@phdthesis{14697, author = {Stopp, Julian A}, isbn = {978-3-99078-038-1}, issn = {2663 - 337X}, pages = {226}, publisher = {Institute of Science and Technology Austria}, title = {{Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function}}, doi = {10.15479/at:ista:14697}, year = {2023}, } @article{14701, author = {Archer, Lynden A. and Bruce, Peter G. and Calvo, Ernesto J. and Dewar, Daniel and Ellison, James H. J. and Freunberger, Stefan Alexander and Gao, Xiangwen and Hardwick, Laurence J. and Horwitz, Gabriela and Janek, Jürgen and Johnson, Lee R. and Jordan, Jack W. and Matsuda, Shoichi and Menkin, Svetlana and Mondal, Soumyadip and Qiu, Qianyuan and Samarakoon, Thukshan and Temprano, Israel and Uosaki, Kohei and Vailaya, Ganesh and Wachsman, Eric D. and Wu, Yiying and Ye, Shen}, issn = {1364-5498}, journal = {Faraday Discussions}, keywords = {Physical and Theoretical Chemistry}, publisher = {Royal Society of Chemistry}, title = {{Towards practical metal–oxygen batteries: General discussion}}, doi = {10.1039/d3fd90062b}, year = {2023}, } @article{14702, author = {Attard, Gary A. and Calvo, Ernesto J. and Curtiss, Larry A. and Dewar, Daniel and Ellison, James H. J. and Gao, Xiangwen and Grey, Clare P. and Hardwick, Laurence J. and Horwitz, Gabriela and Janek, Juergen and Johnson, Lee R. and Jordan, Jack W. and Matsuda, Shoichi and Mondal, Soumyadip and Neale, Alex R. and Ortiz-Vitoriano, Nagore and Temprano, Israel and Vailaya, Ganesh and Wachsman, Eric D. and Wang, Hsien-Hau and Wu, Yiying and Ye, Shen}, issn = {1364-5498}, journal = {Faraday Discussions}, keywords = {Physical and Theoretical Chemistry}, publisher = {Royal Society of Chemistry}, title = {{Materials for stable metal–oxygen battery cathodes: general discussion}}, doi = {10.1039/d3fd90059b}, year = {2023}, } @unpublished{14703, abstract = {We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation.}, author = {Ishida, Sadashige and Lavenant, Hugo}, booktitle = {arXiv}, keywords = {Optimal transport, Hamilton-Jacobi equation, convex optimization}, title = {{Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation}}, doi = {10.48550/arXiv.2312.12213}, year = {2023}, } @article{14709, abstract = {Amid the delays due to the global pandemic, in early October 2022, the auxin community gathered in the idyllic peninsula of Cavtat, Croatia. More than 170 scientists from across the world converged to discuss the latest advancements in fundamental and applied research in the field. The topics, from signalling and transport to plant architecture and response to the environment, show how auxin research must bridge from the molecular realm to macroscopic developmental responses. This is mirrored in this collection of reviews, contributed by participants of the Auxin 2022 meeting.}, author = {Del Bianco, Marta and Friml, Jiří and Strader, Lucia and Kepinski, Stefan}, issn = {1460-2431}, journal = {Journal of Experimental Botany}, number = {22}, pages = {6889--6892}, publisher = {Oxford University Press}, title = {{Auxin research: Creating tools for a greener future}}, doi = {10.1093/jxb/erad420}, volume = {74}, year = {2023}, } @article{14710, abstract = {The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells.}, author = {Curatolo, Agnese I. and Kimchi, Ofer and Goodrich, Carl Peter and Krueger, Ryan K. and Brenner, Michael P.}, issn = {20411723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{A computational toolbox for the assembly yield of complex and heterogeneous structures}}, doi = {10.1038/s41467-023-43168-4}, volume = {14}, year = {2023}, } @article{14715, abstract = {We consider N trapped bosons in the mean-field limit with coupling constant λN = 1/(N − 1). The ground state of such systems exhibits Bose–Einstein condensation. We prove that the probability of finding ℓ particles outside the condensate wave function decays exponentially in ℓ.}, author = {Mitrouskas, David Johannes and Pickl, Peter}, issn = {1089-7658}, journal = {Journal of Mathematical Physics}, number = {12}, publisher = {AIP Publishing}, title = {{Exponential decay of the number of excitations in the weakly interacting Bose gas}}, doi = {10.1063/5.0172199}, volume = {64}, year = {2023}, } @article{14716, abstract = {Background: Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature. Results: In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models’ performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics. Conclusions: Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers.}, author = {Yurtseven, Alper and Buyanova, Sofia and Agrawal, Amay Ajaykumar A. and Bochkareva, Olga and Kalinina, Olga V V.