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Afrotheria, the superorder that includes aardvarks, elephants, elephant shrews, hyraxes, manatees, and tenrecs, is home to some of the most charismatic and well-studied animals on Earth. Here, we assemble a nearly taxonomically complete molecular timetree of Afrotheria using an integrative approach that combines a literature search for published timetrees,de novodating of untimed molecular phylogenies, and inference of timetrees from new alignments. The resulting timetree sheds light on the impact of the Cretaceous-Paleogene (K-Pg) role ∼66 million years ago in the diversification of Afrotherian orders. The earliest divergence in the timetree of Afrotherian mammals predates the K-Pg event by 12 million years, followed by five interordinal divergences that occurred gradually over a 16-million-year period encompassing the K-Pg event. 

Despite considerable work in recent years, pinpointing the time when angiosperms originated has been challenging. However, the rapid development of molecular clock methodology has provided new tools to resolve this conundrum. In particular, the fossilized birth-death model establishes a rich interplay between molecules and stratigraphy by incorporating fossils explicitly into dating analyses. In this study, we apply Bayesian node dating and the skyline fossilized birth-death model, which differ in how the calibration is applied, to estimate the crown age of angiosperms. Node dating analyses with different calibration strategies show that the posterior distribution is strongly constrained by the effective prior at the node of crown angiosperms, dominated by the maximum age constraint. Using the skyline fossilized birth-death model, we reveal that assigning different priors for origin time resulted in similar crown ages for angiosperms. Moreover, the oldest fossils play a significant role in time estimates, and the dating results are robust to sampling assumptions of extant taxa. Our dating analyses indicate a largely Triassic crown age (255–202 Ma) for angiosperms, the period when mammals, dinosaurs, and squamate reptiles first appeared, and highlight the potential of morphological data to redefine the timeline of angiosperms. 

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. 

Primary forests play a crucial role in providing essential ecosystem services and supporting biodiversity compared to secondary forests. With increasing threats from extreme climate events and human activities, monitoring primary forest loss is critical for understanding the impact of these threats on ecosystems and biodiversity. Dense time series data from remotely sensed satellite imagery allow us to track historical disturbances, making it an effective source for mapping primary forests over time. However, distinguishing between primary and secondary forests based on spectral-temporal information remains challenging as primary forests can show high resilience to certain natural disturbances (e.g., drought), and secondary forests may not have experienced any disturbance during the satellite observation period. In this context, this study aims to map primary forests on the Caribbean island of Hispaniola using the time series approach and resilience metrics given that primary forests tend to be more resilient than secondary forests. To achieve this, we used spectral-temporal features from COntinuous monitoring of Land Disturbance (COLD) algorithm based on all available Landsat data between 1984 and 2023. Additionally, a resilience map is generated from deseasonalized and detrended spectral observations using the lag-1 autocorrelation method. Then, a Random Forest model was employed to generate an annual primary forest map. 

Primary forest (PF) is critical in supporting biodiversity and mitigating greenhouse gas emissions. However, the continuous monitoring of PF loss through remote sensing time-series observations remains largely unexplored, particularly in undeveloped and developing countries. In this study, we use the COntinuous monitoring of Land Disturbance (COLD) algorithm and Landsat time-series data to quantify PF loss on the island of Hispaniola, including Haiti and the Dominican Republic, from 1996 to 2022. The major findings include: (1) Haiti experienced a more pronounced PF loss compared to the Dominican Republic despite its lower PF coverage. From 1996 to 2022, PF in Haiti decreased from 0.64% to 0.35%, while PF in Dominican Republic decreased from 7.17% to 4.89%. (2) PF loss is observed both inside and outside protected areas. In Haiti, more PF loss occurs within protected areas than outside those areas. In the Dominican Republic, PF loss rates inside and outside protected areas are comparable. (3) The mean topographic slope of PF shows an increasing trend through time in both Haiti and Dominican Republic, suggesting slope plays a key role in PF loss. Despite the disparities between Haiti and Dominican Republic in preserving PF, urgent conservation policies are needed for the whole island. The land cover maps framework can be extended beyond the island of Hispaniola to larger regions for evaluating the impacts of PF loss on biodiversity conservation and ecosystem services. 

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. 

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 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 

Motivation: Timetrees depict evolutionary relationships between species and the geological times of their divergence. Hundreds of research articles containing timetrees are published in scientific journals every year. The TimeTree project has been manually locating, curating, and synthesizing timetrees from these articles for almost two decades into a TimeTree of Life, delivered through a unique, userfriendly web interface (timetree.org). The manual process of finding articles containing timetrees is becoming increasingly expensive and time-consuming. So, we have explored the effectiveness of textmining approaches and developed optimizations to find research articles containing timetrees automatically. Results: We have developed an optimized machine learning (ML) system to determine if a research article contains an evolutionary timetree appropriate for inclusion in the TimeTree resource. We found that BERT classification fine-tuned on whole-text articles achieved an F1 score of 0.67, which we increased to 0.88 by text-mining article excerpts surrounding the mentioning of figures. The new method is implemented in the TimeTreeFinder tool, TTF, which automatically processes millions of articles to discover timetree-containing articles. We estimate that the TTF tool would produce twice as many timetree-containing articles as those discovered manually, whose inclusion in the TimeTree database would potentially double the knowledge accessible to a wider community. Manual inspection showed that the precision on out-of-distribution recently-published articles is 87%. This automation will speed up the collection and curation of timetrees with much lower human and time costs. Availability: https://github.com/marija-stanojevic/time-tree-classification Contact: {marija.stanojevic, s.kumar, zoran.obradovic}@temple.edu Supplementary information: Supplementary data are available at Bioinformatics online