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| Open AccessThe adaptive value of density-dependent habitat specialization and social network centrality
Social behavior and habitat specialization are often linked through density-dependence and their effects on fitness. Here, the authors show that in caribou, these traits are density-dependent, but only habitat specialization has an effect on fitness.
- Quinn M. R. Webber
- , Michel P. Laforge
- & Eric Vander Wal
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Article
| Open AccessSerial founder effects slow range expansion in an invasive social insect
Invasive populations often have low genetic diversity because they originated from a small number of founding individuals. This study shows that in an invasive honey bee, one consequence of low genetic diversity is a reduced rate of population expansion due to serial founder effects at range edges.
- Thomas Hagan
- , Guiling Ding
- & Rosalyn Gloag
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| Open AccessNatural selection and genetic diversity maintenance in a parasitic wasp during continuous biological control application
Parasitoid wasps are reared and released as biocontrol agents to manage aphids and protect crops. Here, the authors use genomes from 542 wasps to show that, in spite of wide scale release of low-diversity captive individuals, diversity in wild populations is maintained.
- Bingyan Li
- , Yuange Duan
- & Hu Li
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Article
| Open AccessLeucine aminopeptidase1 controls egg deposition and hatchability in male Aedes aegypti mosquitoes
Aedes aegypti transmit several arboviruses and control of the mosquito populations could be beneficial. Here the authors show that deletion of leucine aminopeptidase1 (LAP1) results in mitochondrial defects and abnormal autophagy in sperm, reducing fertility and fecundity of females. LAP1−/− males show no obvious defects in longevity and mating fitness.
- Xiaomei Sun
- , Xueli Wang
- & Zhen Zou
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Article
| Open AccessEarly warning signals have limited applicability to empirical lake data
Abrupt regime shifts could in theory be predicted from early warning signals. Here, the authors show that true critical transitions are challenging to classify in lake planktonic systems, due to mismatches between trophic levels, and reveal uneven performance of early warning signal detection methods.
- Duncan A. O’Brien
- , Smita Deb
- & Christopher F. Clements
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Article
| Open AccessIsolation may select for earlier and higher peak viral load but shorter duration in SARS-CoV-2 evolution
The COVID-19 pandemic has seen the emergence of different variants. Analyzing the evolution from the Wuhan strain to the Delta variant, clinical data reveals a fivefold increase in peak viral load and a 1.5-fold faster time to peak.
- Junya Sunagawa
- , Hyeongki Park
- & Ryo Yamaguchi
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Article
| Open AccessDisrupting cellular memory to overcome drug resistance
Identifying memory and state switching in single cells remains elusive. Here, the authors develop a method, scMemorySeq, by combining cell barcoding and scRNA-seq and apply it to human melanoma cells to track lineages as they switch states between a drug-susceptible state and a state primed for drug resistance.
- Guillaume Harmange
- , Raúl A. Reyes Hueros
- & Sydney M. Shaffer
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Perspective
| Open AccessThe uncertain role of substandard and falsified medicines in the emergence and spread of antimicrobial resistance
Substandard and falsified medicines are a problem, particularly in low- and middle-income countries, and effects on antimicrobial resistance development aren’t well understood. Here, the authors discuss mechanisms by which they can increase or decrease levels of resistance and the need for improved data collection and analytical approaches.
- Sean Cavany
- , Stella Nanyonga
- & Ben S. Cooper
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Article
| Open AccessGrowth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes
Here, the authors present a novel approach for inferring in vivo growth phases of human gut bacteria from metagenomic time series data. These inferences can be used to better-constrain community scale metabolic modeling in the gut.
- Joe J. Lim
- , Christian Diener
- & Sean M. Gibbons
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Article
| Open AccessTop-down identification of keystone taxa in the microbiome
Keystone taxa in ecological communities are native taxa that have an especially important role in the stability of their ecosystem. This study introduces a novel method for detecting keystones in microbial communities by comparing data with and without specific species.