}, issn = {1471-2180}, journal = {BMC Microbiology}, number = {1}, publisher = {Springer Nature}, title = {{Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis}}, doi = {10.1186/s12866-023-03147-7}, volume = {23}, year = {2023}, } @article{14717, abstract = {We count primitive lattices of rank d inside Zn as their covolume tends to infinity, with respect to certain parameters of such lattices. These parameters include, for example, the subspace that a lattice spans, namely its projection to the Grassmannian; its homothety class and its equivalence class modulo rescaling and rotation, often referred to as a shape. We add to a prior work of Schmidt by allowing sets in the spaces of parameters that are general enough to conclude the joint equidistribution of these parameters. In addition to the primitive d-lattices Λ themselves, we also consider their orthogonal complements in Zn⁠, A1⁠, and show that the equidistribution occurs jointly for Λ and A1⁠. Finally, our asymptotic formulas for the number of primitive lattices include an explicit bound on the error term.}, author = {Horesh, Tal and Karasik, Yakov}, issn = {1464-3847}, journal = {Quarterly Journal of Mathematics}, number = {4}, pages = {1253--1294}, publisher = {Oxford University Press}, title = {{Equidistribution of primitive lattices in ℝn}}, doi = {10.1093/qmath/haad008}, volume = {74}, year = {2023}, } @inproceedings{14718, abstract = {Binary decision diagrams (BDDs) are one of the fundamental data structures in formal methods and computer science in general. However, the performance of BDD-based algorithms greatly depends on memory latency due to the reliance on large hash tables and thus, by extension, on the speed of random memory access. This hinders the full utilisation of resources available on modern CPUs, since the absolute memory latency has not improved significantly for at least a decade. In this paper, we explore several implementation techniques that improve the performance of BDD manipulation either through enhanced memory locality or by partially eliminating random memory access. On a benchmark suite of 600+ BDDs derived from real-world applications, we demonstrate runtime that is comparable or better than parallelising the same operations on eight CPU cores. }, author = {Pastva, Samuel and Henzinger, Thomas A}, booktitle = {Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design}, isbn = {9783854480600}, location = {Ames, IA, United States}, pages = {122--131}, publisher = {TU Vienna Academic Press}, title = {{Binary decision diagrams on modern hardware}}, doi = {10.34727/2023/isbn.978-3-85448-060-0_20}, year = {2023}, } @article{14719, abstract = {Lithium–sulfur batteries are regarded as an advantageous option for meeting the growing demand for high-energy-density storage, but their commercialization relies on solving the current limitations of both sulfur cathodes and lithium metal anodes. In this scenario, the implementation of lithium sulfide (Li2S) cathodes compatible with alternative anode materials such as silicon has the potential to alleviate the safety concerns associated with lithium metal. In this direction, here, we report a sulfur cathode based on Li2S nanocrystals grown on a catalytic host consisting of CoFeP nanoparticles supported on tubular carbon nitride. Nanosized Li2S is incorporated into the host by a scalable liquid infiltration–evaporation method. Theoretical calculations and experimental results demonstrate that the CoFeP–CN composite can boost the polysulfide adsorption/conversion reaction kinetics and strongly reduce the initial overpotential activation barrier by stretching the Li–S bonds of Li2S. Besides, the ultrasmall size of the Li2S particles in the Li2S–CoFeP–CN composite cathode facilitates the initial activation. Overall, the Li2S–CoFeP–CN electrodes exhibit a low activation barrier of 2.56 V, a high initial capacity of 991 mA h gLi2S–1, and outstanding cyclability with a small fading rate of 0.029% per cycle over 800 cycles. Moreover, Si/Li2S full cells are assembled using the nanostructured Li2S–CoFeP–CN cathode and a prelithiated anode based on graphite-supported silicon nanowires. These Si/Li2S cells demonstrate high initial discharge capacities above 900 mA h gLi2S–1 and good cyclability with a capacity fading rate of 0.28% per cycle over 150 cycles.}, author = {Mollania, Hamid and Zhang, Chaoqi and Du, Ruifeng and Qi, Xueqiang and Li, Junshan and Horta, Sharona and Ibáñez, Maria and Keller, Caroline and Chenevier, Pascale and Oloomi-Buygi, Majid and Cabot, Andreu}, issn = {1944-8252}, journal = {ACS Applied Materials and Interfaces}, number = {50}, pages = {58462–58475}, publisher = {American Chemical Society}, title = {{Nanostructured Li₂S cathodes for silicon-sulfur batteries}}, doi = {10.1021/acsami.3c14072}, volume = {15}, year = {2023}, } @article{14726, abstract = {Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Zea mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Zea mays LLG 1 and 2 (ZmLLG1/2) and Zea mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants.