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

{"title":"Unbalanced social–ecological acceleration led to state formation failure in early medieval Poland","authors":"Adam Izdebski, Sambor Czerwiński, Marek Jankowiak, Marcin Danielewski, Sabina Fiołna, Raphael Gromig, Piotr Guzowski, Negar Haghipour, Irka Hajdas, Piotr Kołaczek, Mariusz Lamentowicz, Katarzyna Marcisz, Jakub Niebieszczański, Paweł Sankiewicz, Bernd Wagner","doi":"10.1073/pnas.2409056122","DOIUrl":"https://doi.org/10.1073/pnas.2409056122","url":null,"abstract":"Rapid social–ecological intensification is a recurrent feature of human history. It occurred in different forms and contexts; its outcomes may have been sustainable or transient. Until recently, such intensifications usually accompanied state formation: Consolidation of political power was often coupled with exponential increase in human exploitation of the environment of a given area. Here, we study one such case, uniquely well-documented through our rich paleoecological, archaeological, numismatic, and literary data. Triggered by the Eurasian slave trade, the first “Polish” polity was founded in Central Europe c. 900 common era. It undertook unprecedented ecological intensification in its core territory, connected with large construction projects, and engaged in rapid territorial expansion. We provide new crucial evidence on this process by publishing here a high-resolution pollen profile from a location close to the polity’s capital and by an application of social network analysis to numismatic data. This state collapsed within a few generations after its foundation. The collapse of the political elites, however, did not produce a complete social and ecological disintegration of the polity’s former core region. We thus show how collapse and continuity can remain closely intertwined. Last but not least, the rich evidence on the mechanism of the collapse reveals that successful maintenance of social–ecological intensification requires reliance on a number of cultural, economic, religious, and social networks underlying the political expansion. The polity’s elite lacked access to or failed to mobilize such networks, which led to its demise.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"219 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857382","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":"The ins and outs of plant specialized metabolite gene organization.","authors":"Richard A Dixon","doi":"10.1073/pnas.2504934122","DOIUrl":"https://doi.org/10.1073/pnas.2504934122","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"19 1","pages":"e2504934122"},"PeriodicalIF":11.1,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143862021","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":"Nonnative tree invaders lead to declines in native tree species richness","authors":"Yunpeng Liu, Samuel M. Scheiner, J. Aaron Hogan, Matthew B. Thomas, Pamela S. Soltis, Robert P. Guralnick, Douglas E. Soltis, Jeremy W. Lichstein","doi":"10.1073/pnas.2424908122","DOIUrl":"https://doi.org/10.1073/pnas.2424908122","url":null,"abstract":"Biological invasions are profoundly altering Earth’s ecosystems, but generalities about the effects of nonnative species on the diversity and productivity of native communities have been elusive. This lack of generality may reflect the limited spatial and temporal extents of most previous studies. Using >5 million tree measurements across eastern US forests from 1995 to 2023, we quantified temporal trends in tree diversity and biomass. We then analyzed community-level changes in native tree diversity and biomass in relation to nonnative tree invasion and native species colonization. Across the entire eastern United States, native tree species richness decreased over time in plots where nonnatives occurred, whereas nonnative species richness and the biomass of both natives and nonnatives increased over time. At the community scale, native richness tended to decline following nonnative invasion, whereas native biomass and richness-independent measures of trait and phylogenetic diversity tended to remain stable. These patterns can be explained by the rarity of the displaced native species and their functional and phylogenetic similarity to native species that survived nonnative invasions. In contrast, native survivors tended to be functionally distinct from nonnative invaders, suggesting an important role for niche partitioning in community dynamics. Colonization by previously absent native species was associated with an increase in native richness (beyond the addition of native colonizers), which contrasts with declines in native richness that tended to follow nonnative invasion. These results suggest a causal role for nonnative species in the native richness decline of invaded communities.