- Guy Amit
- & Amir Bashan
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Article
| Open AccessCell facilitation promotes growth and survival under drug pressure in breast cancer
In cancer, interactions between treatment-sensitive and resistant cells can influence the effectiveness of therapies. Here, the authors use experimental and mathematical models to explore interactions between ER+ breast cancer cell lineages that are sensitive or resistant to CDK4/6 inhibition, revealing the role of facilitative growth.
- Rena Emond
- , Jason I. Griffiths
- & Andrea H. Bild
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Article
| Open AccessModelling genetic stability in engineered cell populations
Predicting the evolution of engineered cell populations is an increasingly popular topic in biotechnology. Here the authors build a model that explores evolution in engineered cell populations which can generate hypotheses that could lead to important insights into strategies for assessing and mitigating the effects of evolution.
- Duncan Ingram
- & Guy-Bart Stan
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Article
| Open AccessSingularity response reveals entrainment properties in mammalian circadian clock
Current methods to assess circadian biological parameters can be labor intensive. Here, the authors establish a method for estimating circadian entrainment characteristics using simple experiments and mathematical modeling, revealing the responsiveness of circadian rhythms to diverse stimuli in the mammalian circadian clock.
- Kosaku Masuda
- , Naohiro Kon
- & Arisa Hirano
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Article
| Open AccessTradeoff between lag time and growth rate drives the plasmid acquisition cost
Plasmid acquisition imposes a transient burden on bacterial hosts. Here, authors show this burden results in a tradeoff between growth and lag that dictates plasmid fate, favoring intermediate cost plasmids over both low and high cost counterparts.
- Mehrose Ahmad
- , Hannah Prensky
- & Allison J. Lopatkin
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Article
| Open AccessMutation-induced infections of phage-plasmids
Phage-plasmids are bacterial extrachromosomal elements that act both as plasmids and as viruses. Here, Shan et al. show that segregational drift and loss-of-function mutations play key roles in the infection dynamics of a cosmopolitan phage-plasmid, allowing it to create continuous productive infections in marine bacteria.
- Xiaoyu Shan
- , Rachel E. Szabo
- & Otto X. Cordero
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Article
| Open AccessQuantitative dose-response analysis untangles host bottlenecks to enteric infection
Here, using Citrobacter rodentium colonization of mice as a model, the authors characterize the impact of pathogen dose on the number of bacteria that initiate infection in the mouse gut, providing a framework for quantifying the host bottlenecks that eliminate pathogens to protect from infection.
- Ian W. Campbell
- , Karthik Hullahalli
- & Matthew K. Waldor
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Article
| Open AccessMapping lesion-specific response and progression dynamics and inter-organ variability in metastatic colorectal cancer
Understanding the heterogeneity of growth, response to therapy and progression dynamics in metastatic colorectal cancer (mCRC) remains critical. Here, the authors analyse lesion-specific response heterogeneity in 4,308 mCRC patients and find that organ-level progression sequence is associated with long-term survival.
- Jiawei Zhou
- , Amber Cipriani
- & Yanguang Cao
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Article
| Open AccessPopulation fluctuations and synanthropy explain transmission risk in rodent-borne zoonoses
Many rodent species are known as hosts of zoonotic pathogens, but the ecological conditions that trigger spillover are not well-understood. Here, the authors show that population fluctuations and association with human-dominated habitats explain the zoonotic reservoir status of rodents globally.
- Frauke Ecke
- , Barbara A. Han
- & Richard S. Ostfeld
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Article
| Open AccessContrasting life-history responses to climate variability in eastern and western North Pacific sardine populations
Using high-resolution stable isotope and microstructure analyses of otoliths, this study reveals that sardine populations in the western and eastern North Pacific have different early life metabolic and growth rates that respond contrastingly to temperature variations. These findings could explain observations of different responses in these populations to decadal-scale temperature anomalies.
- Tatsuya Sakamoto
- , Motomitsu Takahashi
- & Tomihiko Higuchi
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Article
| Open AccessSpatial structure of city population growth
A new study finds that city growth in the U.S. is spatially heterogeneous. Inter-city flows concentrate in core areas. Intra-city flows are generally directed towards external and low density counties of cities, and is the main contributor to urban sprawl.
