Proceedings of the National Academy of Sciences of the United States of America最新文献

{"title":"Forecasting range shifts of dioecious plants under climate change","authors":"Jacob K. Moutouama, Aldo Compagnoni, Tom E. X. Miller","doi":"10.1073/pnas.2422162122","DOIUrl":"https://doi.org/10.1073/pnas.2422162122","url":null,"abstract":"Global climate change has triggered an urgent need for predicting the reorganization of Earth’s biodiversity. For dioecious species (those with separate sexes), it is unclear how commonly unique climate sensitivities of females and males could influence projections for species-level responses to climate change. We developed demographic models of range limitation, parameterized from geographically distributed common garden experiments, with females and males of a dioecious grass species ( <jats:italic toggle=\"yes\">Poa arachnifera</jats:italic> ) throughout and beyond its range in the south-central U.S. We contrasted predictions of a standard female-dominant model with those of a two-sex model that accounts for feedbacks between sex ratio and vital rates. Both model versions predict that future climate change will induce a poleward shift of niche suitability beyond current northern limits. However, the magnitude of the poleward shift was underestimated by the female-dominant model because females have broader temperature tolerance than males but become mate-limited under female-biased sex ratios, which are forecasted to become more common under future climate. Our results illustrate how explicitly accounting for both sexes can enhance population viability forecasts and conservation planning for dioecious species in response to climate change.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"78 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144104800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ancient DNA suggests a historical demographic decline and genetic erosion in the Atlantic bluefin tuna","authors":"Adam Jon Andrews, Emma Falkeid Eriksen, Bastiaan Star, Kim Præbel, Antonio Di Natale, Estrella Malca, Vedat Onar, Veronica Aniceti, Gabriele Carenti, Gäel Piquès, Svein Vatsvåg Nielsen, Per Persson, Federica Piattoni, Francesco Fontani, Lane M. Atmore, Oliver Kersten, Fausto Tinti, Elisabetta Cilli, Alessia Cariani","doi":"10.1073/pnas.2409302122","DOIUrl":"https://doi.org/10.1073/pnas.2409302122","url":null,"abstract":"Overexploitation has depleted fish stocks during the past century; nonetheless, its genomic consequences remain poorly understood for most species. Characterizing the spatiotemporal patterns of these consequences may provide baseline estimates of past diversity and productivity to aid management targets, help predict future dynamics, and facilitate the identification of evolutionary factors limiting fish population recovery. Here, we evaluate human impacts on the evolution of the iconic Atlantic bluefin tuna ( <jats:italic toggle=\"yes\">Thunnus thynnus</jats:italic> ), one of the longest and most intensely exploited marine fishes, with a tremendous cultural and economic importance. We sequenced whole genomes from modern (n = 49) and ancient (n = 41) specimens dating up to 5,000 y ago, uncovering several findings. First, we identify temporally stable patterns of population admixture, as bluefin tuna caught off Norway and in the eastern Mediterranean share a greater degree of ancestry with Gulf of Mexico bluefin tuna than western and central Mediterranean bluefin tuna. This suggests that Atlantic spawning areas are important mixing grounds for the genetic diversity of Mediterranean bluefin tuna. We model effective population size to show that Mediterranean bluefin tuna began to undergo a demographic decline by the year 1900 to an extent not observed across the previous millennia. Coinciding with this, we found that heterozygosity and nucleotide diversity were significantly lower in modern (2013 to 2020) than ancient (pre-1941) Mediterranean bluefin tuna, suggesting that bluefin tuna underwent a genetic bottleneck. With this work, we show how ancient DNA provides unique perspectives on ecological complexity with the potential to inform the management and conservation of fishes.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"42 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144104802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population size interacts with reproductive longevity to shape the germline mutation rate","authors":"Luke Zhu, Annabel Beichman, Kelley Harris","doi":"10.1073/pnas.2423311122","DOIUrl":"https://doi.org/10.1073/pnas.2423311122","url":null,"abstract":"Mutation rates vary across the tree of life by many orders of magnitude, with fewer mutations occurring each generation in species that reproduce quickly and maintain large effective population sizes. A compelling explanation is that large effective population sizes facilitate selection against weakly deleterious “mutator alleles” such as variants that modulate cell division or interfere with the molecular efficacy of DNA repair. However, while the fidelity of a single cell division largely determines microorganisms’ mutation rates, the relationship of the mutation rate to the molecular determinants of DNA damage and repair is more complex in multicellular species with long generation times. Since long generations leave more time for mutations to accrue each generation, we posit that a long generation time likely amplifies the fitness consequences of any damage agent or DNA repair defect that creates extra mutations in the spermatogonia or oocytes. This leads to the counterintuitive prediction that the species with the highest germline mutation rates per generation are also the species with most effective mechanisms for avoiding and repairing mutations in their reproductive cells. Consistent with this, we show that mutation rates in the reproductive cells are inversely correlated with generation time; in contrast, the number of germline mutations that occur during prepuberty development trends weakly upward as generation time increases. Our results parallel recent findings that the longest-lived species have the lowest mutation rates in adult somatic tissues, potentially due to selection to keep the lifetime mutation load below a harmful threshold.