From the Cover. Contents

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Cover image: Pictured is a fruit of Theobroma cacao. Its seeds are used to make chocolate. To uncover how structural variants affect natural populations, Tuomas Hämälä et al.

analyzed genome assemblies for 31 wild-collected accessions of T. cacao.

Certain structural variants of T. cacao may benefit local adaptation via pathogen resistance, but most structural variants constrain adaptation by reducing fitness, likely because of impaired gene function and suppressed recombination. The findings suggest that structural variants are often selected against due to their accumulation of harmful nucleotides and negative effects on gene expression. See the article by Hämälä et al., e2102914118. Image credit: Mark J. Guiltinan.

From the Cover

e2102914118 Fitness effects of structural variants e2106595118 Inhibiting nitrification in wheat farming e2100765118 Evolution of cannibalism in toads

e2101115118 Circadian clocks and exercise performance e2109643118 Performance of monkeys under pressure

Niels J. Van Doesum, Ryan O. Murphy, Marcello Gallucci, Efrat Aharonov-Majar, Ursula Athenstaedt, Wing Tung Au, Liying Bai, Robert Bo¨hm, Inna Bovina, Nancy R. Buchan, Xiao-Ping Chen, Kitty B. Dumont, Jan B. Engelmann, Kimmo Eriksson, Hyun Euh, Susann Fiedler, Justin Friesen, Simon Ga¨chter, Camilo Garcia, Roberto Gonza´lez, Sylvie Graf, Katarzyna Growiec, Serge Guimond, Martina Hrebıćkova´, Elizabeth Immer-Bernold, Jeff Joireman, Gokhan Karagonlar, Kerry Kawakami, Toko Kiyonari, Yu Kou, D. Michael Kuhlman, Alexandros-Andreas Kyrtsis, Siugmin Lay, Geoffrey J. Leonardelli, Norman P. Li, Yang Li, Boris Maciejovsky, Zoi Manesi, Ali Mashuri, Aurelia Mok, Karin S. Moser, Ladislav Mota´k, Adrian Netedu, Chandrasekhar Pammi, Michael J. Platow, Karolina Raczka-Winkler, Christopher P. Reinders Folmer, Cecilia Reyna, Angelo Romano, Shaul Shalvi, Claúdia Simaõ, Adam W. Stivers, Pontus Strimling, Yannis Tsirbas, Sonja Utz, Leander van der Meij, Sven Waldzus, Yiwen Wang, Bernd Weber, Ori Weisel, Tim Wildschut, Fabian Winter, Junhui Wu, Jose C. Yong, and Paul A. M. Van Lange

e2014781118 Interaction between decision-making and interoceptive representations of bodily arousal in frontal cortex

Atsushi Fujimoto, Elisabeth A. Murray, and Peter H. Rudebeck

SOCIAL SCIENCES

e2106292118 Dynamical system model predicts when social learners impair collective performance Vicky Chuqiao Yang, Mirta Galesic, Harvey McGuinness, and Ani Harutyunyan

e2106357118 Psychological ownership interventions increase interest in claiming

government benefits

Wendy De La Rosa, Eesha Sharma, Stephanie M. Tully, Eric Giannella, and Gwen Rino

e2101724118 Using time-use diaries to track changing behavior across successive stages of COVID-19 social restrictions

Oriel Sullivan, Jonathan Gershuny, Almudena Sevilla, Francesca Foliano, Margarita Vega-Rapun, Juana Lamote de Grignon, Teresa Harms,

and Pierre Walthe´ry

BIOLOGICAL SCIENCES

AGRICULTURAL SCIENCES

e2106595118 Enlisting wild grass genes to combat nitrification in wheat farming: A nature-based solution

Guntur V. Subbarao, Masahiro Kishii, Adrian Bozal- Leorri, Ivan Ortiz-Monasterio, Xiang Gao, Maria Itria Ibba, Hannes Karwat, M. B. Gonzalez-Moro, Carmen Gonzalez-Murua, Tadashi Yoshihashi, Satoshi Tobita, Victor Kommerell, Hans-Joachim Braun,

and Masa Iwanaga

APPLIED BIOLOGICAL SCIENCES

e2100347118 Ultrarapid detection of SARS-CoV-2 RNA using a reverse transcription–free exponential amplification reaction, RTF-EXPAR

Jake G. Carter, Lorea Orueta Iturbe, Jean-Louis H. A.

