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DOE OSTI2019

Adaptive responses of animals to climate change are most likely insufficient

Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Quantifying the local adaptive landscape of a nascent bacterial community

Abstract The fitness effects of all possible mutations available to an organism largely shape the dynamics of evolutionary adaptation. Yet, whether and how this adaptive landscape changes over evolutionary times, especially upon ecological diversification and changes in community composition, remains poorly understood. We sought to fill this gap by analyzing a stable community of two closely related ecotypes (“L” and “S”) shortly after they emerged within the E. coli Long-Term Evolution Experiment (LTEE). We engineered genome-wide barcoded transposon libraries to measure the invasion fitness effects of all possible gene knockouts in the coexisting strains as well as their ancestor, for many different, ecologically relevant conditions. We find consistent statistical patterns of fitness effect variation across both genetic background and community composition, despite the idiosyncratic behavior of individual knockouts. Additionally, fitness effects are correlated with evolutionary outcomes for a number of conditions, possibly revealing shifting patterns of adaptation. Together, our results reveal how ecological and epistatic effects combine to shape the adaptive landscape in a nascent ecological community.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

The dynamics of adaptive genetic diversity during the early stages of clonal evolution

The dynamics of genetic diversity in large clonally evolving cell populations are poorly understood, despite having implications for the treatment of cancer and microbial infections. Here, we combine barcode lineage tracking, sequencing of adaptive clones and mathematical modelling of mutational dynamics to understand adaptive diversity changes during experimental evolution of Saccharomyces cerevisiae under nitrogen and carbon limitation. We find that, despite differences in beneficial mutational mechanisms and fitness effects, early adaptive genetic diversity increases predictably, driven by the expansion of many single-mutant lineages. Furthermore, a crash in adaptive diversity follows, caused by highly fit double-mutant ‘jackpot’ clones that are fed from exponentially growing single mutants, a process closely related to the classic Luria–Delbrück experiment. The diversity crash is likely to be a general feature of asexual evolution with clonal interference; however, both its timing and magnitude are stochastic and depend on the population size, the distribution of beneficial fitness effects and patterns of epistasis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish

Despite deep evolutionary conservation, recombination rates vary greatly across the genome and among individuals, sexes and populations. Yet the impact of this variation on adaptively diverging populations is not well understood. Here we characterized fine-scale recombination landscapes in an adaptively divergent pair of marine and freshwater populations of threespine stickleback from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic locations of almost 50,000 crossovers and built recombination maps for marine, freshwater and hybrid individuals at a resolution of 3.8 kb. We used these maps to quantify the factors driving variation in recombination rates. We found strong heterochiasmy between sexes but also differences in recombination rates among ecotypes. Hybrids showed evidence of significant recombination suppression in overall map length and in individual loci. Recombination rates were lower not only within individual marine–freshwater-adaptive loci, but also between loci on the same chromosome, suggesting selection on linked gene ‘cassettes’. Through temporal sampling along a natural hybrid zone, we found that recombinants showed traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers, whose functions are disrupted in hybrids, may play an important role in maintaining differences among adaptively diverging populations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

The Marchantia polymorpha pangenome reveals ancient mechanisms of plant adaptation to the environment

Plant adaptation to terrestrial life started 450 million years ago and has played a major role in the evolution of life on Earth. The genetic mechanisms allowing this adaptation to a diversity of terrestrial constraints have been mostly studied by focusing on flowering plants. Here, we gathered a collection of 133 accessions of the model bryophyte Marchantia polymorpha and studied its intraspecific diversity using selection signature analyses, a genome-environment association study and a pangenome. We identified adaptive features, such as peroxidases or nucleotide-binding and leucine-rich repeats (NLRs), also observed in flowering plants, likely inherited from the first land plants. The M. polymorpha pangenome also harbors lineage-specific accessory genes absent from seed plants. We conclude that different land plant lineages still share many elements from the genetic toolkit evolved by their most recent common ancestor to adapt to the terrestrial habitat, refined by lineage-specific polymorphisms and gene family evolution.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

A variational framework for residual-based adaptivity in neural PDE solvers and operator learning

Residual-based adaptive strategies are widely used in scientific machine learning yet remain largely heuristic. We introduce a variational framework that formalizes these methods through convex transformations of the residual, where different transformations correspond to distinct objective functionals. For instance, exponential weights target uniform error minimization, while linear weights recover quadratic error minimization. This perspective reveals adaptive weighting as a means of selecting sampling distributions that optimize a primal objective, directly linking discretization choices to error metrics. This principled approach yields three key benefits: it enables systematic design of adaptive schemes, reduces discretization error by lowering estimator variance, and enhances learning dynamics by improving gradient signal-to-noise ratio. Extending the framework to operator learning, we demonstrate substantial performance gains across diverse optimizers and architectures. Our results provide a theoretical perspective for residual-based adaptivity and establish a foundation for principled discretization and training.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Adaptive sparse grid expansions of the vibrational Hamiltonian