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"129 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144104810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kernels of selfhood: GPT-4o shows humanlike patterns of cognitive dissonance moderated by free choice.","authors":"Steven A Lehr, Ketan S Saichandran, Eddie Harmon-Jones, Nykko Vitali, Mahzarin R Banaji","doi":"10.1073/pnas.2501823122","DOIUrl":"10.1073/pnas.2501823122","url":null,"abstract":"<p><p>Large language models (LLMs) show emergent patterns that mimic human cognition. We explore whether they also mirror other, less deliberative human psychological processes. Drawing upon classical theories of cognitive consistency, two preregistered studies tested whether GPT-4o changed its attitudes toward Vladimir Putin in the direction of a positive or negative essay it wrote about the Russian leader. Indeed, GPT displayed patterns of attitude change mimicking cognitive dissonance effects in humans. Even more remarkably, the degree of change increased sharply when the LLM was offered an illusion of choice about which essay (positive or negative) to write, suggesting that GPT-4o manifests a functional analog of humanlike selfhood. The exact mechanisms by which the model mimics human attitude change and self-referential processing remain to be understood.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 20","pages":"e2501823122"},"PeriodicalIF":9.4,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144041812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effective polarization in potassium channel simulations: Ion conductance, occupancy, voltage response, and selectivity","authors":"Chenggong Hui, Reinier de Vries, Wojciech Kopec, Bert L. de Groot","doi":"10.1073/pnas.2423866122","DOIUrl":"https://doi.org/10.1073/pnas.2423866122","url":null,"abstract":"Potassium (K <jats:sup>+</jats:sup> ) channels are widely distributed in many types of organisms. They combine high efficiency (~100 pS) and K <jats:sup>+</jats:sup> /Na <jats:sup>+</jats:sup> selectivity by a conserved selectivity filter (SF). Molecular Dynamics (MD) simulations can provide detailed, atomistic mechanisms of this sophisticated ion permeation. However, currently there are clear inconsistencies between computational predictions and experimental results. First, the ion occupancy of the SF in simulations is lower than expected (~2.5 in MD compared to ~4 in X-ray crystallography). Second, in many reported MD simulations of K <jats:sup>+</jats:sup> channels, K <jats:sup>+</jats:sup> conductance is typically an order of magnitude lower than experimental values. This discrepancy is in part because the force fields used in MD simulations of potassium channels do not account for polarization. One of the proposed solutions is the Electronic Continuum Correction (ECC), a force field modification that scales down formal charges, to introduce the polarization in a mean-field way. When the ECC is used in conjunction with the Charmm36m force field, the simulated K <jats:sup>+</jats:sup> conductance increases 13-fold. Following the analysis of ion occupancy states using Hamiltonian Replica Exchange simulations, we propose a parameter set for Amber14sb, that also leads to a similar increase in conductance. These two force fields are then used to compute the full current–voltage (I-V) curves from MD simulations, approaching quantitative agreement with experiments at all voltages. In general, the ECC-enabled simulations are in excellent agreement with experiment, in terms of ion occupancy, conductance, current–voltage response, and K <jats:sup>+</jats:sup> /Na <jats:sup>+</jats:sup> selectivity.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"62 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144104808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exact and efficient phylodynamic simulation from arbitrarily large populations.","authors":"Michael Celentano, William S DeWitt, Sebastian Prillo, Yun S Song","doi":"10.1073/pnas.2412978122","DOIUrl":"10.1073/pnas.2412978122","url":null,"abstract":"<p><p>Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a comprehensive population tree and is distorted by survivorship and sampling biases. Inferring evolutionary parameters from ascertained trees requires modeling both the underlying population dynamics and the ascertainment process. A crucial component of this phylodynamic modeling involves tree simulation, which is used to benchmark probabilistic inference methods. To simulate an ascertained tree, one must first simulate the full population tree and then prune unobserved lineages. Consequently, the computational cost is determined not by the size of the final simulated tree, but