Key Line Of Evidence Research Articles

Linking and the Role of the Material Citation

Citing the specimens used to describe new species or augment existing taxa is integral to the scholarship of taxonomic and related biodiversity-oriented publications. These so-called material citations (Darwin Core Term MaterialCitation), linked to the natural history collections in which they are archived, are the mechanism by which readers may return to the source material upon which reported observations are based. This is integral to the scientific nature of the project of documenting global biodiversity. Material citation records typically contain such information as the location and date associated with the collection of a specimen, along with other data, and taxonomic identification. Thus, material citations are a key line of evidence for biodiversity informatics, along with other evidence classes such as database records of specimens archived in natural history collections, human observations not linked to specimens, and DNA sequences that may or may not be linked to a specimen. Natural history collections are not completely databased and records of some occurrences are only available as material citations. In other cases, material citations can be linked to the record of the physical specimen in a collections database. Taxonomic treatments, sections of publications documenting the features or distribution of a related group of organisms (Catapano 2019), may contain citations of DNA sequences, which can be linked to database records. There is potential for bidirectional linking that could contribute data elements or entire records to collections and DNA databases, based on content found in material citations. We compare material citations data to other major sources of biodiversity records (preserved specimens, human observations, and material samples). We present pilot project data that reconcile material citations with their database records, and track all material citations across the taxonomic history of a species.

Exploiting the Autozygome to Support Previously Published Mendelian Gene-Disease Associations: An Update.

There is a growing interest in standardizing gene-disease associations for the purpose of facilitating the proper classification of variants in the context of Mendelian diseases. One key line of evidence is the independent observation of pathogenic variants in unrelated individuals with similar phenotypes. Here, we expand on our previous effort to exploit the power of autozygosity to produce homozygous pathogenic variants that are otherwise very difficult to encounter in the homozygous state due to their rarity. The identification of such variants in genes with only tentative associations to Mendelian diseases can add to the existing evidence when observed in the context of compatible phenotypes. In this study, we report 20 homozygous variants in 18 genes (ADAMTS18, ARNT2, ASTN1, C3, DMBX1, DUT, GABRB3, GM2A, KIF12, LOXL3, NUP160, PTRHD1, RAP1GDS1, RHOBTB2, SIGMAR1, SPAST, TENM3, and WASHC5) that satisfy the ACMG classification for pathogenic/likely pathogenic if the involved genes had confirmed rather than tentative links to diseases. These variants were selected because they were truncating, founder with compelling segregation or supported by robust functional assays as with the DUT variant that we present its validation using yeast model. Our findings support the previously reported disease associations for these genes and represent a step toward their confirmation.

Symbiont arrangement and metabolism can explain high δ13C in Eocene planktonic foraminifera

Abstract An important question in climate modeling is whether carbon cycling is fundamentally different in warm versus cold climate states. A key line of evidence regarding this question comes from the unusually large difference in carbon-isotope values (δ13C) between shallow-dwelling muricate foraminifera and foraminifera living deeper in the water column in the Paleogene. This has been interpreted as evidence that warmer temperatures elevated the metabolic rates of carbon-recycling bacteria, resulting in a steeper gradient in the δ13C of dissolved inorganic carbon (δ13CDIC) and reduced carbon export. However, this interpretation depends on the assumption that vital effects—biological processes that bias foraminiferal δ13C—are constant throughout time. We test this assumption using a chemical model of the foraminiferal microenvironment and find that the hypothesized increase in metabolic rates should also increase vital effects, meaning that both Paleogene δ13CDIC gradients and the temperature dependence of metabolism must have been significantly lower than previously estimated. We further propose that muricate foraminifera may have evolved a novel “mat” strategy for photosymbiosis wherein symbionts rested on the muricae in a thin layer surrounding the shell. This hypothesis can explain both the function of muricae and the observed isotopic data without the need for any change in metabolism. Our work thus challenges existing interpretations of δ13C and provides a path forward to empirically test the magnitude of temperature-dependent metabolic change in the deep past.

