Global sequencing of hundreds of thousands of genomes of Severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, has continued to reveal new genetic variants that are the key to unraveling its early evolutionary history and tracking its global spread over time. Here, we present the heretofore cryptic mutational history and spatiotemporal dynamics of SARS-CoV-2 from an analysis of thousands of high-quality genomes. We report the likely most recent common ancestor of SARS-CoV-2, reconstructed through a novel application and advancement of computational methods initially developed to infer the mutational history of tumor cells in a patient. This progenitor genome differs from genomes of the first coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections. However, multiple coronavirus infections in China and the USA harbored the progenitor genetic fingerprint in January 2020 and later, suggesting that the progenitor was spreading worldwide months before and after the first reported cases of COVID-19 in China. Mutations of the progenitor and its offshoots have produced many dominant coronavirus strains, which have spread episodically over time. Fingerprinting based on common mutations reveals that the same coronavirus lineage has dominated North America for most of the pandemic in 2020. There have been multiple replacements of predominant coronavirus strains in Europe and Asia and the continued presence of multiple high-frequency strains in Asia and North America. We have developed a continually updating dashboard of global evolution and spatiotemporal trends of SARS-CoV-2 spread (http://sars2evo.datamonkey.org/).

Severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, was quickly identified as the cause of COVID-19 disease soon after its earliest reports. The knowledge of the contemporary evolution of SARS-CoV-2 is urgently needed not only for a retrospective on how, when, and why COVID-19 has emerged and spread, but also for creating remedies through efforts of science, technology, medicine, and public policy. Global sequencing of thousands of genomes has revealed many common genetic variants, which are the key to unraveling the early evolutionary history of SARS-CoV-2 and tracking its global spread over time. However, our knowledge of fundamental events in the evolution and spread of this coronavirus remains grossly incomplete and highly uncertain. Here, we present the heretofore cryptic mutational history, phylogeny, and dynamics of SARS-CoV-2 from an analysis of tens of thousands of high-quality genomes. The reconstructed mutational progression is highly concordant with the timing of coronavirus sampling dates. It predicts the progenitor genome whose earliest offspring without any non-synonymous mutations were still spreading worldwide months after the report of COVID-19. Over time, mutations gave rise to seven major lineages that spread episodically, some of which arose in Europe and North America after the genesis of the ancestral lineages in China. Mutational barcoding establishes that North American coronaviruses harbor very different genome signatures than coronaviruses prevalent in Europe and Asia that have converged over time. These spatiotemporal patterns continue to evolve as the pandemic progresses and can be viewed live online.

Agathis was present in Patagonia ca. 2 million years after the K-Pg boundary, and the putative latest Cretaceous fossils suggest that the genus survived the K-Pg extinction. Agathis immortalis sp nov. is recovered in a stem position for the genus, while A. zamunerae (Eocene, Patagonia) is recovered as part of the crown. A Mesozoic divergence for the Araucariaceae crown group, previously challenged by molecular divergence estimates, is supported by the combined phylogenetic analyses including the fossil taxa.

Abstract:Pollinator visits to flowers of self-incompatible tropical trees are critical for plant fecundity. However, few studies have examined how much of the variance in tropical tree fecundity is explained by individual attributes of trees (e.g. number of flowers), and how much is due to contextual variables such as distances to nearest flowering neighbours. Using multiple regressions we examined the relative contributions of these factors to the pollination and fecundity of Goetzea elegans, a mainly self-incompatible tree endemic to Puerto Rico. We studied the largest wild population of the species during the peak flowering and collected data on the frequency of pollinator visits (N = 25 trees), and the fecundity of the whole population (N = 105), including the visitation rate of two pollinators (the honey bee Apis mellifera and the bananaquit Coereba flaveola), the total number of flowers produced by each tree, and the total fruit set and seed viability per tree. We also recorded the distance to flowering conspecifics and heterospecifics, and the height for each tree. Flower number had a strong positive effect on pollinator visitation, but distance to nearest neighbours was equally or more important than flower number in influencing fecundity. Also, competition for limited pollinators between G. elegans and other species has a stronger effect than the facilitation that conspecifics may provide. Our results suggest that pollinator visits and aspects of fecundity of G. elegans depend both on the attributes of individual plants, and on those of the community of other nearby plants.

The impact of introduced species on native organisms is one of the main conservation concerns around the world. To fully understand the effect of introduced pollinators on native plants, it is important to know the reproductive biology of the focal species, especially its pollination biology. In this study we examined the breeding system of the endangered tree Goetzea elegans (Solanaceae), and compared pollination effectiveness of the two main floral visitors, Coereba flaveola (an avian nectarivore), and Apis mellifera (the introduced European Honeybee). We assessed the breeding system of G. elegans by applying several pollination treatments to flowers of cultivated trees to test fruit set, seed set, and seed viability. We also examined the pollination efficiency of A. mellifera and C. flaveola , and compared all the treatments with positive and negative controls. Our results indicate that the introduced honeybee A. mellifera is as efficient as the native bird C. flaveola in pollinating the flowers of G. elegans. This study also showed that G. elegans requires cross–pollination for fruit and seed set, and to obtain high seed viability rates. Despite the fact that many studies report exotic species as detrimental for native organisms, we document a case where an introduced insect has a beneficial impact on the reproductive biology of an endangered tropical tree.