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Primates, consisting of apes, monkeys, tarsiers, and lemurs, are among the most charismatic and well-studied animals on Earth, yet there is no taxonomically complete molecular timetree for the group. Combining the latest large-scale genomic primate phylogeny of 205 recognized species with the 400-species literature consensus tree available fromTimeTree.orgyields a phylogeny of just 405 primates, with 50 species still missing despite having molecular sequence data in the NCBI GenBank. In this study, we assemble a timetree of 455 primates, incorporating every species for which molecular data are available. We use a synthetic approach consisting of a literature review for published timetrees,de novodating of untimed trees, and assembly of timetrees from novel alignments. The resulting near-complete molecular timetree of primates allows testing of two long-standing alternate hypotheses for the origins of primate biodiversity: whether species richness arises at a constant rate, in which case older clades have more species, or whether some clades exhibit faster rates of speciation than others, in which case, these fast clades would be more species-rich. Consistent with other large-scale macroevolutionary analyses, we found that the speciation rate is similar across the primate tree of life, albeit with some variation in smaller clades. 

The amount of light produced by nuclear recoils in scintillating targets is strongly quenched compared to that produced by electrons. A precise understanding of the quenching factor is particularly interesting for weakly interacting massive particles (WIMP) searches and coherent elastic neutrino-nucleus scattering ( $\mathrm{CE}\nu \mathrm{NS}$) measurements since both rely on nuclear recoils, whereas energy calibrations are more readily accessible from electron recoils. There is a wide variation among the current measurements of the quenching factor in sodium iodide (NaI) crystals, especially below 10 keV, the energy region of interest for dark matter and $\mathrm{CE}\nu \mathrm{NS}$ studies. A better understanding of the quenching factor in NaI(Tl) is of particular interest for resolving the decades-old puzzle in the field of dark matter between the null results of most WIMP searches and the claim for dark matter detection by the DAMA/LIBRA collaboration. In this work, we measured sodium and iodine quenching factors for five small NaI(Tl) crystals grown with similar thallium concentrations and growth procedures. Unlike previous experiments, multiple crystals were tested, with measurements made in the same experimental setup to control systematic effects. The quenching factors agree in all crystals we investigated, and both sodium and iodine quenching factors are smaller than those reported by DAMA/LIBRA. The dominant systematic effect was due to the electron equivalent energy calibration originating from the nonproportional behavior of the NaI(Tl) light yield at lower energies, potentially the cause for the discrepancies among the previous measurements. Published by the American Physical Society2024 

The primate infraorder Simiiformes, comprising Old and New World monkeys and apes, includes the most well-studied species on earth. Their most comprehensive molecular timetree, assembled from thousands of published studies, is found in the TimeTree database and contains 268 simiiform species. It is, however, missing 38 out of 306 named species in the NCBI taxonomy for which at least one molecular sequence exists in the NCBI GenBank. We developed a three-pronged approach to expanding the timetree of Simiiformes to contain 306 species. First, molecular divergence times were searched and found for 21 missing species in timetrees published across 15 studies. Second, untimed molecular phylogenies were searched and scaled to time using relaxed clocks to add four more species. Third, we reconstructed ten new timetrees from genetic data in GenBank, allowing us to incorporate 13 more species. Finally, we assembled the most comprehensive molecular timetree of Simiiformes containing all 306 species for which any molecular data exists. We compared the species divergence times with those previously imputed using statistical approaches in the absence of molecular data. The latter data-less imputed times were not significantly correlated with those derived from the molecular data. Also, using phylogenies containing imputed times produced different trends of evolutionary distinctiveness and speciation rates over time than those produced using the molecular timetree. These results demonstrate that more complete clade-specific timetrees can be produced by analyzing existing information, which we hope will encourage future efforts to fill in the missing taxa in the global timetree of life. 

The origin of eukaryotes was among the most important events in the history of life, spawning a new evolutionary lineage that led to all complex multicellular organisms. However, the timing of this event, crucial for understanding its environmental context, has been difficult to establish. The fossil and biomarker records are sparse and molecular clocks have thus far not reached a consensus, with dates spanning 2.1–0.91 billion years ago (Ga) for critical nodes. Notably, molecular time estimates for the last common ancestor of eukaryotes are typically hundreds of millions of years younger than the Great Oxidation Event (GOE, 2.43–2.22 Ga), leading researchers to question the presumptive link between eukaryotes and oxygen. We obtained a new time estimate for the origin of eukaryotes using genetic data of both archaeal and bacterial origin, the latter rarely used in past studies. We also avoided potential calibration biases that may have affected earlier studies. We obtained a conservative interval of 2.2–1.5 Ga, with an even narrower core interval of 2.0–1.8 Ga, for the origin of eukaryotes, a period closely aligned with the rise in oxygen. We further reconstructed the history of biological complexity across the tree of life using three universal measures: cell types, genes, and genome size. We found that the rise in complexity was temporally consistent with and followed a pattern similar to the rise in oxygen. This suggests a causal relationship stemming from the increased energy needs of complex life fulfilled by oxygen. 