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"138 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857383","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":"A diverse single-stranded DNA–annealing protein library enables efficient genome editing across bacterial phyla","authors":"Gabriel T. Filsinger, Aaron Mychack, Evan Lyerly, Camilla Henriksen, Thomas M. Bartlett, Helene Kuchwara, Simon Eitzinger, Thomas G. Bernhardt, Suzanne Walker, George M. Church, Timothy M. Wannier","doi":"10.1073/pnas.2414342122","DOIUrl":"https://doi.org/10.1073/pnas.2414342122","url":null,"abstract":"Genome modification is essential for studying and engineering bacteria, yet making efficient modifications to most species remains challenging. Bacteriophage-encoded single-stranded DNA–annealing proteins (SSAPs) can facilitate efficient genome editing by homologous recombination, but their typically narrow host range limits broad application. Here, we demonstrate that a single library of 227 SSAPs enables efficient genome-editing across six diverse bacteria from three divergent classes: Actinomycetia ( <jats:italic>Mycobacterium smegmatis</jats:italic> and <jats:italic>Corynebacterium glutamicum</jats:italic> ), Alphaproteobacteria ( <jats:italic>Agrobacterium tumefaciens</jats:italic> and <jats:italic>Caulobacter crescentus</jats:italic> ), and Bacilli ( <jats:italic>Lactococcus lactis</jats:italic> and <jats:italic>Staphylococcus aureus</jats:italic> ). Surprisingly, the most effective SSAPs frequently originated from phyla distinct from their bacterial hosts, challenging the assumption that phylogenetic relatedness is necessary for recombination efficiency, and supporting the value of a large unbiased library. Across these hosts, the identified SSAPs enable genome modifications requiring efficient homologous recombination, demonstrated through three examples. First, we use SSAPs with Cas9 in <jats:italic>C. crescentus</jats:italic> to introduce single amino acid mutations with &gt;70% efficiency. Second, we adapt SSAPs for dsDNA editing in <jats:italic>C. glutamicum</jats:italic> and <jats:italic>S. aureus</jats:italic> , enabling one-step gene knockouts using PCR products. Finally, we apply SSAPs for multiplexed editing in <jats:italic>S. aureus</jats:italic> to precisely map the interaction between a conserved protein and a small-molecule inhibitor. Overall, this library-based SSAP screen expands engineering capabilities across diverse, previously recalcitrant microbes, enabling efficient genetic manipulation for both fundamental research and biotechnological applications.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"1 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857388","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":"Phase transitions and dimensional cross-over in layered confined solids","authors":"Yong Wang, Junjie Wang, Ge Yao, Zheyong Fan, Enzo Granato, Michael Kosterlitz, Tapio Ala-Nissila, Roberto Car, Jian Sun","doi":"10.1073/pnas.2502980122","DOIUrl":"https://doi.org/10.1073/pnas.2502980122","url":null,"abstract":"The nature of solid phases and cross-over of order–disorder phase transitions from two-dimensional (2D) layers to three-dimensional (3D) bulk in confined atomic systems remain largely unexplained. To this end, we consider noble gases and aluminum confined between graphene sheets at different pressures and temperatures. Using crystal structure search methods and molecular dynamics based on machine-learned potentials with quantum-mechanical accuracy, we identify structures of multilayer confined solids that deviate from simple close packing. Upon heating, we find that confined 2D monolayers melt according to the two-step continuous Kosterlitz–Thouless–Halperin–Nelson–Young theory. However, multilayer solids transition continuously into an intermediate layered-hexatic phase before melting discontinuously into an isotropic liquid. This intermediate phase persists at least up to 12 layers studied here. This change can be qualitatively understood based on the cross-over from 2D topological defects toward 3D ones during melting as the number of layers increases.