}, author = {Zhou, Liang-Zi and Wang, Lele and Chen, Xia and Ge, Zengxiang and Mergner, Julia and Li, Xingli and Küster, Bernhard and Längst, Gernot and Qu, Li-Jia and Dresselhaus, Thomas}, issn = {1532-298X}, journal = {The Plant Cell}, keywords = {Cell Biology, Plant Science}, publisher = {Oxford University Press}, title = {{The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize}}, doi = {10.1093/plcell/koad324}, year = {2023}, } @unpublished{14732, abstract = {Fragmented landscapes pose a significant threat to the persistence of species as they are highly susceptible to heightened risk of extinction due to the combined effects of genetic and demographic factors such as genetic drift and demographic stochasticity. This paper explores the intricate interplay between genetic load and extinction risk within metapopulations with a focus on understanding the impact of eco-evolutionary feedback mechanisms. We distinguish between two models of selection: soft selection, characterised by subpopulations maintaining carrying capacity despite load, and hard selection, where load can significantly affect population size. Within the soft selection framework, we investigate the impact of gene flow on genetic load at a single locus, while also considering the effect of selection strength and dominance coefficient. We subsequently build on this to examine how gene flow influences both population size and load under hard selection as well as identify critical thresholds for metapopulation persistence. Our analysis employs the diffusion, semi-deterministic and effective migration approximations. Our findings reveal that under soft selection, even modest levels of migration can significantly alleviate the burden of load. In sharp contrast, with hard selection, a much higher degree of gene flow is required to mitigate load and prevent the collapse of the metapopulation. Overall, this study sheds light into the crucial role migration plays in shaping the dynamics of genetic load and extinction risk in fragmented landscapes, offering valuable insights for conservation strategies and the preservation of diversity in a changing world.}, author = {Olusanya, Oluwafunmilola O and Khudiakova, Kseniia and Sachdeva, Himani}, booktitle = {bioRxiv}, title = {{Genetic load, eco-evolutionary feedback and extinction in a metapopulation}}, doi = {10.1101/2023.12.02.569702}, year = {2023}, } @article{14733, abstract = {Redox flow batteries (RFBs) rely on the development of cheap, highly soluble, and high-energy-density electrolytes. Several candidate quinones have already been investigated in the literature as two-electron anolytes or catholytes, benefiting from fast kinetics, high tunability, and low cost. Here, an investigation of nitrogen-rich fused heteroaromatic quinones was carried out to explore avenues for electrolyte development. These quinones were synthesized and screened by using electrochemical techniques. The most promising candidate, 4,8-dioxo-4,8-dihydrobenzo[1,2-d:4,5-d′]bis([1,2,3]triazole)-1,5-diide (−0.68 V(SHE)), was tested in both an asymmetric and symmetric full-cell setup resulting in capacity fade rates of 0.35% per cycle and 0.0124% per cycle, respectively. In situ ultraviolet-visible spectroscopy (UV–Vis), nuclear magnetic resonance (NMR), and electron paramagnetic resonance (EPR) spectroscopies were used to investigate the electrochemical stability of the charged species during operation. UV–Vis spectroscopy, supported by density functional theory (DFT) modeling, reaffirmed that the two-step charging mechanism observed during battery operation consisted of two, single-electron transfers. The radical concentration during battery operation and the degree of delocalization of the unpaired electron were quantified with NMR and EPR spectroscopy.}, author = {Jethwa, Rajesh B and Hey, Dominic and Kerber, Rachel N. and Bond, Andrew D. and Wright, Dominic S. and Grey, Clare P.}, issn = {2574-0962}, journal = {ACS Applied Energy Materials}, keywords = {Electrical and Electronic Engineering, Materials Chemistry, Electrochemistry, Energy Engineering and Power Technology, Chemical Engineering (miscellaneous)}, publisher = {American Chemical Society}, title = {{Exploring the landscape of heterocyclic quinones for redox flow batteries}}, doi = {10.1021/acsaem.3c02223}, year = {2023}, } @article{14734, abstract = {Developing cost-effective and high-performance thermoelectric (TE) materials to assemble efficient TE devices presents a multitude of challenges and opportunities. Cu3SbSe4 is a promising p-type TE material based on relatively earth abundant elements. However, the challenge lies in its poor electrical conductivity. Herein, an efficient and