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Th-230 - U-238 series disequilibrium of the Olkaria basalts Gregory Rift Valley, Kenya

U-Th disequilibrium analyses of the Naivasha basalts show a very small (U-238/Th-230) ratios which are lower than any previously analyzed basalts. The broadly positive internal isochron trend from one sample indicates that the basalts may have source heterogeneities, this is supported by earlier work. The Naivasha complex comprises a bimodal suite of basalts and rhyolites. The basalts are divided into two stratigraphic groups each of a transitional nature. The early basalt series (EBS) which were erupted prior to the Group 1 comendites and, the late basalt series (LBS) which erupted temporally between the Broad Acres and the Ololbutot centers. The basalts represent a very small percentage of the overall eruptive volume of material at Naivasha (less than 2 percent). The analyzed samples come from four stratigraphic units in close proximity around Ndabibi, Hell's Gate and Akira areas. The earliest units occur as vesicular flows from the Ndabibi plain. These basalts are olivine-plagioclase phyric with the associated hawaiites being sparsely plagioclase phyric. An absolute age of 0.5Ma was estimated for these basalts. The next youngest basalts flows occur as younger tuft cones in the Ndabibi area and are mainly olivine-plagioclase-clinopyroxcene phyric with one purely plagioclase phyric sample. The final phase of activity at Ndabibi resulted in much younger tuft cones consisting of air fall ashes and lapilli tufts. Many of these contain resorbed plagioclase phenocrysts with sample number 120c also being clinopyroxene phyric. The isotopic evidence for the basalt formation is summarized.

Black, S.↗

Nitrogen and xenon isotopic disequilibrium in Bachmut (L6) chondrule J2689 and matrix

Chondrule J2689, a large (8-mm) RP chondrule from Bachmut (L6) was previously found to be in disequilibrium with its host in a variety of features: (1) It has a fine-grained hornfelsic texture; (2) it contains low amounts of metal with a low-Ni taenite composition not found in the matrix; (3) the Ni/Co ratio of that metal is close to the solar ratio, which is equal to the bulk Ni/Co ratio (23) of the chondrule; (4) the bulk alkali content of the chondrule is high and the Na/K ratio is fractionated with respect to the average L chondrite ratio of 8; (5) Cr is depleted in spite of the high pyroxene content; (6) the siderophile elements are strongly depleted but are fractionated with their abundances increasing with volatility; and (7) the O isotopes of the chondrule and the host are out of equilibrium. However, the (Fe,Mg) silicates, feldspar, and chromite have chemical compositions indistinguishable from that of the host chondrite. We have studied a chip of the chondrite and of adjacent matrix by stepwise heating and by combustion in O for N and Xe isotopic abundances. (1) The chondrule preserved distinct bulk, metal, and O isotopic compositional features. It is therefore unlikely that the 'equilibration' of the major silicates Fe/Mg ratios could have taken place after accretion; (2) the chondrule was well equilibrated before break-up and exposure to cosmic rays; (3) two N signatures in the matrix also indicate that the matrix is not equilibrated; and (4) all data collected so far point toward the presence of unequilibrated Bachmut components. Very few reactions took place after accretion.

Kim, Y.↗

Nucleon-Alpha Particle Disequilibrium and Short-Lived r-Process Radioactivities

r-Process yields can be extremely sensitive to expansion parameters when a persistent disequilibrium between free nucleons and alpha particles is present. This may provide a natural scenario for understanding the variation of heavy and light r-process isotopes in different r-process events. Additional information is contained in the original extended abstract.

Meyer, B. S.↗

Particle excitation, airglow and H2 vibrational disequilibrium in the atmosphere of Jupiter

The extreme ultraviolet EUV emission produced by particle excitation of the hydrogen atmospheres of Jupiter and Saturn is examined using model calculations to determine the nature of the energy deposition process and the effect of such processes on atmospheric structure. Tasks ranging from examination of phenomenologically related processes on Saturn and Titan to analysis of experimental laboratory data required to allow accurate modeling of emissions from hydrogenic atmospheres are investigated. An explanation of the hydrogen H Ly(alpha) bulge in Jupiter's emission from the equatorial region is presented. It is proposed that Saturn, rather then Titan is the major source of the extended hydrogen cloud. The atomic hydrogen detected at the rings of Saturn may originate predominantly from the same source. A cross calibration is obtained between the Pioneer 10 EUV photometer and the Voyager EUV spectrometers, thus providing a direct measure of the temporal morphology of Jupiter between a minimum and a maximum in solar activity. Atomic and molecular data required for the research program are analyzed. An extrapolation of conditions in the upper atmospheres of Jupiter and Saturn produces a predicted condition at Uranus in terms of excitation and hydrogen escape rates that may be observed at Voyager-Uranus encounter.

