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

Freshwater Testate Amoebae (Arcellinida) Response to Eutrophication as Revealed by Test Size and Shape Indices

We review the potential for applying traits-based approaches to freshwater testate amoeba, a diverse protist group that are abundant in lakes and are valuable ecological indicators. We investigated the efficacy of geometric morphometric analysis to define Arcellinida test size and shape indices that could summarize freshwater testate amoeba community dynamics along a temporal gradient of eutrophication in Loch Leven, Scotland (United Kingdom). A cluster analysis of test size and shape indices yielded three clusters, each dominated by a single shape: elongate, spherical and ovoid. When plotted stratigraphically, we observed increases in spherical tests, decreases in elongate tests and shrinking of test size coeval with eutrophication in Loch Leven. Decreases in the elongate cluster may reflect benthic conditions with reduced oxygen levels, while increases in the spherical cluster are likely associated with an expanding macrophyte community that promoted pelagic and epibiotic life habits. Shrinking of test size may be a stress response to eutrophication and/or warming temperatures. Tracking community dynamics using test size and shape indices was found to be as effective as using species-based approaches to summarize key palaeolimnological changes, with the added benefits of being free from taxonomic bias and error. The approach thus shows significant potential for future studies of aquatic community change in nutrient impacted lakes.

A Bayesian extension of phylogenetic generalized least squares: Incorporating uncertainty in the comparative study of trait relationships and evolutionary rates

Phylogenetic comparative methods use tree topology, branch lengths, and models of phenotypic change to take into account nonindependence in statistical analysis. However, these methods normally assume that trees and models are known without error. Approaches relying on evolutionary regimes also assume specific distributions of character states across a tree, which often result from ancestral state reconstructions that are subject to uncertainty. Several methods have been proposed to deal with some of these sources of uncertainty, but approaches accounting for all of them are less common. Here, we show how Bayesian statistics facilitates this task while relaxing the homogeneous rate assumption of the well-known phylogenetic generalized least squares (PGLS) framework. This Bayesian formulation allows uncertainty about phylogeny, evolutionary regimes, or other statistical parameters to be taken into account for studies as simple as testing for coevolution in two traits or as complex as testing whether bursts of phenotypic change are associated with evolutionary shifts in intertrait correlations. A mixture of validation approaches indicates that the approach has good inferential properties and predictive performance. We provide suggestions for implementation and show its usefulness by exploring the coevolution of ankle posture and forefoot proportions in Carnivora.

Evolutionary Transition in the Late Neogene Planktonic Foraminiferal Genus Truncorotalia

The fossil record provides empirical patterns of morphological change through time and is central to the study of the tempo and mode of evolution. Here we apply likelihood-based time-series analyses to the near-continuous fossil record of Neogene planktonic foraminifera and reveal a morphological shift along the Truncorotalia lineage. Based on a geometric morphometric dataset of 1,459 specimens, spanning 5.9–4.5 Ma, we recover a shift in the mode of evolution from a disparate latest Miocene morphospace to a highly constrained early Pliocene morphospace. Our recovered dynamics are consistent with those stipulated by Simpson's quantum evolution and Eldredge-Gould's punctuated equilibria and supports previous suppositions that even within a single lineage, evolutionary dynamics require a multi-parameter model framework to describe. We show that foraminiferal lineages are not necessarily gradual and can experience significant and rapid transitions along their evolutionary trajectories and reaffirm the utility of multivariate datasets for their future research.

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Evolution of planktonic foraminiferal anatomy across Miocene/Pliocene boundary

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Novel application of multivariate analyses to 1,459 specimens

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Evidence for a punctuated anatomical shift associated with the boundary

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.

Evolutionary history biases inferences of ecology and environment from δ13C but not δ18O values

Closely related taxa are, on average, more similar in terms of their physiology, morphology and ecology than distantly related ones. How this biological similarity affects geochemical signals, and their interpretations, has yet to be tested in an explicitly evolutionary framework. Here we compile and analyze planktonic foraminiferal size-specific stable carbon and oxygen isotope values (δ¹³C and δ¹⁸O, respectively) spanning the last 107 million years. After controlling for dominant drivers of size-δ¹³C and size-δ¹⁸O trends, such as geological preservation, presence of algal photosymbionts, and global environmental changes, we identify that shared evolutionary history has shaped the evolution of species-specific vital effects in δ¹³C, but not in δ¹⁸O. Our results lay the groundwork for using a phylogenetic approach to correct species δ¹³C vital effects through time, thereby reducing systematic biases in interpretations of long-term δ¹³C records—a key measure of holistic organismal biology and of the global carbon cycle.

