61st Annual Report on Research 2016

Four major efforts were carried out during the first year of ACS funding towards achieving the major goal of the proposal: the generation of a 72 million year long record of planktonic foraminiferal morphology (including an extensive image library). The four efforts include:

i) technical improvements to software and software usability

ii) completion of modern dataset

iii) ecological calibration and investigation of modern dataset

iv) generation of Cenozoic spanning foraminiferal slides and images

The goals and accomplishments of each target are discussed in turn.

i) Technical improvements to software and software usability

Allison Hsiang, a paid post-doctoral researcher on the grant, carried out major improvements to the 3D data generated by the AutoMorph software (our in-house software) to improve 3D data quality and extraction during the first year of funding. These efforts resulted in one published paper, one paper in review, and a generally more robust data processing pipeline openly available through GitHub: https://github.com/HullLab

Further improvements to our internal processing capacities (including batch image processing on the Yale high performance computing clusters) were facilitated by Kaylea Nelson, a scientific computing specialist supported by our department and by Yale University. These efforts to improve the software were furthered by an expanded range of AutoMorph test cases including limpets (led by S. Kahanamoku-Snelling), fish teeth (led by E. Sibert), and detailed foraminiferal calibrations (led by A. Brombacher). Although all the data for all three projects mentioned above were collected during the first year of the grant (and served to improve the software through expanded image handling routines, robust size checks, and improved glare handling), the manuscripts related to these 3-projects are in various stages of preparation and review and will be reported on during Year 2.

ii) Completion of modern dataset

Paleontological inferences over the past 72 million years depend on strong anchors with regards to modern morphologies and ecologies. To this end, we collected and cleaned an extensive, spatially explicit, dataset of modern planktonic foraminifera. This data was collected by Leanne Elder, a paid post-doctoral researcher on the project, and included sites spread throughout the Atlantic Ocean. Of the more than 124,000 objects imaged, we identified 61,000 planktonic foraminifera. This extensive dataset was completed and classified to the level of major group (e.g., planktonic foraminifera, benthic foraminfera, fragment, etc) during the first year of funding. The dataset is uploaded to the public repository Zenodo (https://zenodo.org) and will be locatable under the AutoMorph community once the manuscript is accepted for publication.

Major lessons were learned with regard to massive data handling, data quality control, and data cleaning, with the completion of this modern calibration dataset, that will be applied to the bulk processing of the Cenozoic dataset in Year 2.

iii) Ecological calibration and investigation of modern dataset

With an eye toward interpreting the Cenozoic results, two major projects were begun to interpret the modern morphological data: a comparison of body size across pelagic taxa and a detailed investigation of the body size trends within species of extant foraminifera. Major progress was made only on the first during Year 1 and is described here. In short, existing interpretations of body size change and morphological change in fossil groups over long periods of time are hampered by an incomplete understanding of the major drivers of these factors in modern taxa. We were surprised to realize that the drivers of body size variation in major pelagic groups (from foraminifera to krill to fish to marine mammals) had yet to be comprehensively investigated. Without this, it is difficult to say what changes in planktonic foraminifera over time mean for pelagic ecosystems as a whole. To bridge this gap, during the first year of the project we (P.M. Hull, L. Elder, A. Hsiang) worked with a macroecologist (E. Saupe from Oxford University) to assemble body size and range maps for pelagic heterotrophs with relatively complete data. The datasets were assembled in Year 1, and are being analyzed in Year 2.

iv) Generation of Cenozoic spanning foraminiferal slides and images

Post-doctoral researcher Leanne Elder also led the data collection efforts for the Cenozoic record in Year 1. Her accomplishments in this year include accumulating and sorting the potential sample set, and preparing and imaging a very low resolution (1 sample per 10 million year) slide collection.