The vibrational Hamiltonian involves two high dimensional operators, the kinetic energy operator (KEO), and the potential energy surface (PES). Both must be approximated for systems involving more than a few atoms. Adaptive approximation schemes are not only superior to truncated Taylor or many-body expansions (MBE), they also allow for error estimates, and thus operators of predefined precision. To this end, modified sparse grids (SG) are developed that can be combined with adaptive MBEs. This MBE/SG hybrid approach yields a unified, fully adaptive representation of the KEO and the PES. Refinement criteria, based on the vibrational self-consistent field (VSCF) and vibrational configuration interaction (VCI) methods, are presented. The combination of the adaptive MBE/SG approach and the VSCF plus VCI methods yields a black box like procedure to compute accurate vibrational spectra. This is demonstrated on a test set of molecules, comprising water, formaldehyde, methanimine, and ethylene. The test set is first employed to prove convergence for semi-empirical PM3-PESs and subsequently to compute accurate vibrational spectra from CCSD(T)-PESs that agree well with experimental values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

The relative entropy is fundamental to adaptive resolution simulations

Adaptive resolution techniques are powerful methods for the efficient simulation of soft matter systems in which they simultaneously employ atomistic and coarse-grained (CG) force fields. In such simulations, two regions with different resolutions are coupled with each other via a hybrid transition region, and particles change their description on the fly when crossing this boundary. Here we show that the relative entropy, which provides a fundamental basis for many approaches in systematic coarse-graining, is also an effective instrument for the understanding of adaptive resolution simulation methodologies. We demonstrate that the use of coarse-grained potentials which minimize the relative entropy with respect to the atomistic system can help achieve a smoother transition between the different regions within the adaptive setup. Furthermore, we derive a quantitative relation between the width of the hybrid region and the seamlessness of the coupling. Our results do not only shed light on the what and how of adaptive resolution techniques but will also help setting up such simulations in an optimal manner.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Numerical study of magnetic island coalescence using magnetohydrodynamics with adaptively embedded particle-in-cell model

Collisionless magnetic reconnection typically requires kinetic treatment that is, in general, computationally expensive compared to fluid-based models. In this study, we use the magnetohydrodynamics with an adaptively embedded particle-in-cell (MHD-AEPIC) model to study the interaction of two magnetic flux ropes. This innovative model embeds one or more adaptive PIC regions into a global MHD simulation domain such that the kinetic treatment is only applied in regions where the kinetic physics is prominent. We compare the simulation results among three cases: (1) MHD with adaptively embedded PIC regions, (2) MHD with statically (or fixed) embedded PIC regions, and (3) a full PIC simulation. The comparison yields good agreement when analyzing their reconnection rates and magnetic island separations as well as the ion pressure tensor elements and ion agyrotropy. In order to reach good agreement among the three cases, large adaptive PIC regions are needed within the MHD domain, which indicates that the magnetic island coalescence problem is highly kinetic in nature, where the coupling between the macro-scale MHD and micro-scale kinetic physics is important.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Learning to learn by using nonequilibrium training protocols for adaptable materials

Evolution in time-varying environments naturally leads to adaptable biological systems that can easily switch functionalities. Advances in the synthesis of environmentally responsive materials therefore open up the possibility of creating a wide range of synthetic materials which can also be trained for adaptability. We consider high-dimensional inverse problems for materials where any particular functionality can be realized by numerous equivalent choices of design parameters. By periodically switching targets in a given design algorithm, we can teach a material to perform incompatible functionalities with minimal changes in design parameters. We exhibit this learning strategy for adaptability in two simulated settings: elastic networks that are designed to switch deformation modes with minimal bond changes and heteropolymers whose folding pathway selections are controlled by a minimal set of monomer affinities. The resulting designs can reveal physical principles, such as nucleation-controlled folding, that enable such adaptability.

