Gregor Hartmann, Tone Blakesley, Paige E. dePolo, Stephen L. Brusatte
Machine learning holds great promise for classifying and identifying fossils, and has recently been marshaled to identify trackmakers of dinosaur footprints and address long-standing debates over whether some dinosaur tracks are the oldest birds or ornithopods (duck-billed herbivores and kin) in the fossil record, or alternatively were made by nonavian theropods. Existing methods in paleontology, however, require supervision and a priori labeling of training data by researchers, which can lead to bias. We employ an unsupervised machine learning technique for recognizing inherent patterns in shape data, using a disentangled variational autoencoder network, to a database of 1,974 footprints, spanning a diversity of dinosaurs across their evolutionary history, including modern birds. Our neural network identified eight features of shape variation that most differentiate these tracks: overall load and shape (amount of ground contact area), digit spread, digit attachment, heel load, digit and heel emphasis, loading position, heel position, and left–right load. With the unsupervised process finished, we a posteriori labeled each track based on published expert judgments, plotted them into morphospace, and applied distance metrics to group means and nearest neighbors, which showed 80 to 93% agreement with expert identifications. Controversial Late Triassic-Early Jurassic bird-like tracks group with fossil and modern birds and some Middle Jurassic three-toed tracks with ornithopods, supporting an older origin for these groups than recorded by body fossils. We provide an app, DinoTracker, to make this process accessible, and source code that can be adapted to other cases where paleontologists or biologists are studying patterns of shape variation.
{"title":"Identifying variation in dinosaur footprints and classifying problematic specimens via unbiased unsupervised machine learning","authors":"Gregor Hartmann, Tone Blakesley, Paige E. dePolo, Stephen L. Brusatte","doi":"10.1073/pnas.2527222122","DOIUrl":"https://doi.org/10.1073/pnas.2527222122","url":null,"abstract":"Machine learning holds great promise for classifying and identifying fossils, and has recently been marshaled to identify trackmakers of dinosaur footprints and address long-standing debates over whether some dinosaur tracks are the oldest birds or ornithopods (duck-billed herbivores and kin) in the fossil record, or alternatively were made by nonavian theropods. Existing methods in paleontology, however, require supervision and a priori labeling of training data by researchers, which can lead to bias. We employ an unsupervised machine learning technique for recognizing inherent patterns in shape data, using a disentangled variational autoencoder network, to a database of 1,974 footprints, spanning a diversity of dinosaurs across their evolutionary history, including modern birds. Our neural network identified eight features of shape variation that most differentiate these tracks: overall load and shape (amount of ground contact area), digit spread, digit attachment, heel load, digit and heel emphasis, loading position, heel position, and left–right load. With the unsupervised process finished, we a posteriori labeled each track based on published expert judgments, plotted them into morphospace, and applied distance metrics to group means and nearest neighbors, which showed 80 to 93% agreement with expert identifications. Controversial Late Triassic-Early Jurassic bird-like tracks group with fossil and modern birds and some Middle Jurassic three-toed tracks with ornithopods, supporting an older origin for these groups than recorded by body fossils. We provide an app, DinoTracker, to make this process accessible, and source code that can be adapted to other cases where paleontologists or biologists are studying patterns of shape variation.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"31 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048218","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}
Annemieke Milks, Maria Ntinou, Stylianos Koutalis, Dimitrios Michailidis, George E. Konidaris, Domenico Giusti, Nicholas Thompson, Georgia Tsartsidou, Eleni Panagopoulou, Vangelis Tourloukis, Panagiotis Karkanas, Katerina Harvati
The Middle Pleistocene (MP; ca. 774 to 129 ka) marks a critical period of human evolution, characterized by increasing behavioral complexity and the first unambiguous evidence of plant-based technologies. Despite this, direct evidence for early wooden tool use remains exceptionally rare. Here, we present the earliest handheld wooden tools, identified from secure contexts at the site of Marathousa 1, Greece, dated to ca. 430 ka (MIS12). Through a systematic morphological, microscopic, taphonomic, and taxonomic analysis of the sampled wood macroremains, two specimens were securely identified as modified by hominins: one small alder ( Alnus sp.) trunk fragment bears clear working and use-wear traces consistent with a multifunctional stick likely used in digging at the paleolakeshore; and one very small willow/poplar ( Salix sp./ Populus sp.) artifact exhibits signs of shaping and potential use-wear. A third specimen, a large alder trunk segment, shows deep, nonanthropogenic striations interpreted here as claw marks from a large carnivoran. The wooden tools were excavated together with butchered elephant remains, small lithic artifacts and debitage, and worked bone, underscoring the diversity of engagement with a variety of different raw materials for technological purposes at Marathousa 1. These finds extend the temporal range of early wooden tools. They represent both the use of expedient larger handheld tools as well as a much smaller, likely finger-held wooden tool, which is uniquely small for the Pleistocene, expanding known functional purposes of early wood technologies. Moreover, they highlight the Megalopolis Basin’s exceptional preservation conditions and its role in understanding the evolution of hominin behavior.
