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December 2019

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Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
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Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, Upham et al. developed sets of trees that capture root-to-tip uncertainty in topology and divergence times. Their use of a “backbone-and-patch” approach to tree building resulted in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. The image shows the node-dated molecular phylogeny of 5,911 extant and recently extinct species shows branches colored with tip-level speciation rates. Radial scale is in millions of years, and the K-Pg boundary is marked with a dashed line.

Image Credit: 10.1371/journal.pbio.3000494

Essay

Can postfertile life stages evolve as an anticancer mechanism?

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PLOS Biology: published December 5, 2019 | https://doi.org/10.1371/journal.pbio.3000565

Primer

Mechanisms of species diversity in birdsong learning

Sarah Cushing Woolley, Jon Tatsuya Sakata

PLOS Biology: published December 2, 2019 | https://doi.org/10.1371/journal.pbio.3000555

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Community Page

Viewing the Invisible: Exploring common methodology across disciplines

Ann Witheridge, Rivka Leah Isaacson

PLOS Biology: published December 16, 2019 | https://doi.org/10.1371/journal.pbio.3000577

Research Articles

High-order interactions distort the functional landscape of microbial consortia

Alicia Sanchez-Gorostiaga, Djordje Bajić, Melisa L. Osborne, Juan F. Poyatos, Alvaro Sanchez

PLOS Biology: published December 12, 2019 | https://doi.org/10.1371/journal.pbio.3000550

Coinfections by noninteracting pathogens are not independent and require new tests of interaction

Frédéric M. Hamelin, Linda J. S. Allen, Vrushali A. Bokil, Louis J. Gross, Frank M. Hilker, Michael J. Jeger, Carrie A. Manore, Alison G. Power, Megan A. Rúa, Nik J. Cunniffe

PLOS Biology: published December 3, 2019 | https://doi.org/10.1371/journal.pbio.3000551

The homeostatic dynamics of feeding behaviour identify novel mechanisms of anorectic agents

Thomas M. McGrath, Eleanor Spreckley, Aina Fernandez Rodriguez, Carlo Viscomi, Amin Alamshah, Elina Akalestou, Kevin G. Murphy, Nick S. Jones

PLOS Biology: published December 5, 2019 | https://doi.org/10.1371/journal.pbio.3000482

Bidirectional cingulate-dependent danger information transfer across rats

Yingying Han, Rune Bruls, Efe Soyman, Rajat Mani Thomas, Vasiliki Pentaraki, Naomi Jelinek, Mirjam Heinemans, Iege Bassez, Sam Verschooren, Illanah Pruis, Thijs Van Lierde, Nathaly Carrillo, Valeria Gazzola, Maria Carrillo, Christian Keysers

PLOS Biology: published December 5, 2019 | https://doi.org/10.1371/journal.pbio.3000524

Spatial encoding in primate hippocampus during free navigation

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PLOS Biology: published December 9, 2019 | https://doi.org/10.1371/journal.pbio.3000546

The deubiquitinase USP6 affects memory and synaptic plasticity through modulating NMDA receptor stability

Fanwei Zeng, Xuehai Ma, Lin Zhu, Qiang Xu, Yuzhe Zeng, Yue Gao, Guilin Li, Tiantian Guo, Haibin Zhang, Xiaoyan Tang, Ziqiang Wang, Zesen Ye, Liangkai Zheng, Hongfeng Zhang, Qiuyang Zheng, Kunping Li, Jinfang Lu, Xueting Qi, Hong Luo, Xian Zhang, Zhanxiang Wang, Yulin Zhou, Yi Yao, Rongqin Ke, Ying Zhou, Yan Liu, Hao Sun, Timothy Huang, Zhicheng Shao, Huaxi Xu, Xin Wang

PLOS Biology: published December 16, 2019 | https://doi.org/10.1371/journal.pbio.3000525

Intestinal peroxisomal fatty acid β-oxidation regulates neural serotonin signaling through a feedback mechanism

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PLOS Biology: published December 5, 2019 | https://doi.org/10.1371/journal.pbio.3000242

Human sperm displays rapid responses to diet

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The tricellular vertex-specific adhesion molecule Sidekick facilitates polarised cell intercalation during Drosophila axis extension

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A conserved regulatory mechanism mediates the convergent evolution of plant shoot lateral organs

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Dynamic trafficking and turnover of JAM-C is essential for endothelial cell migration

Katja B. Kostelnik, Amy Barker, Christopher Schultz, Tom P. Mitchell, Vinothini Rajeeve, Ian J. White, Michel Aurrand-Lions, Sussan Nourshargh, Pedro Cutillas, Thomas D. Nightingale

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Glioblastoma cells vampirize WNT from neurons and trigger a JNK/MMP signaling loop that enhances glioblastoma progression and neurodegeneration

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Cilia-based peptidergic signaling

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PLOS Biology: published December 6, 2019 | https://doi.org/10.1371/journal.pbio.3000566

BMPR2 acts as a gatekeeper to protect endothelial cells from increased TGFβ responses and altered cell mechanics

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PLOS Biology: published December 11, 2019 | https://doi.org/10.1371/journal.pbio.3000557

Mediator MED23 regulates inflammatory responses and liver fibrosis

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Enhanced translation expands the endo-lysosome size and promotes antigen presentation during phagocyte activation

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Transcription-induced formation of extrachromosomal DNA during yeast ageing

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PLOS Biology: published December 3, 2019 | https://doi.org/10.1371/journal.pbio.3000471

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Universal antibiotic tolerance arising from antibiotic-triggered accumulation of pyocyanin in Pseudomonas aeruginosa

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Methods and Resources

Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

Nathan S. Upham, Jacob A. Esselstyn, Walter Jetz

PLOS Biology: published December 4, 2019 | https://doi.org/10.1371/journal.pbio.3000494

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Image-based analysis of living mammalian cells using label-free 3D refractive index maps reveals new organelle dynamics and dry mass flux

Patrick A. Sandoz, Christopher Tremblay, F. Gisou van der Goot, Mathieu Frechin

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A generic cell surface ligand system for studying cell–cell recognition

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