Bone need not remain an elephant in the room for radiocarbon dating

Radiocarbon (14C) analysis of skeletal remains by accelerator mass spectrometry is an essential tool in multiple branches of science. However, bone 14C dating results can be inconsistent and not comparable due to disparate laboratory pretreatment protocols that remove contamination. And, pretreatments are rarely discussed or reported by end-users, making it an ‘elephant in the room’ for Quaternary scientists. Through a questionnaire survey, I quantified consensus on the reliability of collagen pretreatments for 14C dating across 132 experts (25 countries). I discovered that while more than 95% of the audience was wary of contamination and would avoid gelatinization alone (minimum pretreatment used by most 14C facilities), 52% asked laboratories to choose the pretreatment method for them, and 58% could not rank the reliability of at least one pretreatment. Ultrafiltration was highly popular, and purification by XAD resins seemed restricted to American researchers. Isolating and dating the amino acid hydroxyproline was perceived as the most reliable pretreatment, but is expensive, time-consuming and not widely available. Solid evidence supports that only molecular-level dating accommodates all known bone contaminants and guarantees complete removal of humic and fulvic acids and conservation substances, with three key areas of progress: (i) innovation and more funded research is required to develop affordable analytical chemistry that can handle low-mass samples of collagen amino acids, (ii) a certification agency overseeing dating-quality control is needed to enhance methodological reproducibility and dating accuracy among laboratories, and (iii) more cross-disciplinary work with better 14C reporting etiquette will promote the integration of 14C dating across disciplines. Those developments could conclude long-standing debates based on low-accuracy data used to build chronologies for animal domestications, human/megafauna extirpations and migrations, archaeology, palaeoecology, palaeontology and palaeoclimate models.Herrando-Pérez, Salvado

Novel physiological data needed for progress in global change ecology

Studies examining the underlying causes of the distributions of species and their future trajectories under climate change have benefitted from the accumulation of measurements of thermal tolerance across the tree of life. However, gaps in the global coverage of heat-tolerance data for ectotherms persist on four critical fronts. First, most large-scale analyses treat heat tolerance as a fixed species trait despite that population-level variation can equal or exceed cross-species variation. Second, terrestrial non-arthropod invertebrates and aquatic ectotherms other than bony fish have been poorly sampled, particularly in boreal and tropical regions, the Indian Ocean and the mesopelagic-deep ocean. Third, the study of climate impacts on the heat tolerance of terrestrial ectotherms has often neglected the interaction of environmental temperatures with water availability. And fourth, the mechanisms driving the dependence of heat tolerance on oxygen supply-demand remain largely unknown. We contend that filling those data and knowledge gaps requires novel strategies for the ecophysiological sampling of the range of understudied populations and species that occupy the length of climatic gradients globally. Such developments are essential for comprehensively predicting species responses to climate change across aquatic and terrestrial biomes

Spatial climate patterns explain negligible variation in strength of compensatory density feedbacks in birds and mammals

The use of long-term population data to separate the demographic role of climate from density-modified demographic processes has become a major topic of ecological investigation over the last two decades. Although the ecological and evolutionary mechanisms that determine the strength of density feedbacks are now well understood, the degree to which climate gradients shape those processes across taxa and broad spatial scales remains unclear. Intuitively, harsh or highly variable environmental conditions should weaken compensatory density feedbacks because populations are hypothetically unable to achieve or maintain densities at which social and trophic interactions (e.g., competition, parasitism, predation, disease) might systematically reduce population growth. Here we investigate variation in the strength of compensatory density feedback, from long-term time series of abundance over 146 species of birds and mammals, in response to spatial gradients of broad-scale temperature precipitation variables covering 97 localities in 28 countries. We use information-theoretic metrics to rank phylogenetic generalized least-squares regression models that control for sample size (time-series length) and phylogenetic non-independence. Climatic factors explained < 1% of the remaining variation in density-feedback strength across species, with the highest non-control, model-averaged effect sizes related to extreme precipitation variables. We could not link our results directly to other published studies, because ecologists use contrasting responses, predictors and statistical approaches to correlate density feedback and climate--at the expense of comparability in a macroecological context. Censuses of multiple populations within a given species, and a priori knowledge of the spatial scales at which density feedbacks interact with climate, seem to be necessary to determine cross-taxa variation in this phenomenon. Despite the availability of robust modelling tools, the appropriate data have not yet been gathered for most species, meaning that we cannot yet make any robust generalisations about how demographic feedbacks interact with climate.Salvador Herrando-Pe, rez, Steven Delean, Barry W. Brook, Phillip Cassey, Corey J. A. Bradsha