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"91 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857384","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":"Ecologically informed solar enables a sustainable energy transition in US croplands","authors":"Matthew A. Sturchio, Adam Gallaher, Steven M. Grodsky","doi":"10.1073/pnas.2501605122","DOIUrl":"https://doi.org/10.1073/pnas.2501605122","url":null,"abstract":"United States (US) croplands are ideal recipient environments for solar photovoltaic (PV) energy because they are flat and have a high solar resource. Perceived threats of solar to agriculture have led some stakeholders to suggest that croplands be exclusively used to produce food. However, 12 million hectares of US croplands, an area about the size of New York State, are already dedicated to corn grown for ethanol (i.e., biofuel), an energy product that requires significantly more land than solar PV per unit energy. Ecosystem service benefits of an ecologically informed approach to solar development (i.e., ecovoltaics), coupled with significant land-use advantages over corn ethanol, make solar an attractive solution for a sustainable energy transition in croplands. Here, we evaluated how the conversion of a small fraction of corn-ethanol croplands into ecovoltaic solar facilities might improve land-use efficiency of energy generation, enhance ecosystem services, and provide landscape diversification. Through spatial analyses, we determined that converting just 3.2% of land currently used for corn ethanol would increase the share of utility-scale solar energy in the US from 3.9 to 13%. We also identified target locations where strategic conversion of corn ethanol to solar PV colocated with perennial vegetation could filter excess nutrients transported from adjacent farm runoff, diversify and connect agricultural landscapes, and provide local wildlife habitat. In contrast to the common perception of land-use competition and land scarcity in the energy transition, our findings highlight benefits of colocated energy landscapes that integrate fundamental principles of energy development and sustainable agroecosystems.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"68 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857601","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":"Identifying air quality monitoring deserts in the United States","authors":"Nelson A. Roque, Hailey Andrews, Alexis R. Santos-Lozada","doi":"10.1073/pnas.2425310122","DOIUrl":"https://doi.org/10.1073/pnas.2425310122","url":null,"abstract":"Air quality is associated with adverse health outcomes and mortality risk. While most research has focused on the association between air quality estimates and these outcomes, little is known about the presence of air quality monitoring sites across the United States or the place-level characteristics associated with such placements. We classify counties without a monitoring station as air quality monitoring deserts. Using the Environmental Protection Agency’s AirData active sites directory, we determine the number and location of monitoring deserts. We then study whether demographic and socioeconomic characteristics are associated with the likelihood of a county being a monitoring desert. Our results indicate that 1,848 or 58.8% of US counties are an air quality monitoring desert, covering about 40% of the nation’s land area. Our estimates suggest that more than 50 million people or 15.3% of the population live in air quality monitoring deserts. Rural and counties with higher proportions of historically minoritized groups have higher odds of being a monitoring desert. Regionally speaking, air quality monitoring deserts are highly concentrated within the Midwest and the South. These findings highlight gaps in air quality monitoring in the United States. Identifying and addressing air quality monitoring deserts across the United States will allow us to better understand air quality across the nation and expand current knowledge of its impact on national health and well-being.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"56 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857381","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":"Computational analysis of 100 K choice dilemmas: Decision attributes, trade-off structures, and model-based prediction","authors":"Sudeep Bhatia, Simon T. van Baal, Feiyi Wang, Lukasz Walasek","doi":"10.1073/pnas.2406489122","DOIUrl":"https://doi.org/10.1073/pnas.2406489122","url":null,"abstract":"We present a dataset of over 100 K textual descriptions of real-life choice dilemmas, obtained from social media posts and large-scale survey data. Using large language models (LLMs), we extract hundreds of choice attributes at play in these dilemmas and map them onto a common representational space. This representation allows us to quantify the broader themes and specific trade-offs inherent in life choices and analyze how they vary across different contexts. We also present our dilemmas to human participants and find that our LLM pipeline, when combined with established decision models, accurately predicts people’s choices, outperforming models based on unstructured textual content, demographics, and personality. In this way, our research provides insights into the attributes, outcomes, and goals that underpin life choices, and shows how large-scale LLM-based structure extraction can be used in combination with existing scientific theory to study complex real-world human behavior.