scalable solution-based approach is developed to synthesize high-quality Cu3SbSe4 nanocrystals doped with Pb at the Sb site. After ligand displacement and annealing treatments, the dried powders are consolidated into dense pellets, and their TE properties are investigated. Pb doping effectively increases the charge carrier concentration, resulting in a significant increase in electrical conductivity, while the Seebeck coefficients remain consistently high. The calculated band structure shows that Pb doping induces band convergence, thereby increasing the effective mass. Furthermore, the large ionic radius of Pb2+ results in the generation of additional point and plane defects and interphases, dramatically enhancing phonon scattering, which significantly decreases the lattice thermal conductivity at high temperatures. Overall, a maximum figure of merit (zTmax) ≈ 0.85 at 653 K is obtained in Cu3Sb0.97Pb0.03Se4. This represents a 1.6-fold increase compared to the undoped sample and exceeds most doped Cu3SbSe4-based materials produced by solid-state, demonstrating advantages of versatility and cost-effectiveness using a solution-based technology.}, author = {Wan, Shanhong and Xiao, Shanshan and Li, Mingquan and Wang, Xin and Lim, Khak Ho and Hong, Min and Ibáñez, Maria and Cabot, Andreu and Liu, Yu}, issn = {2366-9608}, journal = {Small Methods}, publisher = {Wiley}, title = {{Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4}}, doi = {10.1002/smtd.202301377}, year = {2023}, } @inproceedings{14735, abstract = {Scaling blockchain protocols to perform on par with the expected needs of Web3.0 has been proven to be a challenging task with almost a decade of research. In the forefront of the current solution is the idea of separating the execution of the updates encoded in a block from the ordering of blocks. In order to achieve this, a new class of protocols called rollups has emerged. Rollups have as input a total ordering of valid and invalid transactions and as output a new valid state-transition. If we study rollups from a distributed computing perspective, we uncover that rollups take as input the output of a Byzantine Atomic Broadcast (BAB) protocol and convert it to a State Machine Replication (SMR) protocol. BAB and SMR, however, are considered equivalent as far as distributed computing is concerned and a solution to one can easily be retrofitted to solve the other simply by adding/removing an execution step before the validation of the input. This “easy” step of retrofitting an atomic broadcast solution to implement an SMR has, however, been overlooked in practice. In this paper, we formalize the problem and show that after BAB is solved, traditional impossibility results for consensus no longer apply towards an SMR. Leveraging this we propose a distributed execution protocol that allows reduced execution and storage cost per executor (O(log2n/n)) without relaxing the network assumptions of the underlying BAB protocol and providing censorship-resistance. Finally, we propose efficient non-interactive light client constructions that leverage our efficient execution protocols and do not require any synchrony assumptions or expensive ZK-proofs.}, author = {Stefo, Christos and Xiang, Zhuolun and Kokoris Kogias, Eleftherios}, booktitle = {27th International Conference on Financial Cryptography and Data Security}, isbn = {9783031477539}, issn = {0302-9743}, location = {Bol, Brac, Croatia}, pages = {3--20}, publisher = {Springer Nature}, title = {{Executing and proving over dirty ledgers}}, doi = {10.1007/978-3-031-47754-6_1}, volume = {13950}, year = {2023}, } @inproceedings{14736, abstract = {Payment channel networks (PCNs) are a promising technology to improve the scalability of cryptocurrencies. PCNs, however, face the challenge that the frequent usage of certain routes may deplete channels in one direction, and hence prevent further transactions. In order to reap the full potential of PCNs, recharging and rebalancing mechanisms are required to provision channels, as well as an admission control logic to decide which transactions to reject in case capacity is insufficient. This paper presents a formal model of this optimisation problem. In particular, we consider an online algorithms perspective, where transactions arrive over time in an unpredictable manner. Our main contributions are competitive online algorithms which come with provable guarantees over time. We empirically evaluate our algorithms on randomly generated transactions to compare the average performance of our algorithms to our theoretical bounds. We also show how this model and approach differs from related problems in classic communication networks.