Shemansky, D. E.↗

Thermal disequilibrium at the top of volcanic clouds and its effect on estimates of the column height

Satellite images of large volcanic explosions reveal that the tops of volcanic eruptions columns are much cooler than the surrounding atmosphere. It is proposed that this effect occurs whenever a mixture of hot volcanic ash and entrained air ascends sufficiently high into a stably stratified atmosphere. Although the mixture is initially very hot, it expands and cools as the ambient pressure decreases. It is shown that cloud-top undercoolings in excess of 20 C may develop in clouds that penetrate the stratosphere, and it is predicted that, for a given cloud-top temperature, variations in the initial temperature of 100-200 C may correspond to variations in the column height of 5-10 km. It is deduced that the present practice of converting satellite-based measurements of the temperature at the top of volcanic eruptions columns to estimates of the column height will produce rather inaccurate results and should therefore be discontinued.

Woods, Andrew W.↗

Th-230 - U-238 series disequilibrium of the Olkaria basalts Gregory Rift Valley, Kenya: Petrogenesis

Strong mixing trends on a (Th-230/Th-232) versus Th diagram show that the basalts are mixed magmas which have undergone interaction with the crust. Instantaneous Th/U ratios are less than time integrated ones but these exceed the Th/U ratios in the MORB and OIB sources. This indicates that the mantle may have undergone some metasomatic fluxing, crustal contamination of the basalts will also enhance these ratios. Early activity on the Akira plain is represented by early basalts and hawaiites. The early basalt samples are known to predate the earliest comendites. The most recent phase of activity is represented by another cinder cone 40-50 m high being feldspar and clinopyroxene phyric. Inclusions which occur in the comendites vary in size and distribution. The largest and most porphyritic are the trachytes (up to 40 cm) with alkali feldspar phases up to 6 mm and small pyroxenes in the ground mass. The second set of inclusions are smaller (up to 10 cm) and are largely aphyric. The distribution of the inclusions are not uniform, the Broad Acres (C5) lavas contain 2-5 percent. The size of the inclusions decrease from south to north, as does the abundance of the trachytic inclusions. The major element variations in the Naivasha basalts, hawaiites and magmatic inclusions are discussed.

Black, S.↗

Th-230 - U-238 series disequilibrium of the Olkaria rhyolites Gregory Rift Valley, Kenya: Petrogenesis

Positive correlations of (U-238/Th-230) versus Th show the rhyolites to be products of partial melting. Positive correlations of U and Cl and U and F show that the U enrichment in the rhyolites is associated with the halogen contents which may be related to the minor phenocryst phase fractionation. Instantaneous Th/U ratios exceed time integrated Th/U ratios providing further evidence of the hydrous nature of the Olkaria rhyolite source. Excess (U-238/Th-230) in the subduction related rocks has been associated to the preferential incorporation of uranium in slab derived fluids, but no evaluation of the size of this flux has been made. The majority of the Naivasha samples show a (U-238/Th-230) less than 1 and plot close to the subduction related samples indicating the Naivasha rhyolites may also have been influenced by fluids during their formation. In general samples with high (U-238/Th-230) ratios reflecting recent enrichment of uranium relative to thorium have high thorium contents, thereby the high (U-238/Th-230) ratios are restricted to the most incompatible element enriched magmas and, hence, are a good indication that the rhyolites were formed by partial melting. If a fluid phase had some influence on the formation of the rhyolites then the uranium and thorium may have some correlation with F and Cl contents which can be mirrored by the peralkalinity. Plots of uranium against F and Cl contents are shown. The positive correlation indicates that the uranium enrichments are associated with the halogen contents. There seems to be a greater correlation for U against Cl than F indicating that the U may be transported preferentially as Cl complexes.

Black, S.↗

Internal Variability and Disequilibrium Confound Estimates of Climate Sensitivity from Observations

An emerging literature suggests that estimates of equilibrium climate sensitivity (ECS) derived from recent observations and energy balance models are biased low because models project more positive climate feedback in the far future. Here we use simulations from the Coupled Model Intercomparison Project Phase 5 (CMIP5) to show that across models, ECS inferred from the recent historical period (1979-2005) is indeed almost uniformly lower than that inferred from simulations subject to abrupt increases in CO2-radiative forcing. However, ECS inferred from simulations in which sea surface temperatures are prescribed according to observations is lower still. ECS inferred from simulations with prescribed sea surface temperatures is strongly linked to changes to tropical marine low clouds. However, feedbacks from these clouds are a weak constraint on long-term model ECS. One interpretation is that observations of recent climate changes constitute a poor direct proxy for long-term sensitivity.

