Ecological structure of diversity-dependent diversification in Phanerozoic marine bivalves

Rigorous analysis of diversity-dependence—the hypothesis that the rate of proliferation of new species is inversely related to standing diversity—requires consideration of the ecology of the organisms in question. Differences between infaunal marine bivalves (living entirely within the sediment) and epifaunal forms (living partially or completely above the sediment–water interface) predict that these major ecological groups should have different diversity dynamics: epifaunal species may compete more intensely for space and be more susceptible to predation and physical disturbance. By comparing detrended standing diversity with rates of diversification, origination, and extinction in this exceptional fossil record, we find that epifaunal bivalves experienced significant, negative diversity-dependence in origination and net diversification, whereas infaunal forms show little appreciable relationship between diversity and evolutionary rates. This macroevolutionary contrast is robust to the time span over which dynamics are analysed, whether mass-extinction rebounds are included in the analysis, the treatment of stratigraphic ranges that are not maximally resolved, and the details of detrending. We also find that diversity-dependence persists over hundreds of millions of years, even though diversity itself rises nearly exponentially, belying the notion that diversity-dependence must imply equilibrial diversity dynamics

Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia)

Background Comparative morphology fundamentally relies on the orientation and alignment of specimens. In the era of geometric morphometrics, point-based homologies are commonly deployed to register specimens and their landmarks in a shared coordinate system. However, the number of point-based homologies commonly diminishes with increasing phylogenetic breadth. These situations invite alternative, often conflicting, approaches to alignment. The bivalve shell (Mollusca: Bivalvia) exemplifies a homologous structure with few universally homologous points—only one can be identified across the Class, the shell ‘beak’. Here, we develop an axis-based framework, grounded in the homology of shell features, to orient shells for landmark-based, comparative morphology. Methods Using 3D scans of species that span the disparity of shell morphology across the Class, multiple modes of scaling, translation, and rotation were applied to test for differences in shell shape. Point-based homologies were used to define body axes, which were then standardized to facilitate specimen alignment via rotation. Resulting alignments were compared using pairwise distances between specimen shapes as defined by surface semilandmarks. Results Analysis of 45 possible alignment schemes finds general conformity among the shape differences of ‘typical’ equilateral shells, but the shape differences among atypical shells can change considerably, particularly those with distinctive modes of growth. Each alignment corresponds to a hypothesis about the ecological, developmental, or evolutionary basis of morphological differences, but we suggest orientation via the hinge line for many analyses of shell shape across the Class, a formalization of the most common approach to morphometrics of shell form. This axis-based approach to aligning specimens facilitates the comparison of approximately continuous differences in shape among phylogenetically broad and morphologically disparate samples, not only within bivalves but across many other clades

Measuring Biodiversity and Extinction – Present and Past

How biodiversity is changing in our time represents a major concern for all organismal biologists. Anthropogenic changes to our planet are decreasing species diversity through the negative effects of pollution, habitat destruction, direct extirpation of species, and climate change. But major biotic changes – including those that have both increased and decreased species diversity – have happened before in Earth’s history. Biodiversity dynamics in past eras provide important context to understand ecological responses to current environmental change. The work of assessing biodiversity is woven into ecology, environmental science, conservation, paleontology, phylogenetics, evolutionary and developmental biology, and many other disciplines; yet, the absolute foundation of how we measure species diversity depends on taxonomy and systematics. The aspiration of this symposium, and complementary contributed talks, was to promote better understanding of our common goals and encourage future interdisciplinary discussion of biodiversity dynamics. The contributions in this collection of papers bring together a diverse group of speakers to confront several important themes. How can biologists best respond to the urgent need to identify and conserve diversity? How can we better communicate the nature of species across scientific disciplines? Where are the major gaps in knowledge about the diversity of living animal and plant groups, and what are the implications for understanding potential diversity loss? How can we effectively use the fossil record of past diversity and extinction to understand current biodiversity loss

sedie/bayside 2.0

Modeling the count of species described at first time point in the description series outside the autoregressive terms that model the remainder of the series

Investigations into 3D-printed nautiloid-inspired pressure housings

The shell of the chambered nautilus is one of the few examples in nature of a biologically derived one-atmosphere pressure housing, which the animal uses to maintain neutral buoyancy via a series of sealed chambers. Extant species such as Nautilus pompilius live at depths from 200 to 800 m, and similar depth ranges have been hypothesized for their hyper diverse but extinct relatives, the ammonoids. Given the evolutionary success of these molluscan clades, their complex shell morphologies may reveal pressure-tolerant geometries comparable to the ‘ideal’ ones currently used in deep-sea marine robotics: simple spheres and cylinders, which have minimized surface area to volume ratio and easier manufacturability. We modeled and empirically tested 3D-printed bioinspired pressure housings for deep-sea applications using high resolution stereolithography 3D printing. These designs were modeled on the shells of N. pompilius and were compared to conventional 3D-printed spheres with similar wall thicknesses and implodable volumes. Two nautilus-inspired models with internal supports designed after their septal walls (one concave, one convex) had a higher-pressure tolerance compared to hollow models, but none outperformed spherical models with the same outer-wall thickness. Although spheres outperform the nautilus-inspired housings, the methods developed here show that pressure housings with complex geometries can be printed by additive manufacturing and empirically tested. From a biological perspective, this method can be a new tool for empirically testing viable depth tolerances for extinct coiled cephalopod morphologies

High-throughput micro-CT scanning and deep learning segmentation workflow for analyses of shelly invertebrates and their fossils: Examples from marine Bivalvia

The largest source of empirical data on the history of life largely derives from the marine invertebrates. Their rich fossil record is an important testing ground for macroecological and macroevolutionary theory, but much of this historical biodiversity remains locked away in consolidated sediments. Manually preparing invertebrate fossils out of their matrix can require weeks to months of careful excavation and cannot guarantee the recovery of important features on specimens. Micro-CT is greatly improving our access to the morphologies of these fossils, but it remains difficult to digitally separate specimens from sediments of similar compositions, e.g., calcareous shells in a carbonate rich matrix. Here we provide a workflow for using deep learning—a subset of machine learning based on artificial neural networks—to augment the segmentation of these difficult fossils. We also provide a guide for bulk scanning fossil and Recent shells, with sizes ranging from 1 mm to 20 cm, enabling the rapid acquisition of large-scale 3D datasets for macroevolutionary and macroecological analyses (300–500 shells in 8 hours of scanning). We then illustrate how these approaches have been used to access new dimensions of morphology, allowing rigorous statistical testing of spatial and temporal patterns in morphological evolution, which open novel research directions in the history of life

Supplemental Material from Convergence and contingency in the evolution of a specialized mode of life: multiple origins and high disparity of rock-boring bivalves

Supporting text, figures and tables

Raw bivalve data for PERIL calculation

Raw data including valid taxonomy, extinction rate of families, geographic range size, and thermal niche, for the shallow-marine Recent Bivalvia, provided for calculation of PERIL scores