Science & Technology - Other Topics↗

DOE OSTI2025

Prioritizing urban heat adaptation infrastructure based on multiple outcomes: Comfort, health, and energy

Globally, cities face increasing extreme heat, impacting comfort, health, and energy consumption. Infrastructure-based heat adaptation strategies can improve these outcomes, but each strategy has a unique mix of benefits and drawbacks. Here, we apply an urbanized meteorological model (WRF) with the newly integrated multilayer BEP-Tree street tree model to dynamically downscale Earth System Model projections and a 3-D microclimate model (TUF-Pedestrian) to simulate the street-scale radiation environment impacting pedestrians. We evaluate the performance of five heat adaptation strategies (street trees, cool roofs, green roofs, rooftop photovoltaics (PV), and reflective pavements) during extreme heat events in three cities with contrasting background climates (Toronto, Phoenix, and Miami), under contemporary and end-of-century projected climates, based on three metrics: outdoor heat stress, air conditioning (AC) energy use, and ventilation of vehicular air pollution. No single adaptation strategy improves all three outcomes. While street trees inhibit ventilation, they reduce outdoor heat stress four times more effectively than the next best strategy via shade provision, fully offsetting heat stress increases under a high-emissions end-of-century climate scenario in all cities studied. Cool roofs and green roofs moderately reduce heat stress and energy use. Alternatively, rooftop PV with energy storage can generate sufficient power for space cooling but have marginal effects on heat stress. Reflective pavements are the least effective across metrics. Where the ventilation of street-level emissions is of less concern, our results clearly support the combination of street trees and rooftop PV as a highly complementary and effective means of adaptive mitigation across different climates and neighborhood densities.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Drosophila melanogaster pigmentation demonstrates adaptive phenotypic parallelism over multiple spatiotemporal scales

Abstract Populations are capable of responding to environmental change over ecological timescales via adaptive tracking. However, the translation from patterns of allele frequency change to rapid adaptation of complex traits remains unresolved. We used abdominal pigmentation in Drosophila melanogaster as a model phenotype to address the nature, genetic architecture, and repeatability of rapid adaptation in the field. We show that D. melanogaster pigmentation evolves as a highly parallel and deterministic response to shared environmental variation across latitude and season in natural North American populations. We then experimentally evolved replicate, genetically diverse fly populations in field mesocosms to remove any confounding effects of demography and/or cryptic structure that may drive patterns in wild populations; we show that pigmentation rapidly responds, in parallel, in fewer than 15 generations. Thus, pigmentation evolves concordantly in response to spatial and temporal climatic axes. We next examined whether phenotypic differentiation was associated with allele frequency change at loci with established links to genetic variance in pigmentation in natural populations. We found that across all spatial and temporal scales, phenotypic patterns were associated with variation at pigmentation-related loci, and the sets of genes we identified at each scale were largely nonoverlapping. Therefore, our findings suggest that parallel phenotypic evolution is associated with distinct components of the polygenic architecture shifting across each environmental axis to produce redundant adaptive patterns.

Evolutionary Biology↗

DOE OSTI2025

Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource

Abstract Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009 to 2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species' demographic history and identify novel signs of adaptation across spatial and temporal dimensions. For example, we showed that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatiotemporal patterns of genetic variation in this classic model system.

Biochemistry & Molecular Biology↗

DOE OSTI2025

Genomic insights into local adaptation and migration success in reintroduced Coho Salmon of the Wenatchee River basin

ABSTRACT Objective Reintroduction of salmonids into regions where they have been extirpated is a common conservation strategy that is often implemented through natural recolonization, translocation of natural populations, or hatchery-based programs. Locally adapting to specific environmental conditions is critical for long-term population viability, particularly for species like Coho Salmon Oncorhynchus kisutch, which face diverse selective pressures during their migration. This study focused on the mid-Columbia River Coho Salmon reintroduction program managed by Yakama Nation Fisheries, which has successfully reintroduced Coho Salmon into the Wenatchee and Methow River basins, Washington. Notably, these populations have adapted to the longer migration route than those in the founding stock, with selection favoring individuals with an earlier arrival time and that can navigate a 15-km, high-gradient canyon to reach optimal spawning grounds. The objectives of this study were to investigate whether specific genomic regions are under selection for traits associated with return location and timing in Coho Salmon. Methods Low-coverage whole-genome resequencing data were used to screen for genomic regions associated with the phenotypes of interest. Results A weak polygenic signal in female Coho Salmon was found to be associated with return group, with a subset of candidate adaptive regions occurring across eight chromosomes. Conclusions These findings provide insights into the genomic mechanisms underlying local adaptation in reintroduced salmon populations and inform broodstock selection strategies aimed at promoting natural production and long-term population sustainability.