The effects of biological similarity on geochemical signals recorded in planktonic foraminiferal tests used in paleo-reconstructions remains unclear. Here, the authors embed species-specific vital effect offsets in evolutionary models and show how shared evolutionary history shapes δ¹³C, but not δ¹⁸O values.

Biodiversity-ecosystem functioning relationships in long-term time series and palaeoecological records: deep sea as a test bed

The link between biodiversity and ecosystem functioning (BEF) over long temporal scales is poorly understood. Here, we investigate biological monitoring and palaeoecological records on decadal, centennial and millennial time scales from a BEF framework by using deep sea, soft-sediment environments as a test bed. Results generally show positive BEF relationships, in agreement with BEF studies based on present-day spatial analyses and short-term manipulative experiments. However, the deep-sea BEF relationship is much noisier across longer time scales compared with modern observational studies. We also demonstrate with palaeoecological time-series data that a larger species pool does not enhance ecosystem stability through time, whereas higher abundance as an indicator of higher ecosystem functioning may enhance ecosystem stability. These results suggest that BEF relationships are potentially time scale-dependent. Environmental impacts on biodiversity and ecosystem functioning may be much stronger than biodiversity impacts on ecosystem functioning at long, decadal-millennial, time scales. Longer time scale perspectives, including palaeoecological and ecosystem monitoring data, are critical for predicting future BEF relationships on a rapidly changing planet.

The impact of Cenozoic cooling on assemblage diversity in planktonic foraminifera

The Cenozoic planktonic foraminifera (PF) (calcareous zooplankton) have arguably the most detailed fossil record of any group. The quality of this record allows models of environmental controls on macroecology, developed for Recent assemblages, to be tested on intervals with profoundly different climatic conditions. These analyses shed light on the role of long-term global cooling in establishing the modern latitudinal diversity gradient (LDG)--one of the most powerful generalizations in biogeography and macroecology. Here, we test the transferability of environment-diversity models developed for modern PF assemblages to the Eocene epoch (approx. 56-34 Ma), a time of pronounced global warmth. Environmental variables from global climate models are combined with Recent environment-diversity models to predict Eocene richness gradients, which are then compared with observed patterns. The results indicate the modern LDG--lower richness towards the poles--developed through the Eocene. Three possible causes are suggested for the mismatch between statistical model predictions and data in the Early Eocene: the environmental estimates are inaccurate, the statistical model misses a relevant variable, or the intercorrelations among facets of diversity--e.g. richness, evenness, functional diversity--have changed over geological time. By the Late Eocene, environment-diversity relationships were much more similar to those found today.

The challenges to inferring the regulators of biodiversity in deep time

Attempts to infer the ecological drivers of macroevolution in deep time have long drawn inspiration from work on extant systems, but long-term evolutionary and geological changes complicate the simple extrapolation of such theory. Recent efforts to incorporate a more informed ecology into macroevolution have moved beyond the descriptive, seeking to isolate generating mechanisms and produce testable hypotheses of how groups of organisms usurp each other or coexist over vast timespans. This theme issue aims to exemplify this progress, providing a series of case studies of how novel modelling approaches are helping infer the regulators of biodiversity in deep time. In this Introduction, we explore the challenges of these new approaches. First, we discuss how our choices of taxonomic units have implications for the conclusions drawn. Second, we emphasize the need to embrace the interdependence of biotic and abiotic changes, because no living organism ignores its environment. Third, in the light of parts 1 and 2, we discuss the set of dynamic signatures that we might expect to observe in the fossil record. Finally, we ask whether these dynamics represent the most ecologically informative foci for research efforts aimed at inferring the regulators of biodiversity in deep time. The papers in this theme issue contribute in each of these areas.