Duprey, Ian R. Carter, Craig D. Southern, Marium Rana, Celina M. Whalley, Andrew Bosworth, Andrew D. Beggs, Matthew R. Hicks, James H. R.

Tucker, and Timothy R. Dafforn

e2105972118 Functional heterogeneity of IFN-γ–licensed mesenchymal stromal cell immunosuppressive capacity on biomaterials

Brian J. Kwee, Johnny Lam, Adovi Akue, Mark A. KuKuruga, Kunyu Zhang, Luo Gu, and Kyung E. Sung

BIOCHEMISTRY

e2110797118 Bacterial translation machinery for deliberate mistranslation of the genetic code

Oscar Vargas-Rodriguez, Ahmed H. Badran, Kyle S.

Hoffman, Manyun Chen, Ana Crnkovic, Yousong Ding, Jonathan R. Krieger, Eric Westhof, Dieter So¨ll, and Sergey Melnikov

BIOPHYSICS AND COMPUTATIONAL BIOLOGY e2104559118 Bayesian metamodeling of complex biological

systems across varying representations Barak Raveh, Liping Sun, Kate L. White, Tanmoy Sanyal, Jeremy Tempkin, Dongqing Zheng, Kala Bharath, Jitin Singla, Chenxi Wang, Jihui Zhao, Angdi Li, Nicholas A. Graham, Carl Kesselman, Raymond C.

Stevens, and Andrej Sali

e2107289118 Tardigrades exhibit robust interlimb coordination across walking speeds and terrains

Jasmine A. Nirody, Lisset A. Duran, Deborah Johnston, and Daniel J. Cohen

e2023487118 The N terminus ofα-synuclein dictates fibril formation

Ryan P. McGlinchey, Xiaodan Ni, Jared A. Shadish, Jiansen Jiang, and Jennifer C. Lee

e2111257118 Dissecting the role of interprotomer cooperativity in the activation of oligomeric high-temperature requirement A2 protein

Yuki Toyama, Robert W. Harkness, and Lewis E. Kay e2105961118 Structural basis for the activation of the

DEAD-box RNA helicase DbpA by the nascent ribosome

Jan Philip Wurm, Katarzyna-Anna Glowacz, and Remco Sprangers

e2101657118 Dual-mechanism estrogen receptor inhibitors Jian Min, Jerome C. Nwachukwu, Charles K. Min, Jacqline W. Njeri, Sathish Srinivasan, Erumbi S.

Rangarajan, Charles C. Nettles, Valeria Sanabria Guillen, Yvonne Ziegler, Shunchao Yan, Kathryn E.

Carlson, Yingwei Hou, Sung Hoon Kim, Scott Novick, Bruce D. Pascal, Rene Houtman, Patrick R. Griffin, Tina Izard, Benita S. Katzenellenbogen, John A.

Katzenellenbogen, and Kendall W. Nettles e2026583118 Lipid-based and protein-based interactions

synergize transmembrane signaling stimulated by antigen clustering of IgE receptors

Nirmalya Bag, Alice Wagenknecht-Wiesner, Allan Lee, Sophia M. Shi, David A. Holowka,

and Barbara A. Baird

CELL BIOLOGY

e2101287118 An in vitro vesicle formation assay reveals cargo clients and factors that mediate vesicular trafficking

Yan Huang, Haidi Yin, Baiying Li, Qian Wu, Yang Liu, Kristina Poljak, Julija Maldutyte, Xiao Tang, Mo Wang, Zhixiao Wu, Elizabeth A. Miller, Liwen Jiang, Zhong- Ping Yao, and Yusong Guo

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e2023909118 SLC-30A9 is required for Zn²⁺homeostasis, Zn²⁺mobilization, and mitochondrial health Huichao Deng, Xinhua Qiao, Ting Xie, Wenfeng Fu, Hang Li, Yanmei Zhao, Miaomiao Guo, Yaqian Feng, Ligong Chen, Yan Zhao, Long Miao, Chang Chen, Kang Shen, and Xiangming Wang

e2101590118 Chlamydomonas LZTFL1 mediates phototaxis via controlling BBSome recruitment to the basal body and its reassembly at the ciliary tip Wei-Yue Sun, Bin Xue, Yan-Xia Liu, Rui-Kai Zhang, Rong-Chao Li, Wen Xin, Mingfu Wu, and Zhen-Chuan Fan e2103020118 Catabolism of lysosome-related organelles in