中更新世（MP；约774 - 129 ka）标志着人类进化的一个关键时期，其特征是行为复杂性的增加和植物技术的第一个明确证据。尽管如此，早期使用木制工具的直接证据仍然非常罕见。在这里，我们展示了最早的手持式木制工具，这些工具是在希腊马拉松1号遗址的安全环境中发现的，可追溯到约430 ka （MIS12）。通过系统的形态学、显微学、地语学和分类学分析，两个样本被确定为人类改良过的：一个小桤木（Alnus sp.）树干碎片有明显的工作和使用磨损痕迹，与古湖岸挖掘时可能使用的多功能手杖一致；一件非常小的柳树/杨树（Salix sp./ Populus sp.）人工制品显示出成形和潜在使用磨损的迹象。第三个标本是一大块桤木树干，上面有很深的非人为的条纹，这被解释为是大型食肉动物的爪印。这些木制工具与被屠宰的大象遗骸、小型石器制品和碎片以及加工过的骨头一起被挖掘出来，强调了在马拉松1号，为了技术目的，使用各种不同原材料的多样性。这些发现扩大了早期木制工具的时间范围。它们既代表了权宜之计的大型手持工具的使用，也代表了一种更小的，可能是手指握着的木制工具的使用，这种工具在更新世是独一无二的，扩展了早期木材技术的已知功能目的。此外，他们还强调了特大城市盆地特殊的保存条件及其在理解人类行为进化中的作用。
{"title":"Evidence for the earliest hominin use of wooden handheld tools found at Marathousa 1 (Greece)","authors":"Annemieke Milks, Maria Ntinou, Stylianos Koutalis, Dimitrios Michailidis, George E. Konidaris, Domenico Giusti, Nicholas Thompson, Georgia Tsartsidou, Eleni Panagopoulou, Vangelis Tourloukis, Panagiotis Karkanas, Katerina Harvati","doi":"10.1073/pnas.2515479123","DOIUrl":"https://doi.org/10.1073/pnas.2515479123","url":null,"abstract":"The Middle Pleistocene (MP; ca. 774 to 129 ka) marks a critical period of human evolution, characterized by increasing behavioral complexity and the first unambiguous evidence of plant-based technologies. Despite this, direct evidence for early wooden tool use remains exceptionally rare. Here, we present the earliest handheld wooden tools, identified from secure contexts at the site of Marathousa 1, Greece, dated to ca. 430 ka (MIS12). Through a systematic morphological, microscopic, taphonomic, and taxonomic analysis of the sampled wood macroremains, two specimens were securely identified as modified by hominins: one small alder ( <jats:italic toggle=\"yes\">Alnus</jats:italic> sp.) trunk fragment bears clear working and use-wear traces consistent with a multifunctional stick likely used in digging at the paleolakeshore; and one very small willow/poplar ( <jats:italic toggle=\"yes\">Salix</jats:italic> sp./ <jats:italic toggle=\"yes\">Populus</jats:italic> sp.) artifact exhibits signs of shaping and potential use-wear. A third specimen, a large alder trunk segment, shows deep, nonanthropogenic striations interpreted here as claw marks from a large carnivoran. The wooden tools were excavated together with butchered elephant remains, small lithic artifacts and debitage, and worked bone, underscoring the diversity of engagement with a variety of different raw materials for technological purposes at Marathousa 1. These finds extend the temporal range of early wooden tools. They represent both the use of expedient larger handheld tools as well as a much smaller, likely finger-held wooden tool, which is uniquely small for the Pleistocene, expanding known functional purposes of early wood technologies. Moreover, they highlight the Megalopolis Basin’s exceptional preservation conditions and its role in understanding the evolution of hominin behavior.","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":"2026-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048239","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}
The global transition to sustainable energy demands efficient lithium extraction from brines. While electrochemical lithium extraction using LiMn 2 O 4 (LMO) holds great promise, its practical application is hindered by mechanical degradation caused by anisotropic volume changes and stress accumulation during cycling. Herein, we present an entropy-driven amphiphilic self-assembly strategy that engineers stress-homogenized multilayer core–shell architectures, which innovatively mitigates stress accumulation by tuning the internal geometric structure to optimize stress–strain behavior, thereby synergistically enhancing ion distribution, transport kinetics, and electrochemical stability. This hierarchical interlayer architecture ensures uniform Li + distribution and redistributes internal stresses, mitigating localized stress concentrations and lattice expansion to preserve structural integrity throughout cycling. The optimized LMO establishes a dual benchmark for both capacity and cycling stability in hybrid capacitive deionization, achieving a remarkable lithium extraction capacity of 4.78 mmol g −1 with 96% retention over 100 cycles, outperforming both its unoptimized counterpart and other reported materials of the same type. Finite element simulations further elucidate a 48% reduction in maximum stress compared to disordered counterparts, underscoring the critical coupling between ion diffusion and stress evolution. This paradigm provides a pathway for developing advanced materials with intrinsically stable architectures for sustainable lithium extraction.
