Article
Computer Science, Artificial Intelligence
Feng Zou, Debao Chen, Hui Liu, Siyu Cao, Xuying Ji, Yan Zhang
Summary: Fitness landscape analysis (FLA), as a powerful analytical tool, has been widely applied in various optimization areas. It helps to gain a deep understanding of the characteristics of complex optimization problems and improve algorithm performance on specific problems.
Article
Multidisciplinary Sciences
James T. Stroud, Michael P. Moore, R. Brian Langerhans, Jonathan B. Losos
Summary: Species' phenotypic characteristics often remain unchanged over long stretches of geological time. Stabilizing selection has been widely believed to be responsible for this pattern, but evidence for its role in driving long-term stasis is lacking. By studying natural selection in the wild, we found that different species occupy distinct fitness peaks, which presents a barrier to adaptive evolutionary change. However, instead of persistent stabilizing selection, species were maintained on these peaks by fluctuating periods of selection.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Ecology
Samuel R. Levin, Alan Grafen
Summary: This article discusses the limitations of inclusive fitness theory in application, proposes new modeling assumptions to expand its scope, and demonstrates through reanalysis that inclusive fitness is maximized in certain models. By explaining the mathematical model and individual-level understanding of the definition of inclusive fitness, the gap between empiricists and theoreticians is bridged.
ECOLOGY AND EVOLUTION
(2021)
Article
Computer Science, Artificial Intelligence
Yaxin Li, Jing Liang, Kunjie Yu, Ke Chen, Yinan Guo, Caitong Yue, Leiyu Zhang
Summary: Fitness landscape analysis is a data-driven technique for studying the relationship between problem characteristics and algorithm performance. The proposed adaptive local landscape feature vector (ALLFV) shows excellent performance in problem classification and algorithm selection, with high accuracy, stability, and computational cost advantages, demonstrating superior practicality and reliability.
APPLIED SOFT COMPUTING
(2022)
Review
Agronomy
Jamie C. Freeman, Leticia B. Smith, Juan J. Silva, Yinjun Fan, Haina Sun, Jeffrey G. Scott
Summary: A review of over 170 publications on the fitness costs of insecticide resistance revealed that in 60% of experiments, there is a cost to having resistance, especially in measurements of resistance reversion and reproduction. Differences in fitness costs were observed between classes of insecticides, with organochlorines showing lower costs. Variability in experiments was also noted. Further studies should quantitatively determine resistance levels, identify resistance mechanisms, conduct replicated experiments, use related strains, and measure fitness by multiple metrics to provide maximum value to the community.
PEST MANAGEMENT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Dolph Schluter, Kerry B. Marchinko, Matthew E. Arnegard, Haili Zhang, Shannon D. Brady, Felicity C. Jones, Michael A. Bell, David M. Kingsley
Summary: Most mutations for adaptation to new environments are small-effect, but large-effect beneficial variants can contribute significantly under certain conditions. A study on stickleback populations showed that an ancient freshwater allele near the Eda gene had a large fitness effect, leading to a significant increase in offspring survival and allele frequency in freshwater environments. The findings suggest strong selection on this gene (and/or linked genes) in freshwater habitats, which may increase the prevalence of large-effect fitness variants in adaptive evolution.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Computer Science, Artificial Intelligence
Yaxin Li, Kunjie Yu, Jing Liang, Caitong Yue, Kangjia Qiao
Summary: Photovoltaic systems have the ability to convert solar energy into electricity directly, and the accuracy and stability of their conversion performance depend on the parameters of the photovoltaic model. The landscape-aware particle swarm optimization algorithm (LaPSO) proposed in this study provides an effective solution for parameter identification of photovoltaic systems, offering accurate and stable estimation results under various practical conditions.
APPLIED SOFT COMPUTING
(2022)
Article
Biochemistry & Molecular Biology
Gustavo Burin, Travis Park, Tamora D. James, Graham J. Slater, Natalie Cooper
Summary: This study characterizes the adaptive landscape of cetacean body length and finds that the global landscape is relatively flat, but there are numerous local peaks linked to specific adaptations.
Review
Biochemistry & Molecular Biology
Alvaro Sanchez, Djordje Bajic, Juan Diaz-Colunga, Abigail Skwara, Jean C. C. Vila, Seppe Kuehn
Summary: Quantitatively linking the composition and function of microbial communities is challenging. Inspired by genetics, an ecological community-function landscape could be defined to map community composition and function. Exploiting the parallels between both landscapes could improve our ability to engineer and optimize microbial consortia.
