojo E Drigo, Rafael}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice}}, doi = {10.1038/s41467-024-53127-2}, volume = {15}, year = {2024}, } @misc{22865, abstract = {Dataset for Dos Santos et al, 2024}, author = {Arrojo e Drigo, Rafael}, publisher = {Repository}, title = {{Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity}}, doi = {10.5281/zenodo.6491943}, year = {2024}, } @misc{22866, author = {Hrast, Mateja}, publisher = {Repository}, title = {{Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl}}, doi = {10.5281/zenodo.13833474}, year = {2024}, } @article{14850, abstract = {Elaborate sexual signals are thought to have evolved and be maintained to serve as honest indicators of signaller quality. One measure of quality is health, which can be affected by parasite infection. Cnemaspis mysoriensis is a diurnal gecko that is often infested with ectoparasites in the wild, and males of this species express visual (coloured gular patches) and chemical (femoral gland secretions) traits that receivers could assess during social interactions. In this paper, we tested whether ectoparasites affect individual health, and whether signal quality is an indicator of ectoparasite levels. In wild lizards, we found that ectoparasite level was negatively correlated with body condition in both sexes. Moreover, some characteristics of both visual and chemical traits in males were strongly associated with ectoparasite levels. Specifically, males with higher ectoparasite levels had yellow gular patches with lower brightness and chroma, and chemical secretions with a lower proportion of aromatic compounds. We then determined whether ectoparasite levels in males influence female behaviour. Using sequential choice trials, wherein females were provided with either the visual or the chemical signals of wild-caught males that varied in ectoparasite level, we found that only chemical secretions evoked an elevated female response towards less parasitised males. Simultaneous choice trials in which females were exposed to the chemical secretions from males that varied in parasite level further confirmed a preference for males with lower parasites loads. Overall, we find that although health (body condition) or ectoparasite load can be honestly advertised through multiple modalities, the parasite-mediated female response is exclusively driven by chemical signals.}, author = {Pal, Arka and Joshi, Mihir and Thaker, Maria}, issn = {0022-0949}, journal = {Journal of Experimental Biology}, keywords = {Insect Science, Molecular Biology, Animal Science and Zoology, Aquatic Science, Physiology, Ecology, Evolution, Behavior and Systematics}, number = {1}, publisher = {The Company of Biologists}, title = {{Too much information? Males convey parasite levels using more signal modalities than females utilise}}, doi = {10.1242/jeb.246217}, volume = {227}, year = {2024}, } @article{18908, abstract = {Chromosomal rearrangements can lead to the coupling of reproductive barriers, but whether and how they contribute to the completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between populations segregating for multiple inversion arrangements, providing opportunities to study their barrier effects. Here, we analyzed 2 adjacent transects across hybrid zones between 2 ecotypes of Littorina fabalis (“large” and “dwarf”) adapted to different wave exposure conditions on a Swedish island. Applying whole-genome sequencing, we found 12 putative inversions on 9 of 17 chromosomes. Nine of the putative inversions reached near differential fixation between the 2 ecotypes, and all were in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both transects indicated that the 2 ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact. The bimodality reflects the strong coupling between inversion clines and the extension of the barrier effect across the whole genome. Demographic inference suggests that coupling arose during a period of allopatry and has been maintained for > 1,000 generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Notably, 2 of the putative inversions overlap with inverted genomic regions associated with ecotype differences in a closely related species (Littorina saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species.}, author = {Le Moan, Alan and Stankowski, Sean and Rafajlović, Marina and Ortega-Martinez, Olga and Faria, Rui and Butlin, Roger K and Johannesson, Kerstin}, issn = {2056-3744}, journal = {Evolution Letters}, number = {4}, pages = {575--586}, publisher = {Oxford University Press}, title = {{Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes}}, doi = {10.1093/evlett/qrae014}, volume = {8}, year = {2024}, } @article{18491, abstract = {Predicting the outcomes of adaptation is a major goal of evolutionary biology. When temporal changes in the environment mirror spatial gradients, it opens up the potential for predicting the course of adaptive evolution over time based on patterns of spatial genetic and phenotypic variation. We assessed this approach in a 30-year transplant experiment in the intertidal snail Littorina saxatilis. In 1992, snails were transplanted from a predation-dominated environment to one dominated by wave action. On the basis of spatial patterns, we predicted transitions in shell size and morphology, allele frequencies at positions throughout the genome, and chromosomal rearrangement frequencies. Observed changes closely agreed with predictions and transformation was both dramatic and rapid. Hence, adaptation can be predicted from knowledge of the phenotypic and genetic variation among populations.}, author = {Garcia Castillo, Diego Fernando and Barton, Nicholas H and Faria, Rui and Larsson, Jenny and Stankowski, Sean and Butlin, Roger and Johannesson, Kerstin and Westram, Anja M}, issn = {2375-2548}, journal = {Science Advances}, number = {41}, publisher = {AAAS}, title = {{Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails}}, doi = {10.1126/sciadv.adp2102}, volume = {10}, year = {2024}, } @article{17237, abstract = {The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing their spatial and temporal genomic variations using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at 2 time points, spanning at least 2 generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species’ demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change.}, author = {Reynes, Lauric and Fouqueau, Louise and Aurelle, Didier and Mauger, Stephane and Destombe, Christophe and Valero, Myriam}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {6}, pages = {677--692}, publisher = {Oxford University Press}, title = {{Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations}}, doi = {10.1093/jeb/voae048}, volume = {37}, year = {2024}, } @misc{22870, abstract = {Abstract: Chromosomal rearrangements can lead to the coupling of reproductive barriers, but whether and how they contribute to completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between populations segregating for multiple inversion arrangements, providing opportunities to study their barrier effects. Here, we analysed two adjacent transects across hybrid zones between two ecotypes of Littorina fabalis (‘large’ and ‘dwarf’) adapted to different wave exposure conditions on a Swedish island. Applying whole-genome sequencing, we found 12 putative inversions on nine of 17 chromosomes. Nine of the putative inversions reached near differential fixation between the two ecotypes, and all were in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both transects indicated that the two ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact. The bimodality reflects the strong coupling between inversion clines and the extension of the barrier effect across the whole genome. Demographic inference suggests that coupling arose during a period of allopatry and has been maintained for >1000 generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Notably, two of the putative inversions overlap with inverted genomic regions associated with ecotype differences in a closely-related species (Littorina saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species.}, author = {Le Moan, Alan}, publisher = {Repository}, title = {{Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes}}, doi = {10.5281/zenodo.10790257}, year = {2024}, }