by the size of the population tree in which it is embedded. In most biological scenarios, simulations of the entire population are prohibitively expensive due to computational demands placed on lineages without sampled descendants. Here, we address this challenge by proving that, for any partially ascertained process from a general multitype birth-death-mutation-sampling model, there exists an equivalent process with complete sampling and no death, a property which we leverage to develop a highly efficient algorithm for simulating trees. Our algorithm scales linearly with the size of the final simulated tree and is independent of the population size, enabling simulations from extremely large populations beyond the reach of current methods but essential for various biological applications. We anticipate that this massive speedup will significantly advance the development of novel inference methods that require extensive training data.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 20","pages":"e2412978122"},"PeriodicalIF":9.4,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lane formation in criss-crossing crowds.","authors":"Klaus Kroy","doi":"10.1073/pnas.2505488122","DOIUrl":"https://doi.org/10.1073/pnas.2505488122","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 20","pages":"e2505488122"},"PeriodicalIF":9.4,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144029039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electric field-induced pore constriction in the human K_v2.1 channel.","authors":"Venkata Shiva Mandala, Roderick MacKinnon","doi":"10.1073/pnas.2426744122","DOIUrl":"10.1073/pnas.2426744122","url":null,"abstract":"<p><p>Gating in voltage-dependent ion channels is regulated by the transmembrane voltage. This form of regulation is enabled by voltage-sensing domains (VSDs) that respond to transmembrane voltage differences by changing their conformation and exerting force on the pore to open or close it. Here, we use cryogenic electron microscopy to study the neuronal K_v2.1 channel in lipid vesicles with and without a voltage difference across the membrane. Hyperpolarizing voltage differences displace the positively charged S4 helix in the voltage sensor by one helical turn (~5 Å). When this displacement occurs, the S4 helix changes its contact with the pore at two different interfaces. When these changes are observed in fewer than four voltage sensors, the pore remains open, but when they are observed in all four voltage sensors, the pore constricts. The constriction occurs because the S4 helix, as it displaces inward, squeezes the right-handed helical bundle of pore-lining S6 helices. A similar conformational change occurs upon hyperpolarization of the EAG1 channel but with two helical turns displaced instead of one. Therefore, while K_v2.1 and EAG1 are from distinct architectural classes of voltage-dependent ion channels, called domain-swapped and non-domain-swapped, the way the voltage sensors gate their pores is very similar.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 20","pages":"e2426744122"},"PeriodicalIF":9.4,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144028642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"QnAs with Thomas A. Henzinger.","authors":"Sandeep Ravindran","doi":"10.1073/pnas.2509901122","DOIUrl":"10.1073/pnas.2509901122","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 20","pages":"e2509901122"},"PeriodicalIF":9.4,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144041508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Arteries are finely tuned thermosensors regulating myogenic tone and blood flow","authors":"Thieu X. Phan, Niaz Sahibzada, Marc Freichel, Rosa L. Miyares, Gerard P. Ahern","doi":"10.1073/pnas.2503186122","DOIUrl":"https://doi.org/10.1073/pnas.2503186122","url":null,"abstract":"In response to changing blood pressure, arteries adjust their caliber to control blood flow. This vital autoregulatory property, termed vascular myogenic tone, stabilizes downstream capillary pressure. Here, we reveal that tissue temperature, combined with intraluminal pressure, critically determines myogenic tone. Heating steeply activates tone in skeletal muscle, gut, brain, and skin arteries with temperature coefficients ( <jats:italic toggle=\"yes\">Q</jats:italic> <jats:sub>10</jats:sub> ) of ~11 to 20. Each of these tissues has a distinct resting temperature, and we find that arterial thermosensitivity is tuned to this temperature, making myogenic tone sensitive to small thermal fluctuations. Interestingly, temperature and intraluminal pressure are sensed largely independently and the signals integrated to trigger myogenic tone. We demonstrate that thermosensitive channels TRPV1 and TRPM4 mediate heat-induced tone in skeletal muscle arteries with discrete temperature sensitivities. Similarly, TRPM4 contributes to heat-induced tone in gut and brain arteries. The half-maximal responses occur at approximately 31 °C for TRPV1 and 33 °C for TRPM4. Variations in tissue temperature are known to alter blood fluidity and therefore vascular conductance; remarkably, thermosensitive tone counterbalances this effect, thus protecting capillary integrity and fluid balance. In conclusion, thermosensitive myogenic tone is a fundamental homeostatic mechanism regulating tissue perfusion.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"15 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144104816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}