Article
Biochemistry & Molecular Biology
Menno J. de Jong, Fiona Lovatt, A. Rus Hoelzel
Summary: This study examines genetic signals of selection in founder populations of reindeer on South Georgia Island. Shared genomic regions under selection are identified in the two parallel founder populations, supporting the hypothesis that these outlier regions represent true loci under selection. Wright-Fisher model simulations show that GWDS is most likely to detect loci under selection in small founder populations.
Article
Biochemistry & Molecular Biology
Catia Pereira, Omar M. Warsi, Dan Andersson
Summary: Experimental evolution studies have shown that weak antibiotic selective pressures can select resistant mutants even at concentrations below the minimum inhibitory concentration (MIC). This study addressed several important questions, including the lowest antibiotic concentrations at which de novo resistance mutations can occur, the types of adaptive mutations that are enriched under weak antibiotic selections, and whether the mutations selected in laboratory settings at subMIC are also observed in clinical isolates. The results showed rapid evolution for all antibiotics tested, with selection for resistance observed at concentrations as low as 1/2000th of the MICsusceptible. The evolved resistant mutants showed increased growth yield and outcompeted the susceptible ancestral strain even in the absence of antibiotics, indicating adaptation to the growth environment. Genomic analysis revealed that some of the mutations selected under these conditions are also found in clinical isolates, highlighting the importance of experimental evolution at very low antibiotic levels in identifying novel mutations contributing to bacterial adaptation during subMIC exposure.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Editorial Material
Biology
Carsten K. W. De Dreu, Zegni Triki
Summary: Intergroup conflict and warfare are not limited to humans but are also observed in various group-living species. This theme issue provides novel insights into intergroup conflict across taxa, integrating theory, research, and review from biology, anthropology, and economics. It presents a coherent framework of intergroup conflict as multi-level games of strategy, exploring mechanisms and consequences of participating in intergroup conflict. Additionally, it highlights cutting-edge contributions on within-group heterogeneities, leadership, social organization, and the effects of climate change and environmental degradation on intergroup relations.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Ecology
Mario Blanco-Sanchez, Marina Ramos-Munoz, Beatriz Pias, Jose Alberto Ramirez-Valiente, Laura Diaz-Guerra, Adrian Escudero, Silvia Matesanz
Summary: Natural selection is the major force driving adaptive evolution in Mediterranean ecosystems, but the patterns of selection at the intraspecific level are largely unknown. Studying two Mediterranean endemic species, researchers found that reproductive fitness consistently favored a strategy of drought-escape and resource acquisition.
FUNCTIONAL ECOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Guanlin Luo, Yizhang Guo, Lie Wang, Na Li, Yang Zou
Summary: The study utilized computer three-dimensional simulation technology to create a realistic 3D simulation model, proposed a simulation method for landscape space element layout, and optimized the results through calculations using Ahp and matching tests.
ENVIRONMENTAL TECHNOLOGY & INNOVATION
(2021)
Article
Agronomy
Jennifer Lin, Vivi Arief, Zulfi Jahufer, Juan Osorno, Phil McClean, Diego Jarquin, Valerio Hoyos-Villegas
Summary: This study evaluated multiple breeding scenarios in the common bean and involved five selection strategies, three breeding frameworks, and four different parental population sizes. Results from the study reflect the complexity of breeding programs, with the optimal breeding scenario varying based on trait being selected. Relative genetic gains per cycle of up to 8.69% for seed yield could be obtained under the use of the optimal breeding scenario.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Evolutionary Biology
Brenna R. Forester, Casey C. Day, Kristen Ruegg, Erin L. Landguth
Summary: This study used an individual-based, spatially explicit, dynamic eco-evolutionary simulation model to evaluate the extinction risk of an endangered desert songbird, the southwestern willow flycatcher, in response to climate change. The results showed that incorporating evolutionary potential, population trajectories, and habitat changes can more comprehensively evaluate the extinction risk of threatened and endangered species and the effectiveness of conservation actions in promoting their recovery.
JOURNAL OF HEREDITY
(2023)
Editorial Material
Plant Sciences
Andrew J. Eckert, David B. Neale
Article
Biodiversity Conservation
Casey C. Day, Erin L. Landguth, Ryan K. Simmons, Andrew R. Bearlin
Summary: Multispecies approaches are important in ecology and evolution research, but existing models often lack the ability to consider landscape effects and simulate complex interspecific interactions. We present a simulation model that considers landscape effects and multiple species interactions, allowing for the study of genetic processes in a spatial context.