- Sandro M. Reia
- , P. Suresh C. Rao
- & Satish V. Ukkusuri
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Article
| Open AccessPhylogeographic analysis reveals an ancient East African origin of human herpes simplex virus 2 dispersal out-of-Africa
There are competing hypotheses for human herpes simplex virus 2’s migration out-of-Africa. Here, the authors sequence 65 new herpes simplex virus 2 genomes with a focus on under-sampled sub-Saharan African countries, suggesting an Eastern African origin for global dispersal the virus between 22-29 thousand years ago.
- Jennifer L. Havens
- , Sébastien Calvignac-Spencer
- & Joel O. Wertheim
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| Open AccessModelling the medium-term dynamics of SARS-CoV-2 transmission in England in the Omicron era
This mathematical modelling study projects the dynamics of SARS-CoV-2 in England until the end of 2022 assuming that the Omicron BA.2 sublineage remains dominant. They show that booster vaccination was highly effective in mitigating severe outcomes and that future dynamics will depend greatly on assumptions about waning immunity.
- Rosanna C. Barnard
- , Nicholas G. Davies
- & W. John Edmunds
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Article
| Open AccessDynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback
Communities of microbes play important roles in natural environments and hold great potential for deploying division-of-labor strategies in synthetic biology and bioproduction. Here, in a community of two competing E. coli strains, the authors show that the relative abundances of the strains can be stabilized and steered dynamically with remarkable precision by coupling the cells to an automated computer-controlled feedback-loop.
- Joaquín Gutiérrez Mena
- , Sant Kumar
- & Mustafa Khammash
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Article
| Open AccessDisease-economy trade-offs under alternative epidemic control strategies
Pandemic control policy requires balancing economic and disease outcomes. This study develops a joint modeling approach that allows both aspects to be considered simultaneously and shows that targeted isolation is superior economically and can achieve similar disease outcomes to voluntary isolation or blanket lockdowns.
- Thomas Ash
- , Antonio M. Bento
- & Ana I. Bento
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Article
| Open AccessFrequency modulation of a bacterial quorum sensing response
Quorum-sensing bacteria produce and secrete autoinducers that trigger a behavioral change in the population when reaching a certain threshold. Here, Bettenworth et al. show that autoinducer synthase gene expression in Sinorhizobium meliloti occurs in asynchronous stochastic pulses, and that physiological cues modulate pulse frequency and, consequently, response behavior dynamics. Frequency-modulated pulsing in autoinducer synthase gene expression thus represents a time-based mechanism for information integration and collective decision-making.
- Vera Bettenworth
- , Simon van Vliet
- & Anke Becker
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Article
| Open AccessDesign principles of collateral sensitivity-based dosing strategies
Collateral sensitivity-based antibiotic treatments may have the potential to limit the emergence of antimicrobial resistance. Here, the authors use mathematical modelling to study the effects of pathogen- and drug-specific characteristics for different treatment designs on bacterial population dynamics and resistance evolution.
- Linda B. S. Aulin
- , Apostolos Liakopoulos
- & J. G. Coen van Hasselt
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Article
| Open AccessLandscape heterogeneity buffers biodiversity of simulated meta-food-webs under global change through rescue and drainage effects
Habitat fragmentation and eutrophication have strong impacts on biodiversity but there is limited understanding of their cumulative impacts. This study presents simulations of meta-food-webs and provides a mechanistic explanation of how landscape heterogeneity promotes biodiversity through rescue and drainage effects.
- Remo Ryser
- , Myriam R. Hirt
- & Ulrich Brose
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Article
| Open AccessGene-drive suppression of mosquito populations in large cages as a bridge between lab and field
Experimental analysis of gene drive population dynamics has mostly been limited to small cage trials. Here the authors, to fill the gap between lab based studies and field studies, use large indoor cages and see population suppression without the emergence of resistant alleles
- Andrew Hammond
- , Paola Pollegioni
- & Andrea Crisanti
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Article
| Open AccessThe long lives of primates and the ‘invariant rate of ageing’ hypothesis
The ‘invariant rate of ageing’ hypothesis suggests that the rate of ageing tends to be constant within species. Here, Colchero et al. find support for the hypothesis across primates, including humans, suggesting biological constraints on the rate of ageing.