Abstract Biodiversity analyses of phylogenomic timetrees have produced many high-profile examples of shifts in the rate of speciation across the tree of life. Temporally correlated events in ecology, climate, and biogeography are frequently invoked to explain these rate shifts. In a re-examination of 15 genomic timetrees and 25 major published studies of the pattern of speciation through time, we observed an unexpected correlation between the timing of reported rate shifts and the information content of sequence alignments. Here, we show that the paucity of sequence variation and insufficient species sampling in phylogenomic data sets are the likely drivers of many inferred speciation rate shifts, rather than the proposed biological explanations. Therefore, data limitations can produce predictable but spurious signals of rate shifts even when speciation rates may be similar across taxa and time. Our results suggest that the reliable detection of speciation rate shifts requires the acquisition and assembly of long phylogenomic alignments with near-complete species sampling and accurate estimates of species richness for the clades of study. 

Abstract We present the fifth edition of the TimeTree of Life resource (TToL5), a product of the timetree of life project that aims to synthesize published molecular timetrees and make evolutionary knowledge easily accessible to all. Using the TToL5 web portal, users can retrieve published studies and divergence times between species, the timeline of a species’ evolution beginning with the origin of life, and the timetree for a given evolutionary group at the desired taxonomic rank. TToL5 contains divergence time information on 137,306 species, 41% more than the previous edition. The TToL5 web interface is now Americans with Disabilities Act-compliant and mobile-friendly, a result of comprehensive source code refactoring. TToL5 also offers programmatic access to species divergence times and timelines through an application programming interface, which is accessible at timetree.temple.edu/api. TToL5 is publicly available at timetree.org. 

Abstract The relationships among the four major embryophyte lineages (mosses, liverworts, hornworts, vascular plants) and the timing of the origin of land plants are enigmatic problems in plant evolution. Here, we resolve the monophyly of bryophytes by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions. We then estimate the divergence time of crown embryophytes based on three fossil calibration strategies, and reveal that maximum calibration constraints have a major effect on estimating the time of origin of land plants. Moreover, comparison of priors and posteriors provides a guide for evaluating the optimal calibration strategy. By considering the reliability of fossil calibrations and the influences of molecular data, we estimate that land plants originated in the Precambrian (980–682 Ma), much older than widely recognized. Our study highlights the important contribution of molecular data when faced with contentious fossil evidence, and that fossil calibrations used in estimating the timescale of plant evolution require critical scrutiny. 

Neutrinoless double beta decay is one of the most sensitive probes for new physics beyond the Standard Model of particle physics. One of the isotopes under investigation is ${}^{136}\mathrm{Xe}$, which would double beta decay into ${}^{136}\mathrm{Ba}$. Detecting the single ${}^{136}\mathrm{Ba}$daughter provides a sort of ultimate tool in the discrimination against backgrounds. Previous work demonstrated the ability to perform single atom imaging of Ba atoms in a single-vacancy site of a solid xenon matrix. In this paper, the effort to identify signal from individual barium atoms is extended to Ba atoms in a hexa-vacancy site in the matrix and is achieved despite increased photobleaching in this site. Abrupt fluorescence turn-off of a single Ba atom is also observed. Significant recovery of fluorescence signal lost through photobleaching is demonstrated upon annealing of Ba deposits in the Xe ice. Following annealing, it is observed that Ba atoms in the hexa-vacancy site exhibit antibleaching while Ba atoms in the tetra-vacancy site exhibit bleaching. This may be evidence for a matrix site transfer upon laser excitation. Our findings offer a path of continued research toward tagging of Ba daughters in all significant sites in solid xenon. Published by the American Physical Society2024 

Abstract Testing the DAMA/LIBRA annual modulation result independently of dark matter particle and halo models has been a challenge for twenty years. Using the same target material, NaI(Tl), is required and presently two experiments, ANAIS-112 and COSINE-100, are running for such a goal. A precise knowledge of the detector response to nuclear recoils is mandatory because this is the most likely channel to find the dark matter signal. The light produced by nuclear recoils is quenched with respect to that produced by electrons by a factor that has to be measured experimentally. However, current quenching factor measurements in NaI(Tl) crystals disagree within the energy region of interest for dark matter searches. To disentangle whether this discrepancy is due to intrinsic differences in the light response among different NaI(Tl) crystals, or has its origin in unaccounted for systematic effects will be key in the comparison among the different experiments. We present measurements of the quenching factors for five small NaI(Tl) crystals performed in the same experimental setup to control systematics. Quenching factor results are compatible between crystals and no clear dependence with energy is observed from 10 to 80 keVnr. 

We consider the potential for a 10 kg undoped cryogenic CsI detector operating at the Spallation Neutron Source to measure coherent elastic neutrino-nucleus scattering and its sensitivity to discover new physics beyond the standard model (BSM). Through a combination of increased event rate, lower threshold, and good timing resolution, such a detector would significantly improve on past measurements. We considered tests of several BSM scenarios such as neutrino nonstandard interactions and accelerator-produced dark matter. This detector’s performance was also studied for relevant questions in nuclear physics and neutrino astronomy, namely the weak charge distribution of Cs and I nuclei and detection of neutrinos from a core-collapse supernova. Published by the American Physical Society2024