{"title":"Stress-homogenized spatial architectures via entropy-driven self-assembly enabling high-performance and durable lithium extraction","authors":"Xiaoqian Liu, Zewei Hao, Tongcai Liu, Qipeng Zhao, Xuefei Zhou, Yalei Zhang, Huaqiang Chu","doi":"10.1073/pnas.2525797123","DOIUrl":"https://doi.org/10.1073/pnas.2525797123","url":null,"abstract":"The global transition to sustainable energy demands efficient lithium extraction from brines. While electrochemical lithium extraction using LiMn <jats:sub>2</jats:sub> O <jats:sub>4</jats:sub> (LMO) holds great promise, its practical application is hindered by mechanical degradation caused by anisotropic volume changes and stress accumulation during cycling. Herein, we present an entropy-driven amphiphilic self-assembly strategy that engineers stress-homogenized multilayer core–shell architectures, which innovatively mitigates stress accumulation by tuning the internal geometric structure to optimize stress–strain behavior, thereby synergistically enhancing ion distribution, transport kinetics, and electrochemical stability. This hierarchical interlayer architecture ensures uniform Li <jats:sup>+</jats:sup> distribution and redistributes internal stresses, mitigating localized stress concentrations and lattice expansion to preserve structural integrity throughout cycling. The optimized LMO establishes a dual benchmark for both capacity and cycling stability in hybrid capacitive deionization, achieving a remarkable lithium extraction capacity of 4.78 mmol g <jats:sup>−1</jats:sup> with 96% retention over 100 cycles, outperforming both its unoptimized counterpart and other reported materials of the same type. Finite element simulations further elucidate a 48% reduction in maximum stress compared to disordered counterparts, underscoring the critical coupling between ion diffusion and stress evolution. This paradigm provides a pathway for developing advanced materials with intrinsically stable architectures for sustainable lithium extraction.","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":"2026-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048244","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}
Flamboyant sexual ornaments serve as conspicuous visual signals optimized to the visual receptors and perception of potential mates. While numerous studies have explored the mechanisms and functions of body coloration as a sexual signal, the role of another essential property of light—polarization—remains largely unexplored. Specifically, the question of whether and how polarization signals achieve high conspicuousness under sexual selection, including their visibility and associated behavioral and morphological adaptations, has yet to be thoroughly investigated. Here, we identified a strikingly conspicuous polarization signal used specifically during courtship in the cuttlefish Doratosepion andreanum and investigated the underlying optical mechanism. The signal consists of a pattern of adjacent horizontally and vertically polarized areas, optimizing signal detectability for cephalopod polarization vision. This pattern is generated by reflective cells called iridophores and transparent muscle: light becomes horizontally polarized when reflected by iridophores, and its angle of polarization is then rotated to vertical when transmitted through a birefringent muscle layer. Our findings show the significant contribution of polarization of light to animal communication and reveal that polarization signals—like colorful sexual ornaments—can achieve high conspicuousness through fundamentally different optical mechanisms.
