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Comprehensive Analysis of the Relative Dispersion of Droplet-Size Distributions and Their Relationships to Key Physical Fog Processes Under Different Aerosol Conditions and Evolutionary Stages

The relative dispersion of cloud and fog droplets has significant impacts on aerosol indirect effects, radiative transfer, and microphysical processes. However, previous studies have been mostly concerned with clouds, with limited studies on fog, particularly those that examine the combined influences of all key physical processes and their roles during fog evolution. As such, this study aims to conduct a comprehensive investigation by examining the relationships between relative dispersion and other microphysical variables, as well as the underlying microphysical and dynamic processes, based on field fog campaigns in polluted and clean conditions. In polluted fog, droplet concentrations are higher, leading to smaller droplets and increased dispersion. The correlation between dispersion and droplet volume-mean radius is positive in the polluted fog, but shifts to negative in clean fog. Here, we attribute the difference to various microphysical processes like aerosol activation, condensation, collision-coalescence, and entrainment-mixing. In polluted fog, high aerosol concentrations, low supersaturations, and strong turbulence (entrainment-mixing) provide suitable conditions for the simultaneous occurrence of droplet condensation and aerosol activation, resulting in a positive correlation between dispersion and volume-mean radius, especially during the fog formation stage. In contrast, during the mature stage in clean fog, condensation is dominant with weak aerosol activation leading to a negative correlation between relative dispersion and volume-mean radius. The collision-coalescence process is more active in the mature stage, increasing radii and leading to the negative correlation between dispersion and volume-mean radius. This result sheds new light on understanding the relative dispersion and mechanisms in fog under different aerosol backgrounds.

54 ENVIRONMENTAL SCIENCES

Automated Antenna Design with Evolutionary Algorithms

Current methods of designing and optimizing antennas by hand are time and labor intensive, and limit complexity. Evolutionary design techniques can overcome these limitations by searching the design space and automatically finding effective solutions. In recent years, evolutionary algorithms have shown great promise in finding practical solutions in large, poorly understood design spaces. In particular, spacecraft antenna design has proven tractable to evolutionary design techniques. Researchers have been investigating evolutionary antenna design and optimization since the early 1990s, and the field has grown in recent years as computer speed has increased and electromagnetic simulators have improved. Two requirements-compliant antennas, one for ST5 and another for TDRS-C, have been automatically designed by evolutionary algorithms. The ST5 antenna is slated to fly this year, and a TDRS-C phased array element has been fabricated and tested. Such automated evolutionary design is enabled by medium-to-high quality simulators and fast modern computers to evaluate computer-generated designs. Evolutionary algorithms automate cut-and-try engineering, substituting automated search though millions of potential designs for intelligent search by engineers through a much smaller number of designs. For evolutionary design, the engineer chooses the evolutionary technique, parameters and the basic form of the antenna, e.g., single wire for ST5 and crossed-element Yagi for TDRS-C. Evolutionary algorithms then search for optimal configurations in the space defined by the engineer. NASA's Space Technology 5 (ST5) mission will launch three small spacecraft to test innovative concepts and technologies. Advanced evolutionary algorithms were used to automatically design antennas for ST5. The combination of wide beamwidth for a circularly-polarized wave and wide impedance bandwidth made for a challenging antenna design problem. From past experience in designing wire antennas, we chose to constrain the evolutionary design to a monopole wire antenna. The results of the runs produced requirements-compliant antennas that were subsequently fabricated and tested. The evolved antenna has a number of advantages with regard to power consumption, fabrication time and complexity, and performance. Lower power requirements result from achieving high gain across a wider range of elevation angles, thus allowing a broader range of angles over which maximum data throughput can be achieved. Since the evolved antenna does not require a phasing circuit, less design and fabrication work is required. In terms of overall work, the evolved antenna required approximately three person-months to design and fabricate whereas the conventional antenna required about five. Furthermore, when the mission was modified and new orbital parameters selected, a redesign of the antenna to new requirements was required. The evolutionary system was rapidly modified and a new antenna evolved in a few weeks. The evolved antenna was shown to be compliant to the ST5 mission requirements. It has an unusual organic looking structure, one that expert antenna designers would not likely produce. This antenna has been tested, baselined and is scheduled to fly this year. In addition to the ST5 antenna, our laboratory has evolved an S-band phased array antenna element design that meets the requirements for NASA's TDRS-C communications satellite scheduled for launch early next decade. A combination of fairly broad bandwidth, high efficiency and circular polarization at high gain made for another challenging design problem. We chose to constrain the evolutionary design to a crossed-element Yagi antenna. The specification called for two types of elements, one for receive only and one for transmit/receive. We were able to evolve a single element design that meets both specifications thereby simplifying the antenna and reducing testing and integration costs. The highest performance antenna found using a getic algorithm and stochastic hill-climbing has been fabricated and tested. Laboratory results correspond well with simulation. Aerospace component design is an expensive and important step in space development. Evolutionary design can make a significant contribution wherever sufficiently fast, accurate and capable software simulators are available. We have demonstrated successful real-world design in the spacecraft antenna domain; and there is good reason to believe that these results could be replicated in other design spaces.

