Article
Plant Sciences
Yunsheng Wang, Andrew H. Paterson
Summary: This study re-sequenced and analyzed whole genome data from wild and cultivated Eriobotrya japonica, revealing a two-staged domestication process and enriching knowledge of crop domestication. Cultivated E. japonica showed little reduction in genome-wide nucleotide polymorphism compared with wild forms, and genes responsible for sugar biosynthesis were found to be enriched in regions harboring selective sweeps. An approach based on co-clustering into gene families and evaluating chromosome colinearity of orthologous and paralogous genes identified convergent/parallel selective sweeps among different crops.
Article
Genetics & Heredity
Nandita R. Garud, Philipp W. Messer, Dmitri A. Petrov
Summary: The debate over whether hard sweeps or soft sweeps dominate adaptation has continued, with the authors proposing that soft sweeps are prevalent in North American Drosophila melanogaster. Another study by Harris et al. has raised doubts about the reliability of soft sweeps detected, instead suggesting that hard sweeps may be more likely. However, upon reanalysis, the authors confirm that soft sweeps are the dominant mode of adaptation in North American Drosophila melanogaster.
Review
Physics, Multidisciplinary
Roberto Benzi, David R. Nelson, Suraj Shankar, Federico Toschi, Xiaojue Zhu
Summary: This study reviews recent progress in understanding the growth and evolution of microbial populations under the influence of fluid flows. By solving reaction-diffusion equations, the authors show how flow shear and compressibility effects can interact with selective advantage to impact genetic competition and fixation in spatially distributed populations.
REPORTS ON PROGRESS IN PHYSICS
(2022)
Article
Multidisciplinary Sciences
Sandro M. Reia, P. Suresh C. Rao, Marc Barthelemy, Satish V. Ukkusuri
Summary: A new study reveals that city growth in the U.S. is uneven and concentrated in core areas. Intra-city flows tend to move towards external and low-density counties, contributing to urban sprawl. The study also highlights the significant impact of domestic migration on population growth, surpassing natural demographic growth, and driving the heterogeneity in city growth patterns.
NATURE COMMUNICATIONS
(2022)
Review
Agriculture, Dairy & Animal Science
Manjit Panigrahi, Divya Rajawat, Sonali Sonejita Nayak, Kanika Ghildiyal, Anurodh Sharma, Karan Jain, Chuzhao Lei, Bharat Bhushan, Bishnu Prasad Mishra, Triveni Dutt
Summary: A seminal article half a century ago introduced the concept of selection signatures and their role in shaping evolution and genetic diversity. The development of genomic technologies has led to significant progress in the last two decades in investigating selection signatures.
Article
Ecology
Gregory Thom, Camila C. Ribas, Eduardo Shultz, Alexandre Aleixo, Cristina Y. Miyaki
Summary: This study explores the historical demographic changes of populations occurring on the floodplains of the Solimoes River in the Amazon Basin and finds that habitat specificity might be an important predictor of population connectivity.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Microbiology
Yuki Furuse
Summary: Genetic mutations are crucial in evolution, with significantly beneficial mutations leading to species prospering and dominating through selective sweep. Current methods struggle to identify these mutations in selective sweep. A novel method introduced here can detect mutations responsible for monophyletic selective sweep evolution at the single amino acid/nucleotide level. Applying this method to various viruses has led to the discovery of both known and unrecognized mutations, deepening our understanding of molecular and evolutionary biology.
Article
Plant Sciences
Marin Jezic, Janine Melanie Schwarz, Simone Prospero, Kiril Sotirovski, Mihajlo Risteski, Mirna Curkovic-Perica, Lucija Nuskern, Ljiljana Krstin, Zorana Katanic, Ema Malenicic, Igor Poljak, Marilena Idzojtic, Daniel Rigling
Summary: Chestnut blight caused by Cryphonectria parasitica has shown diversity differences in populations from Switzerland, Croatia, and North Macedonia, with older Swiss and Croatian populations being more diverse compared to more recent North Macedonian populations. Cryphonectria hypovirus 1 (CHV1) also exhibited high diversity, with strains from North Macedonia forming a separate cluster. There was no correlation observed between vc diversity and CHV1 prevalence, indicating established natural hypovirulence in all countries.
