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  1. Betz, Markus ; Elezzabi, Abdulhakem Y. (Ed.)
    Free, publicly-accessible full text available March 8, 2025
  2. Abstract

    Abstract.—Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutionary histories due to incomplete lineage sorting (ILS), introgression, and/or horizontal gene transfer; even single loci may not be treelike due to recombination. To overcome this shortcoming, we introduce an implementation of a multi-tree mixture model that we call mixtures across sites and trees (MAST). This model extends a prior implementation by Boussau et al. (2009) by allowing users to estimate the weight of each of a set of pre-specified bifurcating trees in a single alignment. The MAST model allows each tree to have its own weight, topology, branch lengths, substitution model, nucleotide or amino acid frequencies, and model of rate heterogeneity across sites. We implemented the MAST model in a maximum-likelihood framework in the popular phylogenetic software, IQ-TREE. Simulations show that we can accurately recover the true model parameters, including branch lengths and tree weights for a given set of tree topologies, under a wide range of biologically realistic scenarios. We also show that we can use standard statistical inference approaches to reject a single-tree model when data are simulated under multiple trees (and vice versa). We applied the MAST model to multiple primate datasets and found that it can recover the signal of ILS in the Great Apes, as well as the asymmetry in minor trees caused by introgression among several macaque species. When applied to a dataset of 4 Platyrrhine species for which standard concatenated maximum likelihood (ML) and gene tree approaches disagree, we observe that MAST gives the highest weight (i.e., the largest proportion of sites) to the tree also supported by gene tree approaches. These results suggest that the MAST model is able to analyze a concatenated alignment using ML while avoiding some of the biases that come with assuming there is only a single tree. We discuss how the MAST model can be extended in the future.

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  3. Salicylideneaniline (SA) is an archetypal system for excited-state intramolecular proton transfer (ESIPT) in non-planar systems. Multiple channels for relaxation involving both the keto and enol forms have been proposed after excitation to S1 with near-UV light. Here, we present transient absorption measurements of hot gas-phase SA, jet-cooled SA, and SA in Ar clusters using cavity-enhanced transient absorption spectroscopy (CE-TAS). Assignment of the spectra is aided by simulated TAS spectra, computed by applying time-dependent complete active space configuration interaction (TD-CASCI) to structures drawn from nonadiabatic molecular dynamics simulations. We find prompt ESIPT in all conditions followed by the rapid generation of the trans keto metastable photochrome state and fluorescent keto state in parallel. Increasing the internal energy increases the photochrome yield and decreases the fluorescent yield and fluorescent state lifetime observed in TAS. In Ar clusters, internal conversion of SA is severely hindered, but the photochrome yield is unchanged. Taken together, these results are consistent with the photochrome being produced via the vibrationally excited keto population after ESIPT.

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    Free, publicly-accessible full text available September 14, 2024
  4. Although many studies have examined how taxa responded to Pleistocene climate fluctuations in the Appalachian Mountains, impacts on high-elevation endemics of Central Appalachia are not yet understood. We use mitochondrial (ND4 & Cytb) and nuclear (GAPD) DNA sequences to investigate the phylogeography of the Cow Knob Salamander (Plethodon punctatus), a woodland species from Central Appalachian highlands thought to have origins in the Pleistocene. Data from 72 tail tips representing 25 sites revealed that the species comprises two geographically cohesive mitochondrial clades with a narrow, putative contact zone on Shenandoah Mountain. Molecular clock estimates indicate the clades diverged in the Middle Pleistocene. The population size of the Southern clade appears to have remained stable for at least 50,000 years. Despite spanning several isolated mountain systems, the Northern clade has exceptionally low genetic diversity, probably due to recent demographic expansion. Palaeodemographic hypothesis testing supported a scenario in which a founder effect characterized the Northern clade as it diverged from the Southern clade. Species distribution models predicted no suitable habitat for the species during the Last Glacial Maximum. Ultimately, Pleistocene glacial climates may have driven the species from the northern half of its current range, with recolonization events by members of the Northern clade as climates warmed. Density dependent processes may now maintain a narrow contact zone between the two clades.

