Paleogene Ficus leaves from India and their implications for fig evolution and diversification

PREMISE

Ficus is a scientifically and economically important genus with abundant fossil records from the Paleocene to Pleistocene, but with an intriguing early evolutionary history that remains unresolved. Here, the foliage of three well-preserved figs is described from the early Paleogene succession of the Gurha mine, Rajasthan, India. These fossils provide new morphological data that strengthens our understanding of the past occurrences of Ficus and, alongside all validly published records of fossil figs, helps to trace the evolutionary history of figs.

METHODS

Fossils were identified and described by comparison with their closest modern analogs using the Nearest Living Relative (NLR) technique. Validated fig records are listed and categorized into six geological time frames. Modern precipitation data for the current distributions of NLRs were downloaded from the Climatic Research Unit Timeseries.

RESULTS

Fossil leaves assigned to three new species Ficus paleodicranostyla, F. paleovariegata, and F. paleoauriculata closely resemble their modern analogs based on leaf morphology. Reliable fossil records were used to hypothesize historical fig distributions and paleodispersal pathways. Precipitation data suggest higher precipitations at the fossil locality during the early Paleogene than at present.

CONCLUSIONS

The fossils described herein supplement fig fossil records known from other regions indicating that figs were widely diverse across low latitudes by the early Paleogene. These data support a Eurasian origin for figs, highlight a pivotal role for the Indian subcontinent during the early phase of fig diversification, and depict a perhumid-to-humid climate with high rainfall concordant with paleoclimate evidence from the Gurha mine.

Evidence of fungal decay in petrified legume wood from the Neogene of the Bengal Basin, India

Silicified fossil legume woods of Cynometroxylon Chowdhury & Ghosh collected from the Neogene (late Miocene) sediments of the Bengal Basin, eastern India, exhibit fungal decay seldom found in the fossil record. The wood possesses numerous perforate areas on the surface that seem to be the result of extensive fungal activity. In transverse section, the decayed areas (pockets) appear irregular to ellipsoidal in outline; in longitudinal section these areas of disrupted tissue are somewhat spindle-shaped. Individual pockets are randomly scattered throughout the secondary xylem or are restricted to a narrow zone. The aforesaid patterns of decay in fossil wood show similarities with that of white rot decay commonly produced by higher fungi, specifically basidiomycetes and ascomycetes. The host fossil wood harbors abundant ramifying and septate fungal hyphae with knob like swellings similar to pseudoclamps in basidiomycetes, and three-celled conidia-like reproductive structures. This record expands our current knowledge of wood decaying fungi-host plant interaction in the Neogene tropical forests of Peninsular India.

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it

INTRODUCTION

Data sharing is being increasingly required by journals and has been heralded as a solution to the 'replication crisis'.

OBJECTIVES

(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals' policies to those that publish the most metabolomics papers.

METHODS

A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.

RESULTS

Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.

CONCLUSION

Further efforts are required to improve data sharing in metabolomics.

Compliance with minimum information guidelines in public metabolomics repositories

The Metabolomics Standards Initiative (MSI) guidelines were first published in 2007. These guidelines provided reporting standards for all stages of metabolomics analysis: experimental design, biological context, chemical analysis and data processing. Since 2012, a series of public metabolomics databases and repositories, which accept the deposition of metabolomic datasets, have arisen. In this study, the compliance of 399 public data sets, from four major metabolomics data repositories, to the biological context MSI reporting standards was evaluated. None of the reporting standards were complied with in every publicly available study, although adherence rates varied greatly, from 0 to 97%. The plant minimum reporting standards were the most complied with and the microbial and in vitro were the least. Our results indicate the need for reassessment and revision of the existing MSI reporting standards.

The future of metabolomics in ELIXIR

Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases.

MetaboLights: An Open-Access Database Repository for Metabolomics Data

MetaboLights is the first general purpose, open-access database repository for cross-platform and cross-species metabolomics research at the European Bioinformatics Institute (EMBL-EBI). Based upon the open-source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e.g., MTBLS1) that can be used for publication reference. The MetaboLights Reference Layer associates metabolites with metabolomics studies in the archive and is extensively annotated with data fields such as structural and chemical information, NMR and MS spectra, target species, metabolic pathways, and reactions. The database is manually curated with no specific release schedules. MetaboLights is also recommended by journals for metabolomics data deposition. This unit provides a guide to using MetaboLights, downloading experimental data, and depositing metabolomics datasets using user-friendly submission tools.

Climate change and the evolution of high-latitude terrestrial vegetation and floras

Our understanding of polar vegetation and climate through time has expanded enormously in the past five years as a consequence of improved logistics, detailed studies of plant fossils in their proper sedimentological context, and the development of sophisticated physiognomic methods for extracting the climate signal present in plant fossil assemblages. These revelations are particularly timely in that climate change is most strongly expressed at the poles, and polar conditions play a critical role in determining global climate. By studying the evolution and change in polar vegetation, valuable insights on possible future biotic responses to global warming can be obtained.

Dinosaurs on the north slope, alaska: high latitude, latest cretaceous environments

Abundant skeletal remains demonstrate that lambeosaurine hadrosaurid, tyrannosaurid, and troodontid dinosaurs lived on the Alaskan North Slope during late Campanian-early Maestrichtian time (about 66 to 76 million years ago) in a deltaic environment dominated by herbaceous vegetation. The high ground terrestrial plant community was a mild- to cold-temperate forest composed of coniferous and broad leaf trees. The high paleolatitude (about 70 degrees to 85 degrees North) implies extreme seasonal variation in solar insolation, temperature, and herbivore food supply. Great distances of migration to contemporaneous evergreen floras and the presence of both juvenile and adult hadrosaurs suggest that they remained at high latitudes year-round. This challenges the hypothesis that short-term periods of darkness and temperature decrease resulting from a bolide impact caused dinosaurian extinction.

Uncertainty in predictions of the climate response to rising levels of greenhouse gases

The range of possibilities for future climate evolution needs to be taken into account when planning climate change mitigation and adaptation strategies. This requires ensembles of multi-decadal simulations to assess both chaotic climate variability and model response uncertainty. Statistical estimates of model response uncertainty, based on observations of recent climate change, admit climate sensitivities--defined as the equilibrium response of global mean temperature to doubling levels of atmospheric carbon dioxide--substantially greater than 5 K. But such strong responses are not used in ranges for future climate change because they have not been seen in general circulation models. Here we present results from the 'climateprediction.net' experiment, the first multi-thousand-member grand ensemble of simulations using a general circulation model and thereby explicitly resolving regional details. We find model versions as realistic as other state-of-the-art climate models but with climate sensitivities ranging from less than 2 K to more than 11 K. Models with such extreme sensitivities are critical for the study of the full range of possible responses of the climate system to rising greenhouse gas levels, and for assessing the risks associated with specific targets for stabilizing these levels.