}, author = {Bastankhah, Mahsa and Chatterjee, Krishnendu and Maddah-Ali, Mohammad Ali and Schmid, Stefan and Svoboda, Jakub and Yeo, Michelle X}, booktitle = {27th International Conference on Financial Cryptography and Data Security}, isbn = {9783031477539}, issn = {1611-3349}, location = {Bol, Brac, Croatia}, pages = {309--325}, publisher = {Springer Nature}, title = {{R2: Boosting liquidity in payment channel networks with online admission control}}, doi = {10.1007/978-3-031-47754-6_18}, volume = {13950}, year = {2023}, } @article{14737, abstract = {John’s fundamental theorem characterizing the largest volume ellipsoid contained in a convex body $K$ in $\mathbb{R}^{d}$ has seen several generalizations and extensions. One direction, initiated by V. Milman is to replace ellipsoids by positions (affine images) of another body $L$. Another, more recent direction is to consider logarithmically concave functions on $\mathbb{R}^{d}$ instead of convex bodies: we designate some special, radially symmetric log-concave function $g$ as the analogue of the Euclidean ball, and want to find its largest integral position under the constraint that it is pointwise below some given log-concave function $f$. We follow both directions simultaneously: we consider the functional question, and allow essentially any meaningful function to play the role of $g$ above. Our general theorems jointly extend known results in both directions. The dual problem in the setting of convex bodies asks for the smallest volume ellipsoid, called Löwner’s ellipsoid, containing $K$. We consider the analogous problem for functions: we characterize the solutions of the optimization problem of finding a smallest integral position of some log-concave function $g$ under the constraint that it is pointwise above $f$. It turns out that in the functional setting, the relationship between the John and the Löwner problems is more intricate than it is in the setting of convex bodies.}, author = {Ivanov, Grigory and Naszódi, Márton}, issn = {1687-0247}, journal = {International Mathematics Research Notices}, keywords = {General Mathematics}, number = {23}, pages = {20613--20669}, publisher = {Oxford University Press}, title = {{Functional John and Löwner conditions for pairs of log-concave functions}}, doi = {10.1093/imrn/rnad210}, volume = {2023}, year = {2023}, } @article{14739, abstract = {Attempts to incorporate topological information in supervised learning tasks have resulted in the creation of several techniques for vectorizing persistent homology barcodes. In this paper, we study thirteen such methods. Besides describing an organizational framework for these methods, we comprehensively benchmark them against three well-known classification tasks. Surprisingly, we discover that the best-performing method is a simple vectorization, which consists only of a few elementary summary statistics. Finally, we provide a convenient web application which has been designed to facilitate exploration and experimentation with various vectorization methods.}, author = {Ali, Dashti and Asaad, Aras and Jimenez, Maria-Jose and Nanda, Vidit and Paluzo-Hidalgo, Eduardo and Soriano Trigueros, Manuel}, issn = {1939-3539}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, keywords = {Applied Mathematics, Artificial Intelligence, Computational Theory and Mathematics, Computer Vision and Pattern Recognition, Software}, number = {12}, pages = {14069--14080}, publisher = {IEEE}, title = {{A survey of vectorization methods in topological data analysis}}, doi = {10.1109/tpami.2023.3308391}, volume = {45}, year = {2023}, } @article{14742, abstract = {Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics. While an important role for CRs in speciation has been suggested, evidence primarily stems from theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon pairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at a macroevolutionary level has been supported by associations between species diversity and rates of evolution of CRs across phylogenies, these findings are limited to a restricted range of CRs and taxa. Now that more broadly applicable and precise CR detection approaches have become available, we address the challenges in filling some of the conceptual and empirical gaps between micro- and macroevolutionary studies on the role of CRs in speciation. We synthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.}, author = {Lucek, Kay and Giménez, Mabel D. and Joron, Mathieu and Rafajlović, Marina and Searle, Jeremy B. and Walden, Nora and Westram, Anja M and Faria, Rui}, issn = {1943-0264}, journal = {Cold Spring Harbor Perspectives in Biology}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {11}, publisher = {Cold Spring Harbor Laboratory}, title = {{The impact of chromosomal rearrangements in speciation: From micro- to macroevolution}}, doi = {10.1101/cshperspect.a041447}, volume = {15}, year = {2023}, }