Evaluating Formational Models for Late Archaic Shell Rings of the Southeastern United States Using Vertebrate Fauna From the St. Catherines Shell Ring, St. Catherines Island, Georgia

ABSTRACT Researchers debate the function of Late Archaic (ca. 2550 to 1800 cal BC) shell rings found along the coast of the southeastern United States. Numerous facets of archaeological assemblages have been investigated to resolve this debate; however, zooarchaeological collections, a key line of evidence towards understanding human behaviors resulting in the formation of these sites, often are ignored. To inform functional interpretations of shell rings, I examine and compare several measures of vertebrate collections from three discrete segments of the St. Catherines Shell Ring (9LI231), St. Catherines Island, Georgia, as well as collections from features in the interior of the ring. There are similarities among collections from different segments of this ring, indicating that formational processes were similar throughout the ring. Zooarchaeological collections from features within the interior of the ring differ from those collections of the ring itself. This suggests that activities within the interior of the ring differed from those leading to the ring's formation. These data, interpreted within current shell ring models, suggest that the St. Catherines Shell Ring formed gradually as village refuse accumulated. Evidence from zooarchaeological collections do not support models suggesting this ring formed through rapid accumulation from feasts or displays of social inequality.

Incorporating contaminant bioavailability into sediment quality assessment frameworks

The recently adopted sediment quality assessment framework for evaluating bay and estuarine sediments in the state of California incorporates bulk sediment chemistry as a key line of evidence (LOE) but does not address the bioavailability of measured contaminants. Thus, the chemistry-based LOE likely does not provide an accurate depiction of organism exposure in all cases, nor is it particularly well suited for assessment of causality. In recent years, several methods for evaluating the bioavailability of sediment-associated contaminants have emerged, which, if optimized and validated, could be applied to improve the applicability and broaden the scope of sediment quality assessment. Such methods include equilibrium-based biomimetic extractions using either passive sampling devices (PSDs) or measures of rapidly desorbing contaminant pools, which provide information compatible with existing mechanistic approaches. Currently, these methods show promise in relating bioaccessible chemicals to effects endpoints, including bioaccumulation of hydrophobic organic compounds and/or toxicity due to metals. Using these methods, a bioavailability LOE for organics is proposed based on PSD and equilibrium partitioning theory that can be employed as an independent LOE or in assessing causality in tiered toxicity identification evaluations. Current and future research should be aimed at comparing the performance of PSDs and their relationships with effects concentrations, field validation of the most promising methods, addressing contaminant mixtures, further developing the parameterization of the proposed bioavailability LOE, and providing a better understanding of the underlying diagenetic cycling of metal contaminants that lead to exposure, affect bioavailability, and drive adverse outcomes.

Dating the onset and nature of the Middle Permian Emeishan large igneous province eruptions in SW China using conodont biostratigraphy and its bearing on mantle plume uplift models

The Middle Permian Emeishan large igneous province of SW China has provided the quintessential example of the phenomenon of kilometre-scale pre-eruption domal uplift associated with mantle plume impingement on the base of the lithosphere. One key line of evidence is an interpreted zone of truncation of the platform carbonates belonging to the Maokou Formation that underlies the volcanic pile. Here we test this interpretation by conodont age dating the uppermost beds of the Maokou Formation in sections from Yunnan, Sichuan, Guizhou and Guangxi provinces, which span locations from the inner part of the igneous province to several hundred kilometres beyond its margins. The results show that eruptions began in the Jinogondolella altudaensis Zone (∼ 263 Ma) of the Middle Capitanian Stage and greatly increased in extent and volume in the J. xuanhanensis Zone (∼ 262 Ma). Pre-eruption uplift was muted, and most locations within the terrain and at many locations beyond its margins witnessed platform collapse (not uplift) with deep-water facies (radiolarian cherts and submarine fans) developing in the J. altudaensis Zone. The clearest evidence for an emergence surface occurs around the margins of the province in the J. xuanhanensis Zone. This is after the initial onset of eruptions and marks either a eustatic sequence boundary or a brief pulse of tectonic uplift contemporaneous with volcanism. As with recent studies on the basal volcanic successions of the Emeishan LIP, kilometre-scale plume-related domal uplift prior to Emeishan eruptions is not supported by these data; rather a more complex interaction between plume and lithosphere with minor localized uplift and subsidence is inferred.