- Fernando Colchero
- , José Manuel Aburto
- & Susan C. Alberts
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Article
| Open AccessLate Pleistocene South American megafaunal extinctions associated with rise of Fishtail points and human population
Human arrival in South America predated the extinction of regional megafauna by a substantial margin, which has suggested a different cause for the extinctions. However, here, the authors show that megafaunal extinctions do correspond to the spread of hunting tools and human population shifts.
- Luciano Prates
- & S. Ivan Perez
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Article
| Open AccessHerbaceous perennial plants with short generation time have stronger responses to climate anomalies than those with longer generation time
Plant population growth rate is sensitive to annual temperature and precipitation anomalies. Here the authors analyse time series of population projection models from multiple biomes, finding a relationship between short generation times and strong demographic responses to climate—particularly precipitation—anomalies.
- Aldo Compagnoni
- , Sam Levin
- & Tiffany M. Knight
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Article
| Open AccessHarnessing peak transmission around symptom onset for non-pharmaceutical intervention and containment of the COVID-19 pandemic
Transmission by pre-symptomatic and asymptomatic viral carriers makes intervention and containment of the COVID-19 extremely challenging. Here, the authors construct an epidemiological model that focuses on transmission around the symptom onset, exploring specific transmission control measures.
- Liang Tian
- , Xuefei Li
- & Lei-Han Tang
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Article
| Open AccessAutomated design of synthetic microbial communities
In naturally occurring microbial systems, there is a positive relationship between species diversity and productivity of the community. Here the authors perform model selection to find potential amensal interactions that yield robust stable synthetic microbial consortia.
- Behzad D. Karkaria
- , Alex J. H. Fedorec
- & Chris P. Barnes
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Article
| Open AccessContinued preference for suboptimal habitat reduces bat survival with white-nose syndrome
Temperature-dependent host–pathogen interactions may lead species to shift their thermal preferences under pathogen pressure. However, here the authors show that bats have not altered their microclimate preferences due to temperature-mediated mortality from white-nose syndrome, finding instead a sustained preference for warmer sites with high mortality.
- Skylar R. Hopkins
- , Joseph R. Hoyt
- & Kate E. Langwig
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Article
| Open AccessDemography and the emergence of universal patterns in urban systems
According to Zipf’s law, the population size of a city is inversely proportional to its size rank in any urban system. The authors show how demography explains this law as a time average of balanced migration between cities and how deviations express information about people’s net preferences.
- Luís M. A. Bettencourt
- & Daniel Zünd
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Article
| Open AccessRare and common vertebrates span a wide spectrum of population trends
Conservation biologists often assume that rare (or less abundant) species are more likely to be declining under anthropogenic change. Here, the authors synthesise population trend data for ~2000 animal species to show that population trends cover a wide spectrum of change from losses to gains, which are not related to species rarity.
- Gergana N. Daskalova
- , Isla H. Myers-Smith
- & John L. Godlee
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Matters Arising
| Open AccessHeight-related changes in forest composition explain increasing tree mortality with height during an extreme drought
- Nathan L. Stephenson
- & Adrian J. Das
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Article
| Open AccessThe impact of climate and antigenic evolution on seasonal influenza virus epidemics in Australia
Seasonal influenza epidemics vary in timing and size, but the causes of the variation remain unclear. Here, the authors analyse a 15-year city-level data set, and find that fluctuations in climatic factors do not predict onset timing, and that while antigenic change does not have a consistent effect on epidemic size, the timing of onset and heterosubtypic competition do.
- Edward K. S. Lam
- , Dylan H. Morris
- & Colin A. Russell
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Article
| Open AccessThe stability of mutualism
Mutualism is typically portrayed as a destabilizing process in community ecology. Here, via a random matrix model that considers species density, the author shows that mutualistic interactions can, in fact, enhance population density at equilibrium and increase community resilience to perturbation.