Article
Physics, Fluids & Plasmas
Pintu Patra, Stefan Klumpp
Summary: Bacterial persistence through stochastic phenotype switching against antibiotics is a survival strategy, with benefits in spatially varying environments. The presence of persister cells affects the expansion speed of the population, allowing for deeper spread into antibiotic regions. Optimal switching rates maximize population expansion in environments with alternating growth conditions and antibiotics.
Article
Plant Sciences
Lin Cheng, Mengge Li, Yachao Wang, Qunwei Han, Yanlin Hao, Zhen Qiao, Wei Zhang, Lin Qiu, Andong Gong, Zhihan Zhang, Tao Li, Shanshan Luo, Linshuang Tang, Daliang Liu, Hao Yin, Song Lu, Tiago Santana Balbuena, Yiyong Zhao
Summary: Tea, as one of the world's top three popular non-alcoholic beverages, has significant economic and cultural value. Xinyang Maojian, a famous Chinese tea, has a long history and its cultivation history and genetic differentiation from other tea varieties remain unclear. Through transcriptome analysis, this study successfully resolved the phylogenetic relationships of tea samples and identified selection sweeps during differentiation. This study provides important insights into the cultivation history of Xinyang Maojian and the genetic basis of physiological and ecological differences between the two major tea subspecies.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agronomy
Ramon G. Leon, Jeffrey C. Dunne, Fred Gould
Summary: The evolution of resistance to multiple herbicides and non-target site resistance often involves multiple genes, leading to a polygenic control of weed adaptation. Advances in whole-genome sequencing and bioinformatic tools have enabled a better understanding of genetic control of resistance and other important traits in weed adaptation, allowing for predictions of responses to selection pressure by herbicides and other environmental factors. The use of tools such as quantitative trait loci mapping and genomic prediction will help in explaining how pests adapt to control tools and how specific genotypes thrive and spread.
PEST MANAGEMENT SCIENCE
(2021)
Article
Astronomy & Astrophysics
L. Bisigello, G. Gandolfi, A. Grazian, G. Rodighiero, L. Costantin, A. R. Cooray, A. Feltre, C. Gruppioni, N. P. Hathi, B. W. Holwerda, A. M. Koekemoer, R. A. Lucas, J. A. Newman, P. G. Perez-Gonzalez, L. Y. A. Yung, A. de la Vega, P. Arrabal Haro, M. B. Bagley, M. Dickinson, S. L. Finkelstein, J. S. Kartaltepe, C. Papovich, N. Pirzkal, S. Wilkins
Summary: In this study, the authors utilize NIRCam photometric observations from CEERS to identify and analyze very red sources, leading to the discovery of very dusty star-forming galaxies. They select red galaxies based on their signal-to-noise ratio at specific wavelengths and find that these galaxies exhibit significant dust extinction.
ASTRONOMY & ASTROPHYSICS
(2023)
Article
Genetics & Heredity
Antoine Moinet, Flavia Schlichta, Stephan Peischl, Laurent Excoffier
Summary: This article investigates the shape of neutral valleys of diversity under a model of population size change and compares it to signals of a selective sweep. The results show that selective sweep valleys of diversity are wider than neutral valleys, but it is possible to find a neutral valley with the same width as a given selective valley by parameterizing the model.
Article
Biochemistry & Molecular Biology
Limei Zhong, Youlin Zhu, Kenneth M. Olsen
Summary: This study used genome scans to uncover selection marks of hard and soft sweeps in domesticated soybeans, revealing that hard sweeps are mainly present in domesticated soybeans, while soft sweeps are more common in wild ancestors. The results contribute to a better understanding of genetic characteristics of domestication traits in soybeans.
Article
Entomology
Alihan Katlav, Duong T. Nguyen, Asha Chhagan, Lisa Jamieson, Alexander R. Robertson, Jodie Cheesman, Stewart Learmonth, Piotr Trebicki, James M. Cook, Markus Riegler
Summary: The presence of maternally inherited endosymbionts in invasive pests can affect the phylogeographic patterns and invasion pathways. The study of mitochondrial diversity and endosymbiont prevalence in populations of Kelly's citrus thrips revealed that populations from Victoria in Australia were likely the source of invasive populations in both New Zealand and the Mediterranean region. Surprisingly, invasive populations lacked one of the endosymbionts, Wolbachia, despite its association with cytoplasmic incompatibility. The study also found a linkage pattern between Wolbachia and specific mitochondrial haplotypes in Australian populations. This study highlights the importance of considering endosymbionts in tracing pest invasions, but also warns about the potential confounding effects of endosymbiont-driven selective sweeps on phylogeographic patterns.