Marvel, Kate↗

Mafic explosive volcanism at Llaima Volcano: 3D x-ray microtomography reconstruction of pyroclasts to constrain shallow conduit processes

Abstract Mafic volcanic activity is dominated by effusive to mildly explosive eruptions. Plinian and ignimbrite-forming mafic eruptions, while rare, are also possible; however, the conditions that promote such explosivity are still being explored. Eruption style is determined by the ability of gas to escape as magma ascends, which tends to be easier in low-viscosity, mafic magmas. If magma permeability is sufficiently high to reduce bubble overpressure during ascent, volatiles may escape from the magma, inhibiting violent explosive activity. In contrast, if the permeability is sufficiently low to retain the gas phase within the magma during ascent, bubble overpressure may drive magma fragmentation. Rapid ascent may induce disequilibrium crystallization, increasing viscosity and affecting the bubble network with consequences for permeability, and hence, explosivity. To explore the conditions that promote strongly explosive mafic volcanism, we combine microlite textural analyses with synchrotron x-ray computed microtomography of 10 pyroclasts from the 12.6 ka mafic Curacautín Ignimbrite (Llaima Volcano, Chile). We quantify microlite crystal size distributions (CSD), microlite number densities, porosity, bubble interconnectivity, bubble number density, and geometrical properties of the porous media to investigate the role of magma degassing processes at mafic explosive eruptions. We use an analytical technique to estimate permeability and tortuosity by combing the Kozeny-Carman relationship, tortuosity factor, and pyroclast vesicle textures. The groundmass of our samples is composed of up to 44% plagioclase microlites, > 85% of which are < 10 µm in length. In addition, we identify two populations of vesicles in our samples: (1) a convoluted interconnected vesicle network produced by extensive coalescence of smaller vesicles (> 99% of pore volume), and (2) a population of very small and completely isolated vesicles (< 1% of porosity). Computed permeability ranges from 3.0 × 10 −13 to 6.3 × 10 −12 m 2 , which are lower than the similarly explosive mafic eruptions of Tarawera (1886; New Zealand) and Etna (112 BC; Italy). The combination of our CSDs, microlite number densities, and 3D vesicle textures evidence rapid ascent that induced high disequilibrium conditions, promoting rapid syn-eruptive crystallization of microlites within the shallow conduit. We interpret that microlite crystallization increased viscosity while simultaneously forcing bubbles to deform as they grew together, resulting in the permeable by highly tortuous network of vesicles. Using the bubble number densities for the isolated vesicles (0.1-3 −3 × 10 4 bubbles per mm 3 ), we obtain a minimum average decompression rate of 1.4 MPa/s. Despite the textural evidence that the Curacautín magma reached the percolation threshold, we propose that rapid ascent suppressed outgassing and increased bubble overpressures, leading to explosive fragmentation. Further, using the porosity and permeability of our samples, we estimated that a bubble overpressure > 5 MPa could have been sufficient to fragment the Curacautín magma. Other mafic explosive eruptions report similar disequilibrium conditions induced by rapid ascent rate, implying that syn-eruptive disequilibrium conditions may control the explosivity of mafic eruptions more generally.

Valdivia, Pedro↗

On the Composition of Young, Directly Imaged Giant Planets

The past decade has seen significant progress on the direct detection and characterization of young, self-luminous giant planets at wide orbital separations from their host stars. Some of these planets show evidence for disequilibrium processes like transport-induced quenching in their atmospheres; photochemistry may also be important, despite the typically large orbital distances. Disequilibrium chemical processes such as these can alter the expected composition, spectral behavior, thermal structure, and cooling history of the planets, and can potentially confuse determinations of bulk elemental ratios, which provide important insights into planet-formation mechanisms. Using a thermo/photochemical kinetics and transport model, we investigate the extent to which disequilibrium chemical processes affect the composition and spectra of directly imaged giant exoplanets. Results for specific "young Jupiters" such as HR 8799 b and c and 51 Eri b are presented, as are general trends as a function of planetary effective temperature, surface gravity, incident ultraviolet flux, and strength of deep atmospheric convection. We find that quenching is very important on young Jupiters, leading to CO/CH4 and N2/NH3 ratios much greater than; and H2O mixing ratios a factor of a few less than chemical equilibrium predictions. Photochemistry can also be important on such planets, with CO2 and HCN being key photochemical products. Carbon dioxide becomes a particularly major constituent when stratospheric temperatures are low and recycling of water following H2O photolysis becomes stifled. Young Jupiters with effective temperatures less than 700 degrees Kelvin are in a particularly interesting photochemical regime that differs from both transiting hot Jupiters and our own solar-system giant planets.