Hornby, Gregory S.

Intraspecific Reaction Norm Variation Controls the Eco-Evolutionary Consequences of Environmental Change

As environmental change accelerates globally, understanding concurrent organismal, species, and community responses is increasingly vital. Here, we examine these collective responses by incorporating genotype-specific thermal reaction norms into an eco-evolutionary predator-prey model, allowing us to track simultaneous phenotypic, ecological, and evolutionary responses to environmental change within ecological communities. We show that the reaction norms expressed by genotypes within a population determine how a community switches between different eco-evolutionary outcomes with changes in temperature. We identify how different components of phenotypic variation in thermal reaction norms—environmental (E), additive environmental and genetic (E + G), and gene-by-environment interactions (G × E)—influence eco-evolutionary dynamics and outcomes as temperature changes. Furthermore, our findings underscore how complex eco-evolutionary responses to environmental change ultimately emerge from variation in reaction norms among genotypes, offering new mechanistic insights into environmental impacts on adaptation, the maintenance of phenotypic and genetic variation, and ecological stability, which is crucial for understanding and predicting eco-evolutionary effects of rapid environmental change in the future.

Eco-evolutionary

Bell-Curve Based Evolutionary Strategies for Structural Optimization

Evolutionary methods are exceedingly popular with practitioners of many fields; more so than perhaps any optimization tool in existence. Historically Genetic Algorithms (GAs) led the way in practitioner popularity (Reeves 1997). However, in the last ten years Evolutionary Strategies (ESs) and Evolutionary Programs (EPS) have gained a significant foothold (Glover 1998). One partial explanation for this shift is the interest in using GAs to solve continuous optimization problems. The typical GA relies upon a cumber-some binary representation of the design variables. An ES or EP, however, works directly with the real-valued design variables. For detailed references on evolutionary methods in general and ES or EP in specific see Back (1996) and Dasgupta and Michalesicz (1997). We call our evolutionary algorithm BCB (bell curve based) since it is based upon two normal distributions.

Kincaid, Rex K.

Bell-Curve Based Evolutionary Strategies for Structural Optimization

Evolutionary methods are exceedingly popular with practitioners of many fields; more so than perhaps any optimization tool in existence. Historically Genetic Algorithms (GAs) led the way in practitioner popularity. However, in the last ten years Evolutionary Strategies (ESs) and Evolutionary Programs (EPS) have gained a significant foothold. One partial explanation for this shift is the interest in using GAs to solve continuous optimization problems. The typical GA relies upon a cumbersome binary representation of the design variables. An ES or EP, however, works directly with the real-valued design variables. For detailed references on evolutionary methods in general and ES or EP in specific see Back and Dasgupta and Michalesicz. We call our evolutionary algorithm BCB (bell curve based) since it is based upon two normal distributions.

Kincaid, Rex K.