color-changing spiders supports intracellular turnover of pigments

Florent Figon, Ilse Hurbain, Xavier Heiligenstein, Sylvain Tre´pout, Arnaud Lanoue, Kadda Medjoubi, Andrea Somogyi, Ce´dric Delevoye, Grac¸a Raposo, and Je´roˆme Casas

e2025647118 Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer

Kenichi Miyata, Yoshinori Imai, Satoshi Hori, Mika Nishio, Tze Mun Loo, Ryo Okada, Liying Yang, Tomoyoshi Nakadai, Reo Maruyama, Risa Fujii, Koji Ueda, Li Jiang, Hao Zheng, Shinya Toyokuni, Toyonori Sakata, Katsuhiko Shirahige, Ryosuke Kojima, Mizuho Nakayama, Masanobu Oshima, Satoshi Nagayama, Hiroyuki Seimiya, Toru Hirota, Hideyuki Saya, Eiji Hara, and Akiko Takahashi

DEVELOPMENTAL BIOLOGY

e2106673118 SPATA33 localizes calcineurin to the mitochondria and regulates sperm motility in mice

Haruhiko Miyata, Seiya Oura, Akane Morohoshi, Keisuke Shimada, Daisuke Mashiko, Yuki Oyama, Yuki Kaneda, Takafumi Matsumura, Ferheen Abbasi, and Masahito Ikawa

e2101442118 Histone H3K27 methylation–mediated repression of Hairy regulates insect developmental transition by modulating ecdysone biosynthesis

Yan Yang, Tujing Zhao, Zheng Li, Wenliang Qian, Jian Peng, Ling Wei, Dongqin Yuan, Yaoyao Li, Qingyou Xia, and Daojun Cheng

ECOLOGY

e2105482118 Intensity and frequency of extreme novel epidemics

Marco Marani, Gabriel G. Katul, William K. Pan, and Anthony J. Parolari

e2019591118 Phytoplankton biodiversity is more important for ecosystem functioning in highly variable thermal environments

Elvire Bestion, Bart Haegeman, Soraya Alvarez Codesal, Alexandre Garreau, Miche`le Huet, Samuel Barton, and Jose´ M. Montoya

e2101614118 Variable strategies to solve risk–reward tradeoffs in carnivore communities

Joel Ruprecht, Charlotte E. Eriksson, Tavis D. Forrester, Derek B. Spitz, Darren A. Clark, Michael J. Wisdom, Marcus Bianco, Mary M. Rowland, Joshua B. Smith, Bruce K. Johnson, and Taal Levi

EVOLUTION

e2102467118 Strong within-host selection in a maternally inherited obligate symbiont: Buchnera and aphids Julie Perreau, Bo Zhang, Gerald P. Maeda, Mark Kirkpatrick, and Nancy A. Moran

e2102914118 Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree Tuomas Ha¨ma¨la¨, Eric K. Wafula, Mark J. Guiltinan, Paula E. Ralph, Claude W. dePamphilis, and Peter Tiffin e2100765118 The evolution of targeted cannibalism and

cannibal-induced defenses in invasive populations of cane toads

Jayna L. DeVore, Michael R. Crossland, Richard Shine, and Simon Ducatez

IMMUNOLOGY AND INFLAMMATION

e2109517118 Bromodomain containing 9 (BRD9) regulates macrophage inflammatory responses by potentiating glucocorticoid receptor activity Liu Wang, Tae Gyu Oh, Jason Magida, Gabriela Estepa, S. M. Bukola Obayomi, Ling-Wa Chong, Jovylyn Gatchalian, Ruth T. Yu, Annette R. Atkins, Diana Hargreaves, Michael Downes, Zong Wei, and Ronald M. Evans e2106685118 LRRK2 plays essential roles in maintaining lung

homeostasis and preventing the development of pulmonary fibrosis

Yujie Tian, Jiaoyan Lv, Ziyan Su, Tao Wu, Xiaoguang Li, Xiaoyu Hu, Jianhong Zhang, and Li Wu

e2102374118 Ssu72 phosphatase directly binds to ZAP-70, thereby providing fine-tuning of TCR signaling and preventing spontaneous inflammation Jae Sung Ko, Dongjin Jeong, Jaemoon Koh, Hyeryeon Jung, Kyeong Cheon Jung, Yoon Kyung Jeon, Hye Young Kim, Eugene C. Yi, Ho Lee, Chang-Woo Lee, and Doo Hyun Chung

e2025825118 Hierarchy of signaling thresholds downstream of the T cell receptor and the Tec kinase ITK Michael P. Gallagher, James M. Conley, Pranitha Vangala, Manuel Garber, Andrea Reboldi, and Leslie J. Berg e2107141118 PD-1 preferentially inhibits the activation of

low-affinity T cells

Kenji Shimizu, Daisuke Sugiura, Il-mi Okazaki, Takumi Maruhashi, Tatsuya Takemoto, and Taku Okazaki