{"title":"Transmission through muscle tissue shapes polarization signals during cuttlefish courtship","authors":"Arata Nakayama, Ryosuke Ohnuki, Shinya Yoshioka, Nobuhiro Ogawa, Toshihiko Kushihiki, Shunsuke Momoi, Noriyosi Sato, Tomohiko Kawamura, Yoko Iwata","doi":"10.1073/pnas.2517167123","DOIUrl":"https://doi.org/10.1073/pnas.2517167123","url":null,"abstract":"Flamboyant sexual ornaments serve as conspicuous visual signals optimized to the visual receptors and perception of potential mates. While numerous studies have explored the mechanisms and functions of body coloration as a sexual signal, the role of another essential property of light—polarization—remains largely unexplored. Specifically, the question of whether and how polarization signals achieve high conspicuousness under sexual selection, including their visibility and associated behavioral and morphological adaptations, has yet to be thoroughly investigated. Here, we identified a strikingly conspicuous polarization signal used specifically during courtship in the cuttlefish <jats:italic toggle=\"yes\">Doratosepion andreanum</jats:italic> and investigated the underlying optical mechanism. The signal consists of a pattern of adjacent horizontally and vertically polarized areas, optimizing signal detectability for cephalopod polarization vision. This pattern is generated by reflective cells called iridophores and transparent muscle: light becomes horizontally polarized when reflected by iridophores, and its angle of polarization is then rotated to vertical when transmitted through a birefringent muscle layer. Our findings show the significant contribution of polarization of light to animal communication and reveal that polarization signals—like colorful sexual ornaments—can achieve high conspicuousness through fundamentally different optical mechanisms.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"7 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048394","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}
Wesley Binder, Joel S. Ruprecht, Jack Rabe, Matthew C. Metz, Rebecca Hutchinson, Daniel R. Stahler, Taal Levi
After widespread extirpation, conservation efforts have restored large carnivores to portions of their former range. Substantial research has since focused on their ability to alter ecological communities through effects on herbivores and mesocarnivores, but the principles governing competition among multiple apex carnivores remain unclear. While mesocarnivore scavenging of apex carnivore kills drive “enemies with benefits” dynamics, subordinate apex carnivores seldom rely on scavenging. Instead, they proficiently hunt prey themselves that dominant apex carnivores can steal, fundamentally altering the dynamics of their interactions. We used 9 y of contemporaneous GPS telemetry and 3,929 potential kill site investigations from a reconstituted community of sympatric wolves and cougars in Yellowstone National Park to test whether such apex–apex dynamics instead follow an “enemies without benefits” framework. Wolf movement and resource selection were strongly linked to cougar kills, resulting in carcass theft (i.e., kleptoparasitism) that drove their interactions and led to cougar mortalities. In contrast, cougars avoided wolf kills, were tied to escape terrain, and did not kill wolves, producing an asymmetric dynamic that persisted across distinct seasonal contexts. However, as elk (the shared primary prey) declined longitudinally, cougars shifted their diets to smaller-bodied deer that were kleptoparasitized by wolves at one-sixth the rate of elk kills. Our findings demonstrate that prey diversity and landscape structure are critical for subordinate apex carnivores who experience severe interference competition from their dominant counterparts. This dynamic extends trophic theory and provides a framework for predicting the coexistence outcomes of carnivore restoration and the ongoing recolonization of wolves.
{"title":"Diets, dominance hierarchies, and kleptoparasitism drive asymmetrical interactions between wolves and cougars","authors":"Wesley Binder, Joel S. Ruprecht, Jack Rabe, Matthew C. Metz, Rebecca Hutchinson, Daniel R. Stahler, Taal Levi","doi":"10.1073/pnas.2511397123","DOIUrl":"https://doi.org/10.1073/pnas.2511397123","url":null,"abstract":"After widespread extirpation, conservation efforts have restored large carnivores to portions of their former range. Substantial research has since focused on their ability to alter ecological communities through effects on herbivores and mesocarnivores, but the principles governing competition among multiple apex carnivores remain unclear. While mesocarnivore scavenging of apex carnivore kills drive “enemies with benefits” dynamics, subordinate apex carnivores seldom rely on scavenging. Instead, they proficiently hunt prey themselves that dominant apex carnivores can steal, fundamentally altering the dynamics of their interactions. We used 9 y of contemporaneous GPS telemetry and 3,929 potential kill site investigations from a reconstituted community of sympatric wolves and cougars in Yellowstone National Park to test whether such apex–apex dynamics instead follow an “enemies without benefits” framework. Wolf movement and resource selection were strongly linked to cougar kills, resulting in carcass theft (i.e., kleptoparasitism) that drove their interactions and led to cougar