Evolutionary Optimization of a Quadrifilar Helical Antenna

Automated antenna synthesis via evolutionary design has recently garnered much attention in the research literature. Evolutionary algorithms show promise because, among search algorithms, they are able to effectively search large, unknown design spaces. NASA's Mars Odyssey spacecraft is due to reach final Martian orbit insertion in January, 2002. Onboard the spacecraft is a quadrifilar helical antenna that provides telecommunications in the UHF band with landed assets, such as robotic rovers. Each helix is driven by the same signal which is phase-delayed in 90 deg increments. A small ground plane is provided at the base. It is designed to operate in the frequency band of 400-438 MHz. Based on encouraging previous results in automated antenna design using evolutionary search, we wanted to see whether such techniques could improve upon Mars Odyssey antenna design. Specifically, a co-evolutionary genetic algorithm is applied to optimize the gain and size of the quadrifilar helical antenna. The optimization was performed in-situ in the presence of a neighboring spacecraft structure. On the spacecraft, a large aluminum fuel tank is adjacent to the antenna. Since this fuel tank can dramatically affect the antenna's performance, we leave it to the evolutionary process to see if it can exploit the fuel tank's properties advantageously. Optimizing in the presence of surrounding structures would be quite difficult for human antenna designers, and thus the actual antenna was designed for free space (with a small ground plane). In fact, when flying on the spacecraft, surrounding structures that are moveable (e.g., solar panels) may be moved during the mission in order to improve the antenna's performance.

Lohn, Jason D.

Integration of ultra-low coverage whole-genome sequences for reconstructing the evolutionary history of Galapagos giant tortoises

Genomic data from contemporary and historical samples often need to be coupled for evolutionary reconstructions of multitaxon complexes. However, the genetic data recovered from historical samples may result only in ultra-low coverage whole-genome sequences (ulcWGS; <0.15× depth), leading to inaccurate evolutionary inferences given a preponderance of missing data. Using the Galapagos giant tortoise radiation as a study system (Chelonoidis spp., composed of 13 extant and four extinct lineages), we assembled a novel methodological pipeline that removes potential noise introduced by the missing data and enhances the evolutionary signal from ulcWGS samples. We leveraged existing tools for phylogenomic placement (EPA-ng), population genomic structure (smartsnp) and admixture (Admixfrog, NGSadmix) to demonstrate that the evolutionary history of samples can be uncovered with sequencing depths as low as 0.008–0.139×. Importantly, these approaches do not use genotype imputation of the ulcWGS samples, which would require extensive reference datasets. Our application to two cases of extinct lineages of Galapagos giant tortoises, with and without references from the same lineage, demonstrates the general value of the approach. We confirm where the extinct lineages from San Cristóbal and Santa Fe islands fit into the Galapagos giant tortoise radiation, and that these lineages were evolutionarily distinct entities.

ancient DNA

Evolutionary effects of helium diffusion in population II stars

Evolutionary calculations continuing until well past turnoff are presented for models of low-mass Population II stars which take into account the effects of the diffusion of helium relative to hydrogen. Evolutionary tracks, cluster isochrones and hydrogen distributions were obtained for stellar masses in the range 0.75 to 1.01 solar masses, both in the presence and absence of diffusion. It is found that for a star of a given mass, diffusion speeds up the evolutionary process on the main sequence, although after turnoff evolution is slowed with respect to the case without diffusion. As the stars ascend the red giant branch, their outer regions are remixed so that evidence of helium diffusion is erased, and the evolutionary tracks of the models with and without diffusion converge. Thus, if the age of a globular cluster is determined from the absolute magnitude at turnoff or from fitting isochrones, diffusion results in a 25% reduction in the derived age at a turnoff magnitude of 4.23, and a 14% reduction at a turnoff magnitude of 3.45.

Stringfellow, G. S.

Physical characteristics and evolutionary trends of continental rifts

Rifts may be defined as zones beneath which the entire lithosphere has ruptured in extension. They are widespread and occur in a variety of tectonic settings, and range up to 2,600 m.y. in age. The object of this review is to highlight characteristic features of modern and ancient rifts, to emphasize differences and similarities in order to help characterize evolutionary trends, to identify physical conditions favorable for initiation as well as termination of rifting, and to provide constraints for future modeling studies of rifting. Rifts are characterized on the basis of their structural, geomorphic, magmatic and geophysical features and the diverse character of these features and their evolutionary trends through time are discussed. Mechanisms of rifting are critically examined in terms of the physical characteristics and evolutionary trends of rifts, and it is concluded that while simple models can give valuable insight into specific processes of rifting, individual rifts can rarely, if ever, be characterized by well defined trends predicted by these models. More data are required to clearly define evolutionary trends, and the models require development to incorporate the effects of lithospheric heterogeneities and complex geologic histories.