MEDICAL SCIENCES

e2025948118 METTL14 facilitates global genome repair and suppresses skin tumorigenesis

Zizhao Yang, Seungwon Yang, Yan-Hong Cui, Jiangbo Wei, Palak Shah, Gayoung Park, Xiaolong Cui, Chuan He, and Yu-Ying He

e2100784118 TRIM47 activates NF-κB signaling via PKC- e/PKD3 stabilization and contributes to endocrine therapy resistance in breast cancer Kotaro Azuma, Kazuhiro Ikeda, Takashi Suzuki, Kenjiro Aogi, Kuniko Horie-Inoue, and Satoshi Inoue e2102895118 Identification of a KLF5-dependent program and

drug development for skeletal muscle atrophy Lin Liu, Hiroyuki Koike, Takehito Ono, Shinichiro Hayashi, Fujimi Kudo, Atsushi Kaneda, Hiroyuki Kagechika, Ichiro Manabe, Tomoki Nakashima, and Yumiko Oishi

MICROBIOLOGY

e2100514118 Native structure of the RhopH complex, a key determinant of malaria parasite

nutrient acquisition

Chi-Min Ho, Jonathan Jih, Mason Lai, Xiaorun Li, Daniel E. Goldberg, Josh R. Beck, and Z. Hong Zhou e2107210118 FtsA acts through FtsW to promote cell wall

synthesis during cell division in Escherichia coli Kyung-Tae Park, Sebastien Pichoff, Shishen Du, and Joe Lutkenhaus

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e2108894118 The LpoA activator is required to stimulate the peptidoglycan polymerase activity of its cognate cell wall synthase PBP1a

Marios F. Sardis, Jessica L. Bohrhunter, Neil G. Greene, and Thomas G. Bernhardt

e2105800118 Phosphoenolpyruvate depletion mediates both growth arrest and drug tolerance of Mycobacterium tuberculosis in hypoxia Juhyeon Lim, Jae Jin Lee, Sun-Kyung Lee, Seoyong Kim, Seok-Yong Eum, and Hyungjin Eoh

NEUROSCIENCE

e2014781118 Interaction between decision-making and interoceptive representations of bodily arousal in frontal cortex

Atsushi Fujimoto, Elisabeth A. Murray, and Peter H. Rudebeck

e2009393118 Developmental HCN channelopathy results in decreased neural progenitor proliferation and microcephaly in mice

Anna Katharina Schlusche, Sabine Ulrike Vay, Niklas Kleinenkuhnen, Steffi Sandke, Rafael Campos-Martı´n, Marta Florio, Wieland Huttner, Achim Tresch, Jochen Roeper, Maria Adele Rueger, Igor Jakovcevski, Malte Stockebrand, and Dirk Isbrandt

PHYSIOLOGY

e2107673118 Up-regulation of the manganese transporter SLC30A10 by hypoxia-inducible factors defines a homeostatic response to manganese toxicity Chunyi Liu, Thomas Jursa, Michael Aschner, Donald R.

Smith, and Somshuvra Mukhopadhyay

e2107026118 NMDA receptor–BK channel coupling regulates synaptic plasticity in the barrel cortex

Ricardo Go´mez, Laura E. Maglio, Alberto J. Gonzalez- Hernandez, Belinda Rivero-Pe´rez, David Bartolome´- Martı´n, and Teresa Giraldez

e2100500118 Amino acids activate mTORC1 to release roe deer embryos from decelerated proliferation during diapause

Vera A. van der Weijden, Jochen T. Bick, Stefan Bauersachs, Anna B. Ru¨egg, Thomas B. Hildebrandt, Frank Goeritz, Katarina Jewgenow, Pieter Giesbertz, Hannelore Daniel, Emilie Derisoud, Pascale Chavatte-Palmer, Rupert M.