A comprehensive database of quality-rated fossil ages for Sahul’s Quaternary vertebrates

Published: 19 July 2016The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of individual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery.Marta Rodríguez-Rey, y, Salvador Herrando-Pérez, Barry W. Brook, Frédérik Saltré, John Alroy, Nicholas Beeton, Michael I. Bird, Alan Cooper, Richard Gillespie, Zenobia Jacobs, Christopher N. Johnson, Gifford H. Miller, Gavin J. Prideaux, Richard G. Roberts, Chris S.M. Turney and Corey J.A. Bradsha

A comprehensive database of quality-rated fossil ages for Sahul's Quaternary vertebrates.

The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of individual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery

Ecology needs a convention of nomenclature

Many areas of science have adopted nomenclature rules that facilitate research and communication. In contrast, ecological terminology is constantly redefined across disciplines, plagued with synonymy and polysemy, and foundational terms (and the theories and hypotheses behind them) are overlooked. We contend that this situation handicaps the progress of ecology. We review the causes and consequences of terminological uncertainty and propose a convention of ecological nomenclature (CEN) as an indispensable requirement of ecological synthesis. The core components of a CEN are its endorsement by a transnational institution; a policy framework managed by an advisory committee; and a centralized, peer-reviewed revision of terminology whereby ecologists are proponents and users of a unique, open-access repository of terms, definitions, and ontologies. A CEN should become the basis of a cross-disciplinary platform of communication among ecologists, journals, and the public and aligns with the ongoing initiative toward data globalization in ecology and other disciplines.Salvador Herrando-Pérez, Barry W. Brook, and Corey J. A. Bradsha

ACDC, a global database of amphibian cytochrome-b sequences using reproducible curation for GenBank records

Genetic data are a crucial and exponentially growing resource across all biological sciences, yet curated databases are scarce. The widespread occurrence of sequence and (meta)data errors in public repositories calls for comprehensive improvements of curation protocols leading to robust research and downstream analyses. We collated and curated all available GenBank cytochrome-b sequences for amphibians, a benchmark marker in this globally declining vertebrate clade. The Amphibia’s Curated Database of Cytochrome-b (ACDC) consists of 36,514 sequences representing 2,309 species from 398 genera (median = 2 with 50% interquartile ranges of 1–7 species/genus). We updated the taxonomic identity of >4,800 sequences (ca. 13%) and found 2,359 (6%) conflicting sequences with 84% of the errors originating from taxonomic misidentifications. The database (accessible at https://doi.org/10.6084/m9.figshare.9944759) also includes an R script to replicate our study for other loci and taxonomic groups. We provide recommendations to improve genetic-data quality in public repositories and flag species for which there is a need for taxonomic refinement in the face of increased rate of amphibian extinctions in the Anthropocene

An optimized method for the extraction of ancient eukaryote DNA from marine sediments

Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo-communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead-beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica-solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size-selection of low molecular-weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead-beating, DNA binding in silica-solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post-library LMW size-selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data-processing protocol should improve quantitative paleo-monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.Linda Armbrecht, Salvador Herrando-Pérez, Raphael Eisenhofer, Gustaaf M. Hallegraeff, Christopher J. S. Bolch, Alan Coope