Ramberg, I. B.

Hybrid Co-Evolutionary Motion Planning via Visibility-Based Repair

This paper introduces a hybrid co-evolutionary system for global motion planning within unstructured environments. This system combines the concept of co-evolutionary search along with a concept that we refer to as the visibility-based repair to form a hybrid which quickly transforms infeasible motions into feasible ones. Also, this system makes use of a novel representation scheme for the obstacles within an environment. Our hybrid evolutionary system differs from other evolutionary motion planners in that (1) more emphasis is placed on repairing infeasible motions to develop feasible motions rather than using simulated evolution exclusively as a means of discovering feasible motions, (2) a continuous map of the environment is used rather than a discretized map, and (3) it develops global motion plans for multiple mobile destinations by co-evolving populations of sub-global motion plans. In this paper, we demonstrate the effectiveness of this system by using it to solve two challenging motion planning problems where multiple targets try to move away from a point robot.

Dozier, Gerry

Scheduling Earth Observing Satellites with Evolutionary Algorithms

We hypothesize that evolutionary algorithms can effectively schedule coordinated fleets of Earth observing satellites. The constraints are complex and the bottlenecks are not well understood, a condition where evolutionary algorithms are often effective. This is, in part, because evolutionary algorithms require only that one can represent solutions, modify solutions, and evaluate solution fitness. To test the hypothesis we have developed a representative set of problems, produced optimization software (in Java) to solve them, and run experiments comparing techniques. This paper presents initial results of a comparison of several evolutionary and other optimization techniques; namely the genetic algorithm, simulated annealing, squeaky wheel optimization, and stochastic hill climbing. We also compare separate satellite vs. integrated scheduling of a two satellite constellation. While the results are not definitive, tests to date suggest that simulated annealing is the best search technique and integrated scheduling is superior.

Globus, Al

Reply to “A Comment on ‘an Evolutionary System of Mineralogy: Proposal for A Classification of Planetary Materials Based on Natural Kind Clustering’”

I welcome the “Comment” from Hatert et al. (2021) related to the proposal for an “Evolutionary system of mineralogy” (Hazen 2019) and thank them for their historically informed, conceptually nuanced, and consistently constructive contribution. They offer corrections related to two facets of my paper that seemed unfairly to criticize aspects of the International Mineralogical Association’s Commission on New Minerals, Nomenclature and Classification (IMA-CNMNC) protocols for classifying minerals. First, they note an unfortunate inferred ambivalence with respect to the relationship between the IMA system and the new evolutionary system. If I was once ambivalent, that view has changed. Having spent the past two years in an ongoing effort to develop this new historical approach, I am struck every day by the power of the IMA-CNMNC system of species classification and nomenclature, which is fundamental and indispensable to the science of mineralogy. As Hatert et al. suggest, any new approach to organizing natural solids, including one focused on planetary evolution, must rest on the foundation provided by the IMA-CNMNC and its many volunteers who selflessly bring order to the mineral kingdom. In the best scenario, the evolutionary system may one day emerge as one of several useful approaches that complement and amplify but in no way replace this core IMA-CNMNC foundation, as clearly stated in the abstract of Hazen (2019). Second, Hatert et al. (2021) offer corrections regarding the IMA-CNMNC approach to classification, in particular a mischaracterization of the formal process to incorporate amorphous phases, poorly crystalline materials, and loosely defined “mineraloids.” I am grateful for the clarifications, as well as the implication that IMA protocols may facilitate the embrace of additional such phases in the future. Finally, I welcome the chance to explore further the emerging concept of “natural kinds” as applied to the mineral kingdom. Here, our thoughts differ. I suggest that minerals, considered in their information-rich, idiosyncratic, paragenetic contexts (in contrast to IMA-CNMNC species), have the potential to represent quintessential examples of “natural kinds.” Furthermore, when viewed in their evolutionary context, minerals offer an intriguing opportunity to expand the concept of “historical natural kinds” beyond its present limited and, at times, controversial use in biology, into the realm of the co-evolving geosphere and biosphere.

