TY - JOUR
AB - Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.
AU - Stankowski, Sean
AU - Zagrodzka, Zuzanna B.
AU - Garlovsky, Martin D.
AU - Pal, Arka
AU - Shipilina, Daria
AU - Garcia Castillo, Diego Fernando
AU - Lifchitz, Hila
AU - Le Moan, Alan
AU - Leder, Erica
AU - Reeve, James
AU - Johannesson, Kerstin
AU - Westram, Anja M
AU - Butlin, Roger K.
ID - 14796
IS - 6678
JF - Science
TI - The genetic basis of a recent transition to live-bearing in marine snails
VL - 383
ER -
TY - THES
AB - This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.
Chapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?
Chapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.
Chapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.
Chapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.
AU - Hledik, Michal
ID - 15020
KW - Theoretical biology
KW - Optimality
KW - Evolution
KW - Information
SN - 2663 - 337X
TI - Genetic information and biological optimization
ER -
TY - GEN
AB - Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen, she became a group leader at the Plant Systems Biology Department of the Vlaams Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant Professor position at the Institute of Science and Technology Austria (ISTA) where she was later promoted to Professor. Since 2021, she has served as the Dean of the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling the molecular mechanisms and principles that underlie hormonal interactions in plants. In her current work, she explores the intricate connections between hormones and regulatory pathways that mediate the perception of environmental stimuli, including abiotic stress and nitrate availability.
AU - Benková, Eva
ID - 14842
IS - 1
T2 - Current Biology
TI - Eva Benkova
VL - 34
ER -
TY - JOUR
AB - GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca
2+
-dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.
AU - Koppensteiner, Peter
AU - Bhandari, Pradeep
AU - Önal, Hüseyin C
AU - Borges Merjane, Carolina
AU - Le Monnier, Elodie
AU - Roy, Utsa
AU - Nakamura, Yukihiro
AU - Sadakata, Tetsushi
AU - Sanbo, Makoto
AU - Hirabayashi, Masumi
AU - Rhee, JeongSeop
AU - Brose, Nils
AU - Jonas, Peter M
AU - Shigemoto, Ryuichi
ID - 15084
IS - 8
JF - Proceedings of the National Academy of Sciences
SN - 0027-8424
TI - GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles
VL - 121
ER -
TY - JOUR
AB - Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The very logic of reciprocity, however, seems to require that individuals are symmetric, and that everyone has the same means to influence each others’ payoffs. Yet in many applications, individuals are asymmetric. Herein, we study the effect of asymmetry in linear public good games. Individuals may differ in their endowments (their ability to contribute to a public good) and in their productivities (how effective their contributions are). Given the individuals’ productivities, we ask which allocation of endowments is optimal for cooperation. To this end, we consider two notions of optimality. The first notion focuses on the resilience of cooperation. The respective endowment distribution ensures that full cooperation is feasible even under the most adverse conditions. The second notion focuses on efficiency. The corresponding endowment distribution maximizes group welfare. Using analytical methods, we fully characterize these two endowment distributions. This analysis reveals that both optimality notions favor some endowment inequality: More productive players ought to get higher endowments. Yet the two notions disagree on how unequal endowments are supposed to be. A focus on resilience results in less inequality. With additional simulations, we show that the optimal endowment allocation needs to account for both the resilience and the efficiency of cooperation.
AU - Hübner, Valentin
AU - Staab, Manuel
AU - Hilbe, Christian
AU - Chatterjee, Krishnendu
AU - Kleshnina, Maria
ID - 15083
IS - 10
JF - Proceedings of the National Academy of Sciences
SN - 0027-8424
TI - Efficiency and resilience of cooperation in asymmetric social dilemmas
VL - 121
ER -
TY - GEN
AB - in the research article "Efficiency and resilience of cooperation in asymmetric social dilemmas" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina).
We used different implementations for the case of two and three players, both described below.