mortalities. In contrast, cougars avoided wolf kills, were tied to escape terrain, and did not kill wolves, producing an asymmetric dynamic that persisted across distinct seasonal contexts. However, as elk (the shared primary prey) declined longitudinally, cougars shifted their diets to smaller-bodied deer that were kleptoparasitized by wolves at one-sixth the rate of elk kills. Our findings demonstrate that prey diversity and landscape structure are critical for subordinate apex carnivores who experience severe interference competition from their dominant counterparts. This dynamic extends trophic theory and provides a framework for predicting the coexistence outcomes of carnivore restoration and the ongoing recolonization of wolves.","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":"2026-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048395","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}
Lin Zhu, Xiaoming Liu, Limei Cai, Zhen Li, Chenxi Liu, Xiaoxia Liu
Baculoviruses are large DNA viruses that mainly infect insects. During infection, viral egress from midgut cells and subsequent behavior changes lead to terminally infected insects migrating to higher elevations on plant branches or tree limbs. However, the neural mechanisms driving this hyperactivity remain poorly understood. In this study, we demonstrate that the climbing behavior of Helicoverpa armigera larvae enhances the dispersal of Helicoverpa armigera single nucleopolyhedrovirus (HearNPV). Our findings reveal that HearNPV triggers a calcium response in enteroendocrine cells, leading to the release of midgut-derived tachykinin (TK). Released TK activates its receptor (TKR) in the brain, thereby promoting phototaxis and climbing behavior. Additionally, HaTTD14 functions as a downstream regulator of the TK–TKR signaling pathway. These results provide insights into the neural and molecular mechanisms driving baculovirus-induced hyperactivity, which aids in viral transmission.
{"title":"Baculoviruses hijack host midgut-derived tachykinin to regulate phototactic climbing behavior and promote viral transmission","authors":"Lin Zhu, Xiaoming Liu, Limei Cai, Zhen Li, Chenxi Liu, Xiaoxia Liu","doi":"10.1073/pnas.2524226123","DOIUrl":"https://doi.org/10.1073/pnas.2524226123","url":null,"abstract":"Baculoviruses are large DNA viruses that mainly infect insects. During infection, viral egress from midgut cells and subsequent behavior changes lead to terminally infected insects migrating to higher elevations on plant branches or tree limbs. However, the neural mechanisms driving this hyperactivity remain poorly understood. In this study, we demonstrate that the climbing behavior of <jats:italic toggle=\"yes\">Helicoverpa armigera</jats:italic> larvae enhances the dispersal of <jats:italic toggle=\"yes\">Helicoverpa armigera</jats:italic> single nucleopolyhedrovirus (HearNPV). Our findings reveal that HearNPV triggers a calcium response in enteroendocrine cells, leading to the release of midgut-derived tachykinin (TK). Released TK activates its receptor (TKR) in the brain, thereby promoting phototaxis and climbing behavior. Additionally, <jats:italic toggle=\"yes\">HaTTD14</jats:italic> functions as a downstream regulator of the TK–TKR signaling pathway. These results provide insights into the neural and molecular mechanisms driving baculovirus-induced hyperactivity, which aids in viral transmission.","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":"2026-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048215","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}
Csaba Hefler, Ying Wang, Xiaoli Wang, Xiaoting Zheng, Thomas G. Kaye, Maxime Grosmougin, Matthieu Chotard, Luke Barlow, Huihe Qiu, T. Alexander Dececchi, Michael B. Habib, Wei Shyy, Michael Pittman
Agile and efficient modern flyers like birds and insects rely on complex aerodynamics to increase performance such as leading edge vortices, tip vortices, rapid pitch rotations as well as wing–wake and wing–wing interactions. However, their evolutionary origins are poorly understood. Early birds and their closest relatives like Microraptor had a multiwinged configuration featuring long pennaceous feathers on their arms, legs, and tail, a configuration not seen today. The skill of these early flyers has been debated, centering around what was driving the evolution of this multiwing configuration and its loss in favor of the modern two-winged configuration. In this context, the aerodynamics and wing–wing interactions of Microraptor during gliding flight are investigated. The gliding flight mechanics of Microraptor exhibit flow patterns consistent with those observed and quantitatively assessed in volant living animal species. We analyze leading edge vortices on the forewing and hindwing including beneficial wake interactions between them as well as tip vortices on the distinct distally flared hindwing. The latter is unique in Microraptor as the hindwing’s characteristic outer span flare provides the necessary surface for the tip vortex to be bound to and thus contribute additional lift. These findings suggest that Microraptor evolved toward utilizing leading edge and tip vortices and their aerodynamic interactions. This implies that such utilization was also being exploited by other early multiwinged theropods to differing extents as part of a crucial milestone in early flight evolution.