photochemistry↗

Global Ocean Cooling of 2.3°C During the Last Glacial Maximum

Abstract Quantitative constraints on past mean ocean temperature (MOT) critically inform our historical understanding of Earth's energy balance. A recently developed MOT proxy based on paleoatmospheric Xe, Kr, and N 2 ratios in ice core air bubbles is a promising tool rooted in the temperature dependences of gas solubilities. However, these inert gases are systematically undersaturated in the modern ocean interior, and it remains unclear how air‐sea disequilibrium may have changed in the past. Here, we carry out 30 tracer‐enabled model simulations under varying circulation, sea ice cover, and wind stress regimes to evaluate air‐sea disequilibrium in the Last Glacial Maximum (LGM) ocean. We find that undersaturation of all three gases was likely reduced, primarily due to strengthened high‐latitude winds, biasing reconstructed MOT by −0.38 ± 0.37°C (1σ). Accounting for air‐sea disequilibrium, paleoatmospheric inert gases indicate that LGM MOT was 2.27 ± 0.46°C (1σ) colder than the pre‐industrial era.

Seltzer, A. M.↗

Thermodynamic constraints on the textural evolution of eucrite, EET 90020

Basaltic eucrites, which are possibly parts of the Vestan crust, formed as either lava flows or intrusions, and can offer insights into early crust formation. However most eucrites have experienced thermal metamorphism, which exacerbates the challenges of understanding these samples. A variety of petrogenetic models such as, partial melting of a primitive source, fractional crystallization of magmas emplaced in a primitive crust, and/or partial melting of a eucritic source coupled with melt mixing and assimilation have been proposed in order to explain observed petrologic and chemical characteristics of eucrites. EET 90020 is an unbrecciated eucrite that has experienced significant thermal metamorphism, with temperatures of metamorphic equilibration calculated to be ~840-1040°C. Its petrologic history remains contentious, in part due to differences in trace element analyses [10,17, this work], which has led to multiple metamorphic interpretations [8,10-11]. Here, we combined petrologic observations, chemical analyses, and thermodynamic modeling, to interpret micro-domain textures identified in EET 90020 and better constrain its petrologic history. Ultimately, the development of such textures is a direct result of the geologic processes operating on a young Vesta or similar asteroid. Sample description: We identified three textural domains in EET 90020 (Figure 1); (I) A coarse grain domain with granoblastic plagioclase and pyroxene, (II) a medium grain domain with curved grain boundaries between plagioclase and pyroxene, and (III) a fine grain domain dominated by tridymite that fills in interstitial space between spherical plagioclase. Major element chemistry in phases is consistent across domains. Pyroxene have distinctive high Ca lamellae (Wo40.92En28.1Fs31.0) forming from the low-Ca pigeonite host (Wo3.5En33.7Fs62.8). There are small amounts of fayalitic olivine along pyroxene/oxide grain boundaries, where pyroxenes have reacted with ilmenite/chromite clasts. Plagioclase is anorthitic (Avg ~An88), with little variation (An86-92.5). Trace element bulk rock analyses were collected via ICP-MS and individual mineral analyses with LA-ICP-MS (Figure 2). The bulk sample has an observable enrichment in light rare earth elements, with a notable depletion in Eu. Plagioclase is enriched in LREEs, depleted in HREEs, and has a positive Eu anomaly while pyroxene is enriched in HREEs with a negative Eu anomaly. Variations in trace element analyses is likely influenced by the presence of phosphates because are highly enriched in REEs and have a dramatic effect on the bulk domain compositions. Thermodynamic modeling: The software package, Perple_X, was used to calculate mineral phase equilibria over a range of conditions using a Gibbs free energy minimization approach [12]. Models used all major/minor elements except P2O5. Thermodynamic properties from [13] were used to constrain endmember phase stabilities. Activity models were used to describe mixing in phases with solid solution. Isochemical P-T phase diagrams were constructed for the bulk thin section, and the coarse, medium and fine grain domain compositions. Domain compositions were determined using microprobe analyses of phases identified in each domain and observed modal mineral abundancies. Thermodynamically stable pyroxene compositions were extracted from model results and compared to pyroxene compositions collected via EMPA, allowing us to calculate temperatures for metamorphic equilibrium. Results: Results that use the coarse domain composition (Fig. 3a) demonstrate overlap at T ~ 1020°C indicating high T equilibration. There was no overlap for the medium and fine grain domains, or the bulk composition (e.g., Fig. 3b) indicating that these are not equilibrium assemblages. These results were replicated