AU - Hübner, Valentin
AU - Kleshnina, Maria
ID - 15108
TI - Computer code for "Efficiency and resilience of cooperation in asymmetric social dilemmas"
ER -
TY - JOUR
AB - Global storm-resolving models (GSRMs) use strongly refined horizontal grids compared with the climate models typically used in the Coupled Model Intercomparison Project (CMIP) but employ comparable vertical grid spacings. Here, we study how changes in the vertical grid spacing and adjustments to the integration time step affect the basic climate quantities simulated by the ICON-Sapphire atmospheric GSRM. Simulations are performed over a 45 d period for five different vertical grids with between 55 and 540 vertical layers and maximum tropospheric vertical grid spacings of between 800 and 50 m, respectively. The effects of changes in the vertical grid spacing are compared with the effects of reducing the horizontal grid spacing from 5 to 2.5 km. For most of the quantities considered, halving the vertical grid spacing has a smaller effect than halving the horizontal grid spacing, but it is not negligible. Each halving of the vertical grid spacing, along with the necessary reductions in time step length, increases cloud liquid water by about 7 %, compared with an approximate 16 % decrease for halving the horizontal grid spacing. The effect is due to both the vertical grid refinement and the time step reduction. There is no tendency toward convergence in the range of grid spacings tested here. The cloud ice amount also increases with a refinement in the vertical grid, but it is hardly affected by the time step length and does show a tendency to converge. While the effect on shortwave radiation is globally dominated by the altered reflection due to the change in the cloud liquid water content, the effect on longwave radiation is more difficult to interpret because changes in the cloud ice concentration and cloud fraction are anticorrelated in some regions. The simulations show that using a maximum tropospheric vertical grid spacing larger than 400 m would increase the truncation error strongly. Computing time investments in a further vertical grid refinement can affect the truncation errors of GSRMs similarly to comparable investments in horizontal refinement, because halving the vertical grid spacing is generally cheaper than halving the horizontal grid spacing. However, convergence of boundary layer cloud properties cannot be expected, even for the smallest maximum tropospheric grid spacing of 50 m used in this study.
AU - Schmidt, Hauke
AU - Rast, Sebastian
AU - Bao, Jiawei
AU - Cassim, Amrit
AU - Fang, Shih Wei
AU - Jimenez-De La Cuesta, Diego
AU - Keil, Paul
AU - Kluft, Lukas
AU - Kroll, Clarissa
AU - Lang, Theresa
AU - Niemeier, Ulrike
AU - Schneidereit, Andrea
AU - Williams, Andrew I.L.
AU - Stevens, Bjorn
ID - 15097
IS - 4
JF - Geoscientific Model Development
SN - 1991-959X
TI - Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model
VL - 17
ER -
TY - JOUR
AB - In this note, we prove a formula for the cancellation exponent kv,n between division polynomials ψn and ϕn associated with a sequence {nP}n∈N of points on an elliptic curve E defined over a discrete valuation field K. The formula greatly generalizes the previously known special cases and treats also the case of non-standard Kodaira types for non-perfect residue fields.
AU - Naskręcki, Bartosz
AU - Verzobio, Matteo
ID - 12311
JF - Proceedings of the Royal Society of Edinburgh Section A: Mathematics
KW - Elliptic curves
KW - Néron models
KW - division polynomials
KW - height functions
KW - discrete valuation rings
SN - 0308-2105
TI - Common valuations of division polynomials
ER -
TY - JOUR
AB - Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.
AU - Johannesson, Kerstin
AU - Faria, Rui
AU - Le Moan, Alan
AU - Rafajlović, Marina
AU - Westram, Anja M
AU - Butlin, Roger K.
AU - Stankowski, Sean
ID - 15099
JF - Trends in Genetics
SN - 0168-9525
TI - Diverse pathways to speciation revealed by marine snails
ER -
TY - JOUR
AB - The paper is devoted to the analysis of the global well-posedness and the interior regularity of the 2D Navier–Stokes equations with inhomogeneous stochastic boundary conditions. The noise, white in time and coloured in space, can be interpreted as the physical law describing the driving mechanism on the atmosphere–ocean interface, i.e. as a balance of the shear stress of the ocean and the horizontal wind force.
AU - Agresti, Antonio
AU - Luongo, Eliseo
ID - 15098
JF - Mathematische Annalen
SN - 0025-5831
TI - Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions
ER -