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  1. 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.
    Free, publicly-accessible full text available August 1, 2023
  2. Tamura, Koichiro (Ed.)
    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.
    Free, publicly-accessible full text available March 1, 2023
  3. Abstract

    Cryptogenic species are those whose native and introduced ranges are unknown. The extent and long history of human migration rendered numerous species cryptogenic. Incomplete knowledge regarding the origin and native habitat of a species poses problems for conservation management and may confound ecological and evolutionary studies. The Lesser Antilles pose a particular challenge with regard to cryptogenic species because these islands have been anthropogenically connected since before recorded history. Here, we use population genetic and phylogeographic tools in an attempt to determine the origin ofEleutherodactylus johnstonei, a frog species with a potentially widespread introduced range and whose native range within the Lesser Antilles is unknown. Based on elevated estimates of genetic diversity and within-island geographic structure not present elsewhere in the range, we identify Montserrat as the native island ofE. johnstonei. We also document two major clades withinE. johnstonei, only one of which is the primary source of introduced populations throughout the Americas. Our results demonstrate the utility of genetic tools for resolving cryptogenic species problems and highlightE. johnstoneias a potential system for understanding differences in invasive potential among sister lineages.

  4. 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.
    Free, publicly-accessible full text available December 1, 2022
  5. Battistuzzi, Fabia Ursula (Ed.)
    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.
  6. Free, publicly-accessible full text available August 1, 2023
  7. Free, publicly-accessible full text available August 1, 2023
  8. Abstract We present the analysis and results of the first datasetcollected with the MARS neutron detectordeployed at the Oak Ridge NationalLaboratory Spallation Neutron Source (SNS) for the purpose ofmonitoring and characterizing the beam-related neutron (BRN) backgroundfor the COHERENT collaboration. MARS was positionednext to the COH-CsI coherent elastic neutrino-nucleus scattering detectorin the SNS basement corridor. This is the basement location ofclosest proximity to the SNS target and thus, of highest neutrino flux,but it is also well shielded from the BRN flux by infill concreteand gravel. These data show the detector registered roughly one BRN per day.Using MARS' measured detection efficiency, the incomingBRN flux is estimated to be 1.20 ± 0.56 neutrons/m^2/MWhfor neutron energies above ∼3.5 MeV and up to a few tens of MeV.We compare our results with previous BRN measurements in the SNS basement corridorreported by other neutron detectors.
    Free, publicly-accessible full text available March 1, 2023