using data from [8,20]. Discussion: The disequilibrium results from the bulk rock, fine grain and medium grain models imply that EET 90020 was modified during and/or after peak metamorphism (open system behavior). However, this is in contrast to the coarse domain where it appears as if equilibrium was maintained. We suggest that this conflict is explained by highly localized equilibrium occurring at millimeter length-scales, which has been observed in terrestrial metamorphism where aqueous fluid infiltrate [14] or melt loss occurs [15]. It is unlikely that aqueous alteration was significant in modifying the bulk composition of EET 90020, because it lacks hydrated minerals. However, the presence of melt is supported by the presence of an abundance of curved grain boundaries and spherical grains in the medium and fine grain domains This contrasts the coarse domain, where grain boundaries are angular. Given the evidence for disequilibrium in the medium and fine grain domains, it would be inappropriate to draw additional conclusions about textural evolution using thermodynamic models of those domains. However, modeling results of the coarse grain domain, where equilibrium was maintained, can provide useful insights into the geologic evolution of EET 90020. We approximate maximum metamorphic temperatures, using the Ca component in pyroxene, at ~1020°C (Fig. 4), which is consistent with previous two-pyroxene thermometry [11]. At this temperature, up to 10 vol % melt can be produced in the coarse grain domain, which is at the boundary of minimum melt needed in order to segregate and form a melt network [16]. Tridymite and plagioclase would be the first minerals to melt out during heating starting ~990°C. This is consistent with the observed melt textures formed by tridymite and plagioclase in the fine grain domain. We suggest that a partial melting model best explains the textural development of EET 90020. Upon heating, melt generated was either trapped, resulting in no net change in the localized rock composition, or migrated, resulting in disequilibrium between pyroxene and the surrounding matrix. A positive Eu anomaly in plagioclase indicates that all of the plagioclase was melted previously. This is consistent with previous studies that have suggested that EET 90020 represents a residual eucrite that experienced partial melting and subsequent melt loss [8]. We speculate that partial melting could have occurred when EET 90020 was heated in the asteroid’s lower crust or adjacent to an intrusion [7]. Future work will study other, texturally heterogeneous samples to see if EET 90020 presents a unique circumstance or whether crustal partial melting was ubiquitous on the eucrite asteroid.

Eucrites↗

Understanding and Controlling Hybrid Electric Gas Turbine Engine Transient Dynamics

The electrification of the gas turbine engine is known to increase the flexibility of aircraft architectures by enabling the generation of electrical power to distribute to other electrically based, thrust producing subsystems. It also has potential for direct performance benefits in the gas turbine engine itself, both at steady state and dynamically. Although the design focus of the gas turbine engine performance is primarily at steady state, it is often the instabilities occurring during transients that cause disequilibrium and constrain performance improvements. Instabilities arise due to the disequilibrium of the energy storage mechanisms within the traditional engine system and likewise for the electrified engine system. The primary energy storage mechanisms in the traditional system are the rotational inertia, gas path volumes, the thermal masses that make up the mechanical structure, and now, the electrical power system will provide additional contributions. Understanding the effect each of these energy storage mechanisms has on the others and controlling them appropriately allows for the suppression of state changes within the turbomachinery components to the degree that the components remain near steady state, thus reducing the disequilibrium within the system. The ability to tightly regulate the state changes of turbomachinery components, such as the compressor, minimizes the excursion of the compressor operating point from the operating line (operability), allowing for higher performing, more efficient compressor designs by decreasing the amount of stall margin needed for safe engine power level changes. Preliminary studies with the electrification of the turbine engine have shown that this is possible, and this concept can lead to design trades benefitting engine performance, weight, and volume. This paper explores in detail the energy storage mechanisms and control approaches for coordinating their state changes, and ultimately proposes that a higher performing, more efficient compressor design can result.

transient dynamics↗

Dynamic Surface Incorporation of Pb 2+ Ions at the Actively Dissolving Calcite (104) Surface

