Allison Y. Hsiang

Towards a morphological metric of assemblage dynamics in the fossil record: a test case using planktonic foraminifera.

With a glance, even the novice naturalist can tell you something about the ecology of a given ecosystem. This is because the morphology of individuals reflects their evolutionary history and ecology, and imparts a distinct ‘look’ to communities—making it possible to immediately discern between deserts and forests, or coral reefs and abyssal plains. Once quantified, morphology can provide a common metric for characterizing communities across space and time and, if measured rapidly, serve as a powerful tool for quantifying biotic dynamics. Here, we present and test a new high-throughput approach for analysing community shape in the fossil record using semi-three-dimensional (3D) morphometrics from vertically stacked images (light microscopic or photogrammetric). We assess the potential informativeness of community morphology in a first analysis of the relationship between 3D morphology, ecology and phylogeny in 16 extant species of planktonic foraminifera—an abundant group in the marine fossil record—and in a preliminary comparison of four assemblages from the North Atlantic. In the species examined, phylogenetic relatedness was most closely correlated with ecology, with all three ecological traits examined (depth habitat, symbiont ecology and biogeography) showing significant phylogenetic signal. By contrast, morphological trees (based on 3D shape similarity) were relatively distantly related to both ecology and phylogeny. Although improvements are needed to realize the full utility of community morphometrics, our approach already provides robust volumetric measurements of assemblage size, a key ecological characteristic.

AutoMorph: Accelerating morphometrics with automated 2D and 3D image processing and shape extraction

Large-scale, comparative studies of morphological variation are rare due to the time-intensive nature of shape quantification. This data gap is important to address, as intraspecific and interspecific morphological variation underpins and reflects ecological and evolutionary processes. Here, we detail a novel software package, AutoMorph, for high-throughput object and shape extraction. AutoMorph can batch image many types of organisms (e.g. foraminifera, molluscs and fish teeth), allowing for rapid generation of assemblage-scale morphological data. We used AutoMorph to image and generate 2D and 3D morphological data for >100,000 marine microfossils in about a year. Our collaborators have used AutoMorph to process >12,000 patellogastropod shells and >50,000 fish teeth. AutoMorph allows users to rapidly produce large amounts of morphological data, facilitating community-scale evolutionary and ecological studies. To hasten the adoption of automated approaches, we have made AutoMorph freely available and open source. AutoMorph runs on all UNIX-like systems; future versions will run across all platforms.

Sixty-one thousand recent planktonic foraminifera from the Atlantic Ocean

Marine microfossils record the environmental, ecological, and evolutionary dynamics of past oceans in temporally expanded sedimentary archives. Rapid imaging approaches provide a means of exploiting the primary advantage of this archive, the vast number of fossils, for evolution and ecology. Here we provide the first large scale image and 2D and 3D shape dataset of modern planktonic foraminifera, a major microfossil group, from 34 Atlantic Ocean sediment samples. Information on more than 124,000 objects is provided, including general object classification for 4/5ths of the dataset (~ 99,000 objects). Of the ~ 99,000 classifications provided, more than 61,000 are complete or damaged planktonic foraminifera. Objects also include benthic foraminifera, ostracods, pteropods, spicules, and planktonic foraminifera test fragments, among others. This dataset is the first major microfossil output of a new high-throughput imaging method (AutoMorph) developed to extract 2D and 3D data from photographic images of fossils. Our sample preparation and imaging techniques are described in detail. The data provided here comprises the most extensive publically available archive of planktonic foraminiferal morphology and morphological variation to date.

Twelve thousand recent patellogastropods from a northeastern Pacific latitudinal gradient

Body size distributions can vary widely among communities, with important implications for ecological dynamics, energetics, and evolutionary history. Here we present a dataset of body size and shape for 12,035 extant Patellogastropoda (true limpet) specimens from the collections of the University of California Museum of Paleontology, compiled using a novel high-throughput morphometric imaging method. These specimens were collected over the past 150 years at 355 localities along a latitudinal gradient ranging from Alaska to Baja California, Mexico and are presented here with individual images, 2D outline coordinates, and 2D measurements of body size and shape. This dataset provides a resource for assemblage-scale macroecological questions and documents the size and diversity of recent patellogastropods in the northeastern Pacific.

A North American stem turaco, and the complex biogeographic history of modern birds

BackgroundEarth’s lower latitudes boast the majority of extant avian species-level and higher-order diversity, with many deeply diverging clades restricted to vestiges of Gondwana. However, palaeontological analyses reveal that many avian crown clades with restricted extant distributions had stem group relatives in very different parts of the world.ResultsOur phylogenetic analyses support the enigmatic fossil bird Foro panarium Olson 1992 from the early Eocene (Wasatchian) of Wyoming as a stem turaco (Neornithes: Pan-Musophagidae), a clade that is presently endemic to sub-Saharan Africa. Our analyses offer the first well-supported evidence for a stem musophagid (and therefore a useful fossil calibration for avian molecular divergence analyses), and reveal surprising new information on the early morphology and biogeography of this clade. Total-clade Musophagidae is identified as a potential participant in dispersal via the recently proposed ‘North American Gateway’ during the Palaeogene, and new biogeographic analyses illustrate the importance of the fossil record in revealing the complex historical biogeography of crown birds across geological timescales.ConclusionsIn the Palaeogene, total-clade Musophagidae was distributed well outside the range of crown Musophagidae in the present day. This observation is consistent with similar biogeographic observations for numerous other modern bird clades, illustrating shortcomings of historical biogeographic analyses that do not incorporate information from the avian fossil record.