Bruckmaier, Barbara Drews, and Susanne E. Ulbrich e2101115118 Clock proteins and training modify exercise

capacity in a daytime-dependent manner Yaarit Adamovich, Vaishnavi Dandavate, Saar Ezagouri, Gal Manella, Ziv Zwighaft, Jonathan Sobel, Yael Kuperman, Marina Golik, Asher Auerbach, Maxim Itkin, Sergey Malitsky, and Gad Asher

PLANT BIOLOGY

e2107320118 Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability

Li He, Cheng Zhao, Qingzhu Zhang, Gaurav Zinta, Dong Wang, Rosa Lozano-Dura´n, and Jian-Kang Zhu e2103895118 TEM1 combinatorially binds to FLOWERING

LOCUS T and recruits a Polycomb factor to repress the floral transition in Arabidopsis Hongmiao Hu, Shu Tian, Guohui Xie, Rui Liu, Nana Wang, Sisi Li, Yuehui He, and Jiamu Du

e2105274118 The radish Ogura fertility restorer impedes translation elongation along its cognate CMS-causing mRNA

Chuande Wang, Lina Lezhneva, Nade`ge Arnal, Martine Quadrado, and Hakim Mireau

e2103378118 A poplar short-chain dehydrogenase reductase plays a potential key role in biphenyl detoxification Ańgela Contreras, Irene Merino, Enrique A´lvarez, David Bolonio, Jose´-Eugenio Ortiz, Luis Onãte- Sańchez, and Luis Go´mez

e2101526118 ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF–containing protein that controls root growth angle in barley and wheat

Gwendolyn K. Kirschner, Serena Rosignoli, Li Guo, Isaia Vardanega, Jafargholi Imani, Janine Altmu¨ller, Sara G. Milner, Raffaella Balzano, Kerstin A. Nagel, Daniel Pflugfelder, Cristian Forestan, Riccardo Bovina, Robert Koller, Tyll G. Sto¨cker, Martin Mascher, James Simmonds, Cristobal Uauy, Heiko Schoof, Roberto Tuberosa, Silvio Salvi, and Frank Hochholdinger

PSYCHOLOGICAL AND COGNITIVE SCIENCES e2109643118 Monkeys exhibit a paradoxical decrease in

performance in high-stakes scenarios Adam L. Smoulder, Nicholas P. Pavlovsky, Patrick J.

Marino, Alan D. Degenhart, Nicole T. McClain, Aaron P. Batista, and Steven M. Chase

CORRECTIONS

PHYSICS

e2112849118 Emergence of homochirality in large molecular systems

Gabin Laurent, David Lacoste, and Pierre Gaspard

ECOLOGY, ENGINEERING

e2113284118 Infrared optical and thermal properties of microstructures in butterfly wings Anirudh Krishna, Xiao Nie, Andrew D. Warren, Jorge E. Llorente-Bousquets, Adriana D. Briscoe, and Jaeho Lee

IMMUNOLOGY AND INFLAMMATION

e2112934118 T-cell responses to hybrid insulin peptides prior to type 1 diabetes development Angela M. Mitchell, Aimon A. Alkanani, Kristen A.

McDaniel, Laura Pyle, Kathleen Waugh, Andrea K.

Steck, Maki Nakayama, Liping Yu, Peter A. Gottlieb, Marian J. Rewers, and Aaron W. Michels

MICROBIOLOGY

e2112850118 The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2

Donald J. Benton, Antoni G. Wrobel, Chloe¨ Roustan, Annabel Borg, Pengqi Xu, Stephen R. Martin, Peter B.

Rosenthal, John J. Skehel, and Steven J. Gamblin

PSYCHOLOGICAL AND COGNITIVE SCIENCES e2112851118 Omega-3 deficiency impairs honey bee learning

Yael Arien, Arnon Dag, Shlomi Zarchin, Tania Masci, and Sharoni Shafir

SI CORRECTION

NEUROSCIENCE

e2113007118 Temporally chimeric mice reveal flexibility of circadian period-setting in the

suprachiasmatic nucleus

Nicola J. Smyllie, Johanna E. Chesham, Ryan Hamnett, Elizabeth S. Maywood, and Michael H. Hastings

From the Cover. Contents

From the Cover

Contents

THIS WEEK IN PNAS —This week’s research highlights

OPINION—Leading scientists discuss current issues

RETROSPECTIVE

COMMENTARIES

PERSPECTIVE

LETTERS

INAUGURAL ARTICLE

PHYSICAL SCIENCES

SOCIAL SCIENCES

BIOLOGICAL SCIENCES

CORRECTIONS

SI CORRECTION