{"title":"Microraptor reveals specialized gliding capabilities in multiwinged early paravians","authors":"Csaba Hefler, Ying Wang, Xiaoli Wang, Xiaoting Zheng, Thomas G. Kaye, Maxime Grosmougin, Matthieu Chotard, Luke Barlow, Huihe Qiu, T. Alexander Dececchi, Michael B. Habib, Wei Shyy, Michael Pittman","doi":"10.1073/pnas.2518106123","DOIUrl":"https://doi.org/10.1073/pnas.2518106123","url":null,"abstract":"Agile and efficient modern flyers like birds and insects rely on complex aerodynamics to increase performance such as leading edge vortices, tip vortices, rapid pitch rotations as well as wing–wake and wing–wing interactions. However, their evolutionary origins are poorly understood. Early birds and their closest relatives like <jats:italic toggle=\"yes\">Microraptor</jats:italic> had a multiwinged configuration featuring long pennaceous feathers on their arms, legs, and tail, a configuration not seen today. The skill of these early flyers has been debated, centering around what was driving the evolution of this multiwing configuration and its loss in favor of the modern two-winged configuration. In this context, the aerodynamics and wing–wing interactions of <jats:italic toggle=\"yes\">Microraptor</jats:italic> during gliding flight are investigated. The gliding flight mechanics of <jats:italic toggle=\"yes\">Microraptor</jats:italic> exhibit flow patterns consistent with those observed and quantitatively assessed in volant living animal species. We analyze leading edge vortices on the forewing and hindwing including beneficial wake interactions between them as well as tip vortices on the distinct distally flared hindwing. The latter is unique in <jats:italic toggle=\"yes\">Microraptor</jats:italic> as the hindwing’s characteristic outer span flare provides the necessary surface for the tip vortex to be bound to and thus contribute additional lift. These findings suggest that <jats:italic toggle=\"yes\">Microraptor</jats:italic> evolved toward utilizing leading edge and tip vortices and their aerodynamic interactions. This implies that such utilization was also being exploited by other early multiwinged theropods to differing extents as part of a crucial milestone in early flight evolution.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"8 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048212","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}
William C. Schmidt, Ava Mousavi, Jiahui Li, Rena Yang, Gerson Gonzalez Marin, Henry L. Schreiber, Rachael E. S. Hammann, Chloe L. P. Obernuefemann, Karla Bergeron, Aleksandra Klim, Daniel Wong, Kefu Du, Scott J. Hultgren, Qian Chen, Aaron Celestian, Gerard C. L. Wong, Kymora B. Scotland
Calcium oxalate stones comprise greater than 70% of all kidney stones. In the current conceptual framework, the initial stone nidus is thought to include the aggregation of inorganic crystallites, the formation of which is favored by elevated concentrations of dissolved constituents. Here, we show that this highly prevalent stone type comprises a form of organic–inorganic polycrystalline biocomposite with integrated bacterial biofilms. Evidence from electron microscopy and fluorescence microscopy reveal the unanticipated internal structure of kidney stones from human patients, where bacterial biofilms are intercalated between polycrystalline mineral layers, even in stones identified as “noninfectious” clinically, including those in patients without underlying urinary tract infections. We observe similar bacterial biofilm architectures on the surfaces of stone fragments obtained due to lithotripsy, suggesting that bacteria are intrinsic to the process of nephrolithiasis. Crystallites proximal to biofilm layers exhibit significantly smaller grain sizes, which indicate a larger local concentration of nucleation sites. Staining reveals that biofilm areas of these stones are enriched with bacterial DNA. That bacteria are now observed so broadly in kidney stones (including even in less prevalent struvite stones) may be conceptually salient: Based on the evidence adduced here, we propose a model in which the urine-rich environment of the kidney can impinge on bacterial calcium homeostasis and amplify bacterial production of nucleation templates such as extracellular DNA. The resultant counterion condensation intrinsic to polyelectrolytes charged beyond the Manning criterion (such as DNA) drastically enhances the probability of heterogeneous nucleation, thereby amplifying calcium oxalate stone formation.