- Lewi Stone
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Article
| Open AccessCausal effects of population dynamics and environmental changes on spatial variability of marine fishes
Extracting causality from time series on natural populations is challenging. Here the authors apply empirical dynamical modeling to 25 years of fish survey data from North Sea fisheries to quantify causal effects of age structure, abundance, and environment on population spatial variability, finding both common and species-specific patterns.
- Jheng-Yu Wang
- , Ting-Chun Kuo
- & Chih-hao Hsieh
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Article
| Open AccessDensity-dependence tips the change of plant–plant interactions under environmental stress
Density-dependence is rarely accounted for in plant-plant facilitation studies. Here the authors develop a framework that incorporates density-dependence in the stress-gradient hypothesis, and test it first through modeling and then empirically on Arabidopsis thaliana along salt stress gradients.
- Ruichang Zhang
- & Katja Tielbörger
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Article
| Open AccessTurbulent coherent structures and early life below the Kolmogorov scale
Models of the origin of life generally require a mechanism to structure emerging populations. Here, Krieger et al. develop spatial models showing that coherent structures arising in turbulent flows in aquatic environments could have provided compartments that facilitated the origin of life.
- Madison S. Krieger
- , Sam Sinai
- & Martin A. Nowak
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Article
| Open AccessDynamics of bacterial population growth in biofilms resemble spatial and structural aspects of urbanization
Bacterial biofilms develop from initial colonizers on surfaces that subsequently evolve into structured communities. Here, Paula et al. study this process in Streptococcus mutans and show growth dynamics that display spatial and structural patterns that are analogous to urbanization.
- Amauri J. Paula
- , Geelsu Hwang
- & Hyun Koo
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Article
| Open AccessInducible cell-to-cell signaling for tunable dynamics in microbial communities
Biotechnology innovations require the precise control over microbial dynamics. Here the authors engineer an inducible quorum sensing system to fine tune population and community level behaviour.
- Arianna Miano
- , Michael J. Liao
- & Jeff Hasty
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Article
| Open AccessEnhanced heat tolerance of viral-infected aphids leads to niche expansion and reduced interspecific competition
Organisms living on and inside of plants—such as microbes and herbivorous insects—can interact in complex ways. Here the authors show that a plant virus increases the temperature of the plant and also the thermal tolerance of an aphid species feeding on the plant; this change in thermal tolerance also affects competition with another aphid species.
- Mitzy F. Porras
- , Carlos A. Navas
- & Tomás A. Carlo
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Article
| Open AccessMigration, hotspots, and dispersal of HIV infection in Rakai, Uganda
HIV prevalence varies throughout Africa, but the contribution of migration remains unclear. Using population-based data from ~22,000 persons, Grabowski et al. show that HIV-positive migrants selectively migrate to high prevalence areas and that out-migrants from these areas geographically disperse.
- Mary Kate Grabowski
- , Justin Lessler
- & Ronald H. Gray
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Article
| Open AccessSystematic selection between age and household structure for models aimed at emerging epidemic predictions
Models of emerging epidemics can be exceedingly helpful in planning the response, but early on model selection is a difficult task. Here, the authors explore the joint contribution of age stratification and household structure on epidemic spread, and provides a rule of thumb to guide model choice.
- Lorenzo Pellis
- , Simon Cauchemez
- & Christophe Fraser
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Article
| Open AccessMarket integration reduces kin density in women’s ego-networks in rural Poland
Market integration may loosen the dense kinship networks maintaining high fertility among agriculturalists, but data are lacking. Here, Colleran shows that in 22 rural Polish communities, women’s ego networks are less kin-oriented, but not less dense, as market integration increases, potentially enabling low fertility values to spread.
- Heidi Colleran
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Article
| Open AccessDemographic amplification is a predictor of invasiveness among plants
Prior studies have examined fixed traits that correlate with plant invasiveness. Here the authors use a database of population matrices to compare demographic traits of invasive species in their native and invaded ranges, finding that demographic amplification is an important predictor of invasiveness.
- Kim Jelbert
- , Danielle Buss
- & Dave Hodgson