Article
Biochemistry & Molecular Biology
Thais A. Bernos, Casey Day, Jaclyn Hill, Olivier Morissette, Kenneth M. Jeffries, Nicholas E. Mandrak
Summary: Predicting the expansion and genetic diversity of populations introduced to new regions or tracking environmental conditions is a significant challenge. This study used simulations to examine the relationships between dispersal, expansion rates, and genetic diversity for an invasive fish species in eastern North America. Results showed that populations with greater dispersal distances expanded faster but exhibited more variability in expansion rates among local populations. However, they tended to retain genetic diversity during expansion. On the other hand, populations with smaller dispersal distances spread predictably but showed more variability in genetic diversity losses. These findings have conservation implications, as populations with shorter dispersal distances spreading in narrower landscapes are less predictable in their evolutionary trajectories.
Article
Ecology
Thais A. Bernos, Sarah L. L. Chang, Rachael M. M. Giglio, Kaeli Davenport, Jeff Fisher, Erin Lowery, Andrew Bearlin, Ryan Simmons, Marie-Josee Fortin, Casey C. C. Day, Erin L. L. Landguth
Summary: This study investigated the influence of female mating preference, sneaker-specific mortality, and variation in age-at-maturity on the persistence of distinct alternative mating strategies in bull trout. The results showed that without other selective mechanisms, strong female preference for mating with territorial males and differences in reproductive lifespan allow the stable coexistence of distinct alternative mating strategies.
ECOLOGY AND EVOLUTION
(2023)
Article
Ecology
Adriana Lozada, Casey C. Day, Erin L. Landguth, Angeline Bertin
Summary: This study aimed to elucidate the processes underlying community uniqueness in fragmented landscapes and understand how habitat characteristics and community characteristics affect this beta-based diversity indicator. The results showed that patch quality was the strongest factor influencing community uniqueness, connectivity promoted singular assemblages with high species richness, and patch size increased community uniqueness in species replacement over time.
Article
Biochemistry & Molecular Biology
D. R. Trumbo, B. M. Hardy, H. J. Crockett, E. Muths, B. R. Forester, R. G. Cheek, S. J. Zimmerman, S. Corey-Rivas, L. L. Bailey, W. C. Funk
Summary: Wildlife diseases pose a major global threat to biodiversity. This study focuses on the endangered boreal toads in the southern Rocky Mountains, which suffer from lethal skin infections caused by the amphibian chytrid fungus. By using genomic analyses, researchers found low genetic diversity and population sizes, likely due to founder effects and population crashes caused by the fungus. The study also identified specific environmental factors that facilitate gene flow in the boreal toad population. Furthermore, the analysis revealed that the toads experienced stronger selection pressure from the disease than from broad-scale environmental variations.
Article
Biochemistry & Molecular Biology
Eric C. Palm, Erin L. Landguth, Zachary A. Holden, Casey C. Day, Clayton T. Lamb, Paul F. Frame, Andrea T. Morehouse, Garth Mowat, Michael F. Proctor, Michael A. Sawaya, Gordon Stenhouse, Jesse Whittington, Katherine A. Zeller
Summary: Understanding the impact of human infrastructure and landscape attributes on genetic differentiation in animals is crucial for identifying and maintaining dispersal corridors. In this study, we used a multiscale approach to predict landscape-level genetic connectivity for grizzly bears across a large area in Canada's southern Rocky Mountains. Our results indicate that geographic distance and human footprint significantly affect genetic differentiation in grizzly bears, while open canopies also inhibit genetic connectivity at large scales. This study highlights the negative effect of human activities on genetic connectivity and provides important insights for landscape genetics analysis.
Article
Mathematical & Computational Biology
Leonid Kalachev, Erin L. Landguth, Jon Graham
Summary: This study aims to assess the appropriateness of model parameter estimation and prediction results in classical infectious disease modeling frameworks, focusing on the classification of data for fitting the model when only one data type is available. The research findings highlight the importance of correctly assigning data to the model compartments for accurate prediction results.
INFECTIOUS DISEASE MODELLING
(2023)
Article
Ecology
Amanda S. Cicchino, Alisha A. Shah, Brenna R. Forester, Jason B. Dunham, N. LeRoy Poff, Cameron K. Ghalambor, W. Chris Funk
Summary: Adaptive plasticity in thermal tolerance traits can buffer organisms against changing temperatures, but there is significant variation among populations. Thus, considering population variation is crucial when assessing physiological vulnerability to future warming.