{"title":"Intercalated bacterial biofilms are intrinsic internal components of calcium-based kidney stones","authors":"William C. Schmidt, Ava Mousavi, Jiahui Li, Rena Yang, Gerson Gonzalez Marin, Henry L. Schreiber, Rachael E. S. Hammann, Chloe L. P. Obernuefemann, Karla Bergeron, Aleksandra Klim, Daniel Wong, Kefu Du, Scott J. Hultgren, Qian Chen, Aaron Celestian, Gerard C. L. Wong, Kymora B. Scotland","doi":"10.1073/pnas.2517066123","DOIUrl":"https://doi.org/10.1073/pnas.2517066123","url":null,"abstract":"Calcium oxalate stones comprise greater than 70% of all kidney stones. In the current conceptual framework, the initial stone nidus is thought to include the aggregation of inorganic crystallites, the formation of which is favored by elevated concentrations of dissolved constituents. Here, we show that this highly prevalent stone type comprises a form of organic–inorganic polycrystalline biocomposite with integrated bacterial biofilms. Evidence from electron microscopy and fluorescence microscopy reveal the unanticipated internal structure of kidney stones from human patients, where bacterial biofilms are intercalated between polycrystalline mineral layers, even in stones identified as “noninfectious” clinically, including those in patients without underlying urinary tract infections. We observe similar bacterial biofilm architectures on the surfaces of stone fragments obtained due to lithotripsy, suggesting that bacteria are intrinsic to the process of nephrolithiasis. Crystallites proximal to biofilm layers exhibit significantly smaller grain sizes, which indicate a larger local concentration of nucleation sites. Staining reveals that biofilm areas of these stones are enriched with bacterial DNA. That bacteria are now observed so broadly in kidney stones (including even in less prevalent struvite stones) may be conceptually salient: Based on the evidence adduced here, we propose a model in which the urine-rich environment of the kidney can impinge on bacterial calcium homeostasis and amplify bacterial production of nucleation templates such as extracellular DNA. The resultant counterion condensation intrinsic to polyelectrolytes charged beyond the Manning criterion (such as DNA) drastically enhances the probability of heterogeneous nucleation, thereby amplifying calcium oxalate stone formation.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"33 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048236","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}
Chunyan Jiang, Lei Yue, Dacheng Jin, Ruting Zou, Yu Wang, Biao Li, Xuexiao Du, Xianliang Huang, Yingmin Sun, Renze Wang, Jiandong An, Lijun Cao, Huilong Du, Jiaxing Huang, Bing Chen
The Qinghai–Tibet Plateau (QTP) region is the greatest hotspot of social bumblebee diversity worldwide. However, how the high diversity of bumblebees in the QTP evolved and contributed to their diversification in adjacent and far-reaching regions remains unclear. Here, we explored this question using a widespread bumblebee species, Bombus pyrosoma . Phylogenomic analysis revealed a history of dispersal out of the QTP and distinct lineage divergence along elevations within the species. Four major chromosomal inversion variants were identified, and shifts in their frequency with altitude were consistent with patterns of lineage divergence. The highland bumblebees showed stronger metabolic robustness and better flight performance under cold environments, whereas lowland ones excelled under warm conditions. Forty-one percent of the positively selected genes were located in the inversion regions and were mostly associated with fatty acid metabolism and information processing. Mutation with a strong candidate gene, elovl6 , possibly modulated long-chain fatty acid elongation, which facilitated bumblebee flight under thermal stress. Finally, genomic inversion analyses across 22 bumblebee species–17 native to the QTP–corroborate the widespread involvement of inversions in the elevational diversification of bumblebees. Overall, our findings revealed that chromosomal inversions play a pivotal role in facilitating local adaptation and dispersal out of the QTP in a bumblebee, providing insights into the genomic underpinnings of bumblebees’ diversification.