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"64 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857386","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":"Thermal homogenization of boreal communities in response to climate warming","authors":"Jussi Mäkinen, Emilie E. Ellis, Laura H. Antão, Andréa Davrinche, Anna-Liisa Laine, Marjo Saastamoinen, Irene Conenna, Maria Hällfors, Andrea Santangeli, Elina Kaarlejärvi, Janne Heliölä, Ida-Maria Huikkonen, Mikko Kuussaari, Reima Leinonen, Aleksi Lehikoinen, Juha Pöyry, Anna Suuronen, Maija Salemaa, Tiina Tonteri, Kristiina M. Vuorio, Birger Skjelbred, Marko Järvinen, Stina Drakare, Laurence Carvalho, Erik Welk, Gunnar Seidler, Pieter Vangansbeke, František Máliš, Radim Hédl, Alistair G. Auffret, Jan Plue, Pieter De Frenne, Jesse M. Kalwij, Jarno Vanhatalo, Tomas Roslin","doi":"10.1073/pnas.2415260122","DOIUrl":"https://doi.org/10.1073/pnas.2415260122","url":null,"abstract":"Globally, rising temperatures are increasingly favoring warm-affiliated species. Although changes in community composition are typically measured by the mean temperature affinity of species (the community temperature index, CTI), they may be driven by different processes and accompanied by shifts in the diversity of temperature affinities and breadth of species thermal niches. To resolve the pathways to community warming in Finnish flora and fauna, we examined multidecadal changes in the dominance and diversity of temperature affinities among understory forest plant, freshwater phytoplankton, butterfly, moth, and bird communities. CTI increased for all animal communities, with no change observed for plants or phytoplankton. In addition, the diversity of temperature affinities declined for all groups except butterflies, and this loss was more pronounced for the fastest-warming communities. These changes were driven in animals mainly by a decrease in cold-affiliated species and an increase in warm-affiliated species. In plants and phytoplankton the decline of thermal diversity was driven by declines of both cold- and warm-affiliated species. Plant and moth communities were increasingly dominated by thermal specialist species, and birds by thermal generalists. In general, climate warming outpaced changes in both the mean and diversity of temperature affinities of communities. Our results highlight the complex dynamics underpinning the thermal reorganization of communities across a large spatiotemporal gradient, revealing that extinctions of cold-affiliated species and colonization by warm-affiliated species lag behind changes in ambient temperature, while communities become less thermally diverse. Such changes can have important implications for community structure and ecosystem functioning under accelerating rates of climate change.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"43 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857389","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":"Structure in conversation: Evidence for the vocabulary, semantics, and syntax of prosody","authors":"Nadav Matalon, Eyal Weinreb, Dominik Freche, Erez Volk, Tirza Biron, Elisha Moses, David Biron","doi":"10.1073/pnas.2403262122","DOIUrl":"https://doi.org/10.1073/pnas.2403262122","url":null,"abstract":"Prosody, the musical facet of speech, is pivotal in human communication, and its structure and meaning remain subjects of ongoing research. In this study, we introduce a data-driven model for English prosody, based on large-scale analysis of spontaneous conversations. As a first step, we identify approximately 200 discernible prosodic patterns—which we view as building blocks of the prosodic vocabulary—and outline their properties and range of meanings. Next, we reveal a Markovian logic, akin to a syntax, for concatenating these elementary building blocks into coherent utterances. We identify distinct compound functions associated with pairs of consecutive patterns and show that the Markovian syntax is more prevalent in spontaneous prosody, as compared to scripted speech. These findings offer invaluable insights into the underlying mechanisms of conversational prosody: They empirically inform and refine existing theoretical concepts. The methodology we present, combining unsupervised analysis of large datasets of spontaneous speech with manual sampling of the results, could guide future research aimed at refining our model and expanding it to other languages.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"67 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857573","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}