Philosophy of mineralogy

Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation

Evolutionary changes in transcriptional regulation undoubtedly play an important role in creating morphological diversity. However, there is little information about the evolutionary dynamics of cis-regulatory sequences. This study examines the functional consequence of evolutionary changes in the Endo16 promoter of sea urchins. The Endo16 gene encodes a large extracellular protein that is expressed in the endoderm and may play a role in cell adhesion. Its promoter has been characterized in exceptional detail in the purple sea urchin, Strongylocentrotus purpuratus. We have characterized the structure and function of the Endo16 promoter from a second sea urchin species, Lytechinus variegatus. The Endo16 promoter sequences have evolved in a strongly mosaic manner since these species diverged approximately 35 million years ago: the most proximal region (module A) is conserved, but the remaining modules (B-G) are unalignable. Despite extensive divergence in promoter sequences, the pattern of Endo16 transcription is largely conserved during embryonic and larval development. Transient expression assays demonstrate that 2.2 kb of upstream sequence in either species is sufficient to drive GFP reporter expression that correctly mimics this pattern of Endo16 transcription. Reciprocal cross-species transient expression assays imply that changes have also evolved in the set of transcription factors that interact with the Endo16 promoter. Taken together, these results suggest that stabilizing selection on the transcriptional output may have operated to maintain a similar pattern of Endo16 expression in S. purpuratus and L. variegatus, despite dramatic divergence in promoter sequence and mechanisms of transcriptional regulation.

NASA Discipline Evolutionary Biology

Evolutionary Multiobjective Design Targeting a Field Programmable Transistor Array

This paper introduces the ISPAES algorithm for circuit design targeting a Field Programmable Transistor Array (FPTA). The use of evolutionary algorithms is common in circuit design problems, where a single fitness function drives the evolution process. Frequently, the design problem is subject to several goals or operating constraints, thus, designing a suitable fitness function catching all requirements becomes an issue. Such a problem is amenable for multi-objective optimization, however, evolutionary algorithms lack an inherent mechanism for constraint handling. This paper introduces ISPAES, an evolutionary optimization algorithm enhanced with a constraint handling technique. Several design problems targeting a FPTA show the potential of our approach.

global optimization

Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem

Giant viruses play crucial ecological roles in aquatic ecosystems, yet their evolutionary dynamics in response to environmental changes, particularly in freshwater environments, are not well understood. We analyzed a 20-year time series (2000-2019) of 471 co-assembled metagenomes from Lake Mendota (USA) to reconstruct 1512 giant virus metagenome-assembled genomes, providing insights into viral genome evolution. Viruses in the order Imitervirales dominate the virome, remaining consistent across seasons and years. Our findings reveal gene duplication (23% of genes) and horizontal gene transfer (29% of genes) as key drivers of genomic innovation. A co-occurrence network analysis indicates increased virus-host interactions following the introduction of an invasive predatory zooplankton in 2009, highlighting potential hosts in Bigyra, Perkinsea, and Euglenozoa. While single nucleotide polymorphism analysis shows predominantly purifying selection in viral genes, there is a significant increase in positively selected genes post-invasion, particularly those related to infection. Comparative evolutionary analyses reveal that giant viruses exhibit genome-wide substitution rates similar to co-occurring bacteria but significantly slower than smaller dsDNA phages, suggesting both stability and adaptability. Our study demonstrates that freshwater giant viruses employ various evolutionary strategies to respond to environmental change. These results underscore their significant yet often underappreciated role in freshwater ecosystem dynamics.