The reaction of dissolved Pb 2+ with calcite surfaces at near-equilibrium conditions involves adsorption of Pb 2+ and precipitation of secondary heteroepitaxial Pb-carbonate minerals. A more complex behavior is observed under far-from-equilibrium conditions, including strong inhibition of calcite dissolution, development of microtopography, and near-surface incorporation of multiple monolayers (ML) of Pb 2+ without precipitation of secondary phases [where 1 ML ≡ 1 Ca/20.2 Å 2 , the crystallographic site density of the calcite (104) lattice plane]. However, the mechanistic controls governing far-from-equilibrium reactivity are not well understood. Here, in this study, we observe the interfacial incorporation of dissolved Pb 2+ during the dissolution of calcite (104) surfaces at pH ~3.7 in a flow-through reaction cell, revealing the formation of a ~1 nm thick Pb-rich calcite layer with a total Pb coverage of ~1.4 ML. These observations of the sorbed Pb distribution used resonant anomalous X-ray reflectivity, X-ray fluorescence, and nanoinfrared atomic force microscopy. We propose that this altered surface layer represents a novel sorption mode that is stabilized by conditions of sustained disequilibrium. This behavior may significantly impact the transport of dissolved metals during disequilibrium processes occurring in acid mine drainage and subsurface CO 2 injection and, if appropriately accounted for, could improve the predictive capability of geochemical reactive-transport models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure-informed clustering for population stratification in association studies

Background: Identifying variants associated with complex traits is a challenging task in genetic association studies due to linkage disequilibrium (LD) between genetic variants and population stratification, unrelated to the disease risk. Existing methods of population structure correction use principal component analysis or linear mixed models with a random effect when modeling associations between a trait of interest and genetic markers. However, due to stringent significance thresholds and latent interactions between the markers, these methods often fail to detect genuinely associated variants. Results: To overcome this, we propose CluStrat, which corrects for complex arbitrarily structured populations while leveraging the linkage disequilibrium induced distances between genetic markers. It performs an agglomerative hierarchical clustering using the Mahalanobis distance covariance matrix of the markers. In simulation studies, we show that our method outperforms existing methods in detecting true causal variants. Applying CluStrat on WTCCC2 and UK Biobank cohorts, we found biologically relevant associations in Schizophrenia and Myocardial Infarction. CluStrat was also able to correct for population structure in polygenic adaptation of height in Europeans. Conclusions: CluStrat highlights the advantages of biologically relevant distance metrics, such as the Mahalanobis distance, which captures the cryptic interactions within populations in the presence of LD better than the Euclidean distance.

59 BASIC BIOLOGICAL SCIENCES↗

pyFLANK, a graph neural network based null distribution inference model for F ST outlier detection

Detecting genomic regions under selection is essential for understanding how populations adapt to different environments, yet it remains challenging due to the confounding effects of demographic history and linkage disequilibrium (LD). Fixation index (F ST ) is a widely used statistic to identify genomic regions under adaptation. However, identifying genes under selection by defining F ST outliers often remains challenging, owing to confounding effects of underlying demographic history. Traditional methods assume independence among loci and rely on simple demographic models, while newer models perform much better but are computationally expensive and not easily scalable. Here, we present pyFLANK, an open-source and automated Python implementation which detects F ST outliers using a null distribution inferred from quasi-independent loci. Our tool integrates three approaches to identify loci obeying a null distribution: graph neural network (GNN) inference, linkage disequilibrium (LD)-based inference, and user-defined input. Because pyFLANK uses GNN-based inference of quasi-independent loci, it yields a more accurate null model with less need for user parameter input. In simulation experiments, pyFLANK achieved lower false positive rates than current methods while maintaining comparable detection power, indicating that its refined null model better distinguishes true adaptive loci from background variation. The GNN-based model, in particular, detected additional loci associated with phenotypic variance that were not identified by existing methods. Assessments of simulation and real data from different species demonstrate that pyFLANK achieves lower false positive rates compared with other commonly used F ST outlier detectors, while maintaining comparable detection power and excellent computational performance, providing a robust and user-friendly tool for identifying loci under divergent selection. It extends existing F ST outlier frameworks by incorporating explicit LD-aware strategies for null model calibration. The method is intended as a practical and scalable complement to existing genome scan approaches.

FST↗

PyPop: a mature open-source software pipeline for population genomics

Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations.

59 BASIC BIOLOGICAL SCIENCES↗