Horn, Rebekah L.↗

DOE OSTI2021

Adaptive variational quantum eigensolvers for highly excited states

Highly excited states of quantum many-body systems are central objects in the study of quantum dynamics and thermalization that challenge classical computational methods due to their volume-law entanglement content. In this work, we explore the potential of variational quantum algorithms to approximate such states. We propose an adaptive variational quantum eigensolver (VQE) for excited states (X) that self-generates a variational ansatz for arbitrary eigenstates of a many-body Hamiltonian H by attempting to minimize the energy variance with respect to H. We benchmark the method by applying it to an Ising spin chain with integrable and nonintegrable regimes, where we calculate various quantities of interest, including the total energy, magnetization density, and entanglement entropy. We also compare the performance of adaptive VQE-X to an adaptive variant of the folded-spectrum method. For both methods, we find a strong dependence of the algorithm's performance on the choice of operator pool used for the adaptive construction of the ansatz. In particular, an operator pool including long-range two-body gates accelerates the convergence of both algorithms in the nonintegrable regime. Here, we also study the scaling of the number of variational parameters with system size, finding that an exponentially large number of parameters may be necessary to approximate individual highly excited states. Nevertheless, we argue that these methods lay a foundation for the use of quantum algorithms to study finite-energy-density properties of many-body systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Scaling adaptive quantum simulation algorithms via operator pool tiling

Adaptive variational quantum simulation algorithms use information from a quantum computer to dynamically create optimal trial wave functions for a given problem Hamiltonian. A key ingredient in these algorithms is a predefined operator pool from which trial wave functions are constructed. Finding suitable pools is critical for the efficiency of the algorithm as the problem size increases. Here, we present a technique called operator pool tiling that facilitates the construction of problem-tailored pools for arbitrarily large problem instances. By first performing an Adaptive Derivative-Assembled Problem-Tailored Ansatz Variational Quantum Eigensolver (ADAPT-VQE) calculation on a smaller instance of the problem using a large, but computationally inefficient, operator pool, we extract the most relevant operators and use them to design more efficient pools for larger instances. We demonstrate the method here on strongly correlated quantum spin models in one and two dimensions, finding that ADAPT automatically finds a highly effective ansatz for these systems. Given that many problems, such as those arising in condensed matter physics, have a naturally repeating lattice structure, we expect the pool tiling method to be a widely applicable technique apt for such systems. Published by the American Physical Society 2024

Van Dyke, John S. (ORCID:0000000167815480)↗

DOE OSTI2024

Constant-Depth Preparation of Matrix Product States with Adaptive Quantum Circuits

Adaptive quantum circuits, which combine local unitary gates, midcircuit measurements, and feedforward operations, have recently emerged as a promising avenue for efficient state preparation, particularly on near-term quantum devices limited to shallow-depth circuits. Matrix product states (MPS) comprise a significant class of many-body entangled states, efficiently describing the ground states of one-dimensional gapped local Hamiltonians and finding applications in a number of recent quantum algorithms. Recently, it has been shown that the Affleck-Kennedy-Lieb-Tasaki state—a paradigmatic example of an MPS—can be exactly prepared with an adaptive quantum circuit of constant depth, an impossible feat with local unitary gates alone due to its nonzero correlation length [Smith , PRX Quantum 4, 020315 (2023)]. In this work, we broaden the scope of this approach and demonstrate that a diverse class of MPS can be exactly prepared using constant-depth adaptive quantum circuits, outperforming theoretically optimal preparation with unitary circuits. We show that this class includes short- and long-ranged entangled MPS, symmetry-protected topological (SPT) and symmetry-broken states, MPS with finite Abelian, non-Abelian, and continuous symmetries, resource states for MBQC, and families of states with tunable correlation length. Moreover, we illustrate the utility of our framework for designing constant-depth sampling protocols, such as for random MPS or for generating MPS in a particular SPT phase. We present sufficient conditions for particular MPS to be preparable in constant time, with global on-site symmetry playing a pivotal role. Altogether, this work demonstrates the immense promise of adaptive quantum circuits for efficiently preparing many-body entangled states and provides explicit algorithms that outperform known protocols to prepare an essential class of states. Published by the American Physical Society 2024

Smith, Kevin C. (ORCID:0000000223971518)↗

DOE OSTI2026

Predicting Adaptively Chosen Observables in Quantum Systems

Recent advances have demonstrated that 𝒪⁡(log 𝑀) measurements suffice to predict 𝑀 properties of arbitrarily large quantum many-body systems. However, these remarkable findings assume that the properties to be predicted are chosen independently of the data. This assumption can be violated in practice, where scientists adaptively select properties after looking at previous predictions. This work investigates the adaptive setting for three classes of observables: local, Pauli, and bounded-Frobenius-norm observables. We prove that Ω⁡(√𝑀) samples of an arbitrarily large unknown quantum state are necessary to predict expectation values of 𝑀 adaptively chosen local and Pauli observables, where the system size scales exponentially and polynomially in 𝑀, respectively. We also present computationally efficient algorithms that achieve this information-theoretic lower bound. In contrast, for bounded-Frobenius-norm observables, we devise an algorithm requiring only 𝒪⁡(log 𝑀) samples, independent of system size. These results highlight the potential pitfalls of adaptivity in analyzing data from quantum experiments and provide algorithmic tools to safeguard against erroneous predictions in quantum experiments.

Machine learning↗