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    Free, publicly-accessible full text available August 10, 2024
  5. Hydrologic loads can stimulate seismicity in the Earth’s crust1. However, evidence for the triggering of large earthquakes remains elusive. The southern San Andreas Fault (SSAF) in Southern California lies next to the Salton Sea2, a remnant of ancient Lake Cahuilla that periodically filled and desiccated over the past millennium3,4,5. Here we use new geologic and palaeoseismic data to demonstrate that the past six major earthquakes on the SSAF probably occurred during highstands of Lake Cahuilla5,6. To investigate possible causal relationships, we computed time-dependent Coulomb stress changes7,8 due to variations in the lake level. Using a fully coupled model of a poroelastic crust9,10,11 overlying a viscoelastic mantle12,13, we find that hydrologic loads increased Coulomb stress on the SSAF by several hundred kilopascals and fault-stressing rates by more than a factor of 2, which is probably sufficient for earthquake triggering7,8. The destabilizing effects of lake inundation are enhanced by a nonvertical fault dip14,15,16,17, the presence of a fault damage zone18,19 and lateral pore-pressure diffusion20,21. Our model may be applicable to other regions in which hydrologic loading, either natural8,22 or anthropogenic1,23, was associated with substantial seismicity. 
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  6. Abstract

    We present an in-depth analysis of gas morphologies for a sample of 25 Milky Way–like galaxies from the IllustrisTNG TNG50 simulation. We constrain the morphology of cold, warm, hot gas, and gas particles as a whole using a local shell iterative method and explore its observational implications by computing the hard-to-soft X-ray ratio, which ranges between 10−3and 10−2in the inner ∼50 kpc of the distribution and 10−5–10−4at the outer portion of the hot gas distribution. We group galaxies into three main categories: simple, stretched, and twisted. These categories are based on the radial reorientation of the principal axes of the reduced inertia tensor. We find that a vast majority (77%) of the galaxies in our sample exhibit twisting patterns in their radial profiles. Additionally, we present detailed comparisons between (i) the gaseous distributions belonging to individual temperature regimes, (ii) the cold gas distributions and stellar distributions, and (iii) the gaseous distributions and dark matter (DM) halos. We find a strong correlation between the morphological properties of the cold gas and stellar distributions. Furthermore, we find a correlation between gaseous distributions with a DM halo that increases with gas temperature, implying that we may use the warm–hot gaseous morphology as a tracer to probe the DM morphology. Finally, we show gaseous distributions exhibit significantly more prolate morphologies than the stellar distributions and DM halos, which we hypothesize is due to stellar and active galactic nucleus feedback.

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  7. The origins of maize were the topic of vigorous debate for nearly a century, but neither the current genetic model nor earlier archaeological models account for the totality of available data, and recent work has highlighted the potential contribution of a wild relative,Zea maysssp.mexicana. Our population genetic analysis reveals that the origin of modern maize can be traced to an admixture between ancient maize andZea maysssp.mexicanain the highlands of Mexico some 4000 years after domestication began. We show that variation in admixture is a key component of maize diversity, both at individual loci and for additive genetic variation underlying agronomic traits. Our results clarify the origin of modern maize and raise new questions about the anthropogenic mechanisms underlying dispersal throughout the Americas.

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    Free, publicly-accessible full text available December 1, 2024
  8. Materials that rectify light into current in their bulk are desired for optoelectronic applications. In Weyl semimetals that break inversion symmetry, bulk photocurrents may arise due to nonlinear optical processes that are enhanced near the Weyl nodes. However, the photoresponse of these materials is commonly studied by scanning photocurrent microscopy, which convolves the effects of photocurrent generation and collection. Here we directly image the photocurrent flow inside the type-II Weyl semimetals WTe2 and TaIrTe4 using high-sensitivity quantum magnetometry with nitrogen-vacancy centre spins. We elucidate a mechanism for bulk photocurrent generation, which we call the anisotropic photothermoelectric effect, where unequal thermopowers along different crystal axes drive intricate circulations of photocurrent around the photoexcitation. Using overlapping scanning photocurrent microscopy and magnetic imaging at the interior and edges of the sample, we visualize how the anisotropic photothermoelectric effect stimulates the long-range photocurrent collected in our WTe2 and TaIrTe4 devices through the Shockley–Ramo mechanism. Our results highlight a widely relevant source of current flow and will inspire photodetectors that utilize bulk materials with thermoelectric anisotropy. 
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