Vasquez, Yumary M

A compendium of human gene functions derived from evolutionary modelling

A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating a structured body of information about gene functions, which now includes experimental findings reported in more than 175,000 publications for human genes and genes in experimentally tractable model organisms 1,2 . Here, we describe the results of a large, international effort to integrate all of these findings to create a representation of human gene functions that is as complete and accurate as possible. Specifically, we apply an expert-curated, explicit evolutionary modelling approach to all human protein-coding genes. This approach integrates available experimental information across families of related genes into models that reconstruct the gain and loss of functional characteristics over evolutionary time. The models and the resulting set of 68,667 integrated gene functions cover approximately 82% of human protein-coding genes. The functional repertoire reveals a marked preponderance of molecular regulatory functions, and the models provide insights into the evolutionary origins of human gene functions. We show that our set of descriptions of functions can improve the widely used genomic technique of Gene Ontology enrichment analysis. The experimental evidence for each functional characteristic is recorded, thereby enabling the scientific community to help review and improve the resource, which we have made publicly available.

59 BASIC BIOLOGICAL SCIENCES

Specialization Restricts the Evolutionary Paths Available to Yeast Sugar Transporters

Functional innovation at the protein level is a key source of evolutionary novelties. The constraints on functional innovations are likely to be highly specific in different proteins, which are shaped by their unique histories and the extent of global epistasis that arises from their structures and biochemistries. These contextual nuances in the sequence–function relationship have implications both for a basic understanding of the evolutionary process and for engineering proteins with desirable properties. Here, we have investigated the molecular basis of novel function in a model member of an ancient, conserved, and biotechnologically relevant protein family. These Major Facilitator Superfamily sugar porters are a functionally diverse group of proteins that are thought to be highly plastic and evolvable. By dissecting a recent evolutionary innovation in an α-glucoside transporter from the yeast Saccharomyces eubayanus, we show that the ability to transport a novel substrate requires high-order interactions between many protein regions and numerous specific residues proximal to the transport channel. To reconcile the functional diversity of this family with the constrained evolution of this model protein, we generated new, state-of-the-art genome annotations for 332 Saccharomycotina yeast species spanning ~400 My of evolution. By integrating phylogenetic and phenotypic analyses across these species, we show that the model yeast α-glucoside transporters likely evolved from a multifunctional ancestor and became subfunctionalized. The accumulation of additive and epistatic substitutions likely entrenched this subfunction, which made the simultaneous acquisition of multiple interacting substitutions the only reasonably accessible path to novelty.

59 BASIC BIOLOGICAL SCIENCES

Pangenomes suggest ecological-evolutionary responses to experimental soil warming

ABSTRACT Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive to climate stress may alter microbial feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment where, for over three decades, temperate forest soils are continuously heated at 5°C above ambient. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect adaptations related to growth and carbon utilization. From our bacterial culture collection isolated from experimental heated and control plots, we sequenced genomes representing dominant taxa sensitive to warming, including lineages of Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. We investigated genomic attributes and functional gene content to identify signatures of adaptation. Comparative pangenomics revealed accessory gene clusters related to central metabolism, competition, and carbon substrate degradation, with few functional annotations explicitly associated with long-term warming. Trends in functional gene patterns suggest genomes from heated plots were relatively enriched in central carbohydrate and nitrogen metabolism pathways, while genomes from control plots were relatively enriched in amino acid and fatty acid metabolism pathways. We observed that genomes from heated plots had less codon bias, suggesting potential adaptive traits related to growth or growth efficiency. Codon usage bias varied for organisms with similar 16S rrn operon copy number, suggesting that these organisms experience different selective pressures on growth efficiency. Our work suggests the emergence of lineage-specific trends as well as common ecological-evolutionary microbial responses to climate change. IMPORTANCE Anthropogenic climate change threatens soil ecosystem health in part by altering below-ground carbon cycling carried out by microbes. Microbial evolutionary responses are often overshadowed by community-level ecological responses, but adaptive responses represent potential changes in traits and functional potential that may alter ecosystem function. We predict that microbes are adapting to climate change stressors like soil warming. To test this, we analyzed the genomes of bacteria from a soil warming experiment where soil plots have been experimentally heated 5°C above ambient for over 30 years. While genomic attributes were unchanged by long-term warming, we observed trends in functional gene content related to carbon and nitrogen usage and genomic indicators of growth efficiency. These responses may represent new parameters in how soil ecosystems feedback to the climate system.

Choudoir, Mallory J. (ORCID:0000000291175150)