JOURNAL OF PEST SCIENCE
(2023)
Article
Ecology
Francesco Carrara, Andrea Giometto, Mathew Seymour, Andrea Rinaldo, Florian Altermatt
Article
Multidisciplinary Sciences
Andrea Giometto, Florian Altermatt, Amos Maritan, Roman Stocker, Andrea Rinaldo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Multidisciplinary Sciences
Andrea Giometto, Marco Formentin, Andrea Rinaldo, Joel E. Cohen, Amos Maritan
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Ecology
Francesco Carrara, Andrea Giometto, Mathew Seymour, Andrea Rinaldo, Florian Altermatt
METHODS IN ECOLOGY AND EVOLUTION
(2015)
Article
Ecology
Andrea Giometto, Florian Altermatt, Andrea Rinaldo
Article
Multidisciplinary Sciences
Silvia Zaoli, Andrea Giometto, Amos Maritan, Andrea Rinaldo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Multidisciplinary Sciences
Emanuele Strano, Andrea Giometto, Saray Shai, Enrico Bertuzzo, Peter J. Mucha, Andrea Rinaldo
ROYAL SOCIETY OPEN SCIENCE
(2017)
Article
Biology
Silvia Zaoli, Andrea Giometto, Jonathan Giezendanner, Amos Maritan, Andrea Rinaldo
JOURNAL OF THEORETICAL BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Silvia Zaoli, Andrea Giometto, Emilio Maranon, Stephane Escrig, Anders Meibom, Arti Ahluwalia, Roman Stocker, Amos Maritan, Andrea Rinaldo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Review
Biochemical Research Methods
Fangchen Liu, Andrea Giometto, Mingming Wu
Summary: Aquatic microbial communities play a fundamental role in biogeochemical transformations in natural ecosystems, with their composition and function tightly controlled by environmental factors. Microfluidic platforms provide a unique opportunity for quantitative studies and theoretical modeling of microbial communities, which can be applied beyond aquatic ecosystems.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Ecology
Leonardo Pacciani-Mori, Samir Suweis, Amos Maritan, Andrea Giometto
Summary: Microbial communities are crucial for natural processes and are closely linked to species metabolism. Researchers are reevaluating consumer-resource models to better understand the dynamics of microbial communities. The study explores proteome allocation in relation to microbial growth and aims to determine conditions for species coexistence in systems with multiple resources.
Article
Biology
Andrea Giometto, David R. Nelson, Andrew W. Murray
Summary: Antagonistic interactions are common in the microbial world, impacting microbial evolutionary dynamics. Spatial structure in natural microbial communities affects biological interactions. Experimental and theoretical findings show that a stronger antagonist can only invade a weaker one if the initial invading population exceeds a critical frequency or size. Spatially structured competitions between toxin-producing strains can lead to the emergence of toxin-resistant cells and weaker killers, suggesting that adaptive evolution plays a role in microbial antagonism outcomes in spatial settings.
Article
Biotechnology & Applied Microbiology
Hyun Yoon, Andrea Giometto, Martin P. Pothier, Xuhui Zhang, Alexandre J. Poulain, Matthew C. Reid
Summary: The uptake of arsenic by microbes is influenced by variations in water chemistry, particularly dissolved organic matter (DOM). This study explores the effects of different forms of DOM on arsenic uptake and reveals that thiol-containing compounds significantly inhibit the uptake of arsenite into cells. Additionally, labile DOM fractions may inhibit arsenite uptake through a catabolite repression-like mechanism. These findings suggest that DOM plays an important role in regulating arsenic uptake and biotransformation in the environment.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Ecology
Nicky Lustenhouwer, Felix Moerman, Florian Altermatt, Ronald D. D. Bassar, Greta Bocedi, Dries Bonte, Sutirth Dey, Emanuel A. A. Fronhofer, Erika Garcez da Rocha, Andrea Giometto, Lesley T. T. Lancaster, Robert B. B. Prather Jr, Marjo Saastamoinen, Justin M. J. Travis, Carla A. A. Urquhart, Christopher Weiss-Lehman, Jennifer L. L. Williams, Luca Borger, David Berger
Summary: Experimental evolution studies can provide valuable proofs of concept that reinforce the links between theoretical predictions and empirical observations, advancing our understanding of the ecological and evolutionary consequences of dispersal.
JOURNAL OF ANIMAL ECOLOGY
(2023)