{"title":"Ancestral and local adaptation contribute to dispersal out of the Qinghai–Tibet Plateau in a bumblebee","authors":"Chunyan Jiang, Lei Yue, Dacheng Jin, Ruting Zou, Yu Wang, Biao Li, Xuexiao Du, Xianliang Huang, Yingmin Sun, Renze Wang, Jiandong An, Lijun Cao, Huilong Du, Jiaxing Huang, Bing Chen","doi":"10.1073/pnas.2513080122","DOIUrl":"https://doi.org/10.1073/pnas.2513080122","url":null,"abstract":"The Qinghai–Tibet Plateau (QTP) region is the greatest hotspot of social bumblebee diversity worldwide. However, how the high diversity of bumblebees in the QTP evolved and contributed to their diversification in adjacent and far-reaching regions remains unclear. Here, we explored this question using a widespread bumblebee species, <jats:italic toggle=\"yes\">Bombus pyrosoma</jats:italic> . Phylogenomic analysis revealed a history of dispersal out of the QTP and distinct lineage divergence along elevations within the species. Four major chromosomal inversion variants were identified, and shifts in their frequency with altitude were consistent with patterns of lineage divergence. The highland bumblebees showed stronger metabolic robustness and better flight performance under cold environments, whereas lowland ones excelled under warm conditions. Forty-one percent of the positively selected genes were located in the inversion regions and were mostly associated with fatty acid metabolism and information processing. Mutation with a strong candidate gene, <jats:italic toggle=\"yes\">elovl6</jats:italic> , possibly modulated long-chain fatty acid elongation, which facilitated bumblebee flight under thermal stress. Finally, genomic inversion analyses across 22 bumblebee species–17 native to the QTP–corroborate the widespread involvement of inversions in the elevational diversification of bumblebees. Overall, our findings revealed that chromosomal inversions play a pivotal role in facilitating local adaptation and dispersal out of the QTP in a bumblebee, providing insights into the genomic underpinnings of bumblebees’ diversification.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"274 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048242","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}
Pyroptosis, an inflammatory form of cell death, is characterized by massive cell swelling and plasma membrane rupture. Although swelling was recently shown to occur in two steps, the molecular and biophysical mechanisms driving this process remained unclear. Using fast quantitative microscopy, we reveal that between the two swelling phases, cell volume transiently stabilizes despite sustained plasma membrane permeability to ions and small molecules. From a biophysical perspective, the existence of such a plateau is puzzling, as ion pumps should not be able to regulate cell volume under these conditions. To address this, we developed a physical model based on an ion pump and leak framework that incorporates the dynamics of nonselective pore formation. Experimentally, we demonstrate that the plateau phase is controlled by the dynamics of the gasdermin D (GSDMD) pore enlargement, which is modulated by ninjurin-1 (Ninj1) activation, possibly through intracellular calcium. Ninj1-mediated lesions are also required for the second swelling phase. We further show that fully opened GSDMD pores display an effective hydrodynamic radius slightly above 1.9 nm, providing an in situ upper bound for pore size. Together, our findings demonstrate that pyroptotic volume dysregulation emerges from the successive and interdependent actions of GSDMD and Ninj1, each imparting distinct permeability regimes associated with increased water filtration and decreased ion selectivity due to pore opening. These insights bridge molecular and biophysical perspectives on lytic cell death and may inform the broader understanding of membrane rupture in inflammatory and pathological contexts.
{"title":"Pore size dynamics control complex volume swelling in pyroptosis.","authors":"Estelle Bastien,Guillaume Duprez,Hélène Delanoë-Ayari,Hubert Leloup,Charlotte Rivière,Virginie Petrilli,Pierre Recho,Sylvain Monnier","doi":"10.1073/pnas.2508022123","DOIUrl":"https://doi.org/10.1073/pnas.2508022123","url":null,"abstract":"Pyroptosis, an inflammatory form of cell death, is characterized by massive cell swelling and plasma membrane rupture. Although swelling was recently shown to occur in two steps, the molecular and biophysical mechanisms driving this process remained unclear. Using fast quantitative microscopy, we reveal that between the two swelling phases, cell volume transiently stabilizes despite sustained plasma membrane permeability to ions and small molecules. From a biophysical perspective, the existence of such a plateau is puzzling, as ion pumps should not be able to regulate cell volume under these conditions. To address this, we developed a physical model based on an ion pump and leak framework that incorporates the dynamics of nonselective pore formation. Experimentally, we demonstrate that the plateau phase is controlled by the dynamics of the gasdermin D (GSDMD) pore enlargement, which is modulated by ninjurin-1 (Ninj1) activation, possibly through intracellular calcium. Ninj1-mediated lesions are also required for the second swelling phase. We further show that fully opened GSDMD pores display an effective hydrodynamic radius slightly above 1.9 nm, providing an in situ upper bound for pore size. Together, our findings demonstrate that pyroptotic volume dysregulation emerges from the successive and interdependent actions of GSDMD and Ninj1, each imparting distinct permeability regimes associated with increased water filtration and decreased ion selectivity due to pore opening. These insights bridge molecular and biophysical perspectives on lytic cell death and may inform the broader understanding of membrane rupture in inflammatory and pathological contexts.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"36 1","pages":"e2508022123"},"PeriodicalIF":11.1,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146033971","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}
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