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Abstract Siphons in bivalves have been postulated as a key adaptive trait, enabling modes of life inaccessible to asiphonate lineages, that afford better protection from predation and dislodgement, thereby enhancing their taxonomic diversification. To test the impact of siphons on diversity, we compared two bivalve clades with similar shell forms and life positions that differ in the presence/absence of this supposed key trait: the asiphonate Archiheterodonta (origin ~ 420 Myr ago) and the siphonate Veneridae (origin ~ 170 Myr ago). We measured three characters relevant to burrowing (shell length, cross-sectional area, and proportional shell volume) in these two groups, finding that siphonate venerids occupy more modes of life than archiheterodonts because they can live at a greater range of distances from the sediment–water interface, with the thinnest shells occurring in the deepest-burrowing groups. Asiphonate taxa have thicker shells, perhaps as a compensatory adaptation in response to the potential for exposure and attack because they are limited to shallower depths of burial. The lack of siphons may have impeded morphologic and taxonomic diversification in archiheterodonts. In contrast, siphons are consistent with a key adaptive trait in the Veneridae, evidently enabling taxonomic diversification into a greater range of morphologies. 

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. 

Evolutionary adaptation to novel, specialized modes of life is often associated with a close mapping of form to the new function, resulting in narrow morphological disparity. For bivalve molluscs, endolithy (rock-boring) has biomechanical requirements thought to diverge strongly from those of ancestral functions. However, endolithy in bivalves has originated at least eight times. Three-dimensional morphometric data representing 75 species from approximately 94% of extant endolithic genera and families, along with 310 non-endolithic species in those families, show that endolithy is evolutionarily accessible from many different morphological starting points. Although some endoliths appear to converge on certain shell morphologies, the range of endolith shell form is as broad as that belonging to any other bivalve substrate use. Nevertheless, endolithy is a taxon-poor function in Bivalvia today. This limited richness does not derive from origination within source clades having significantly low origination or high extinction rates, and today's endoliths are not confined to low-diversity biogeographic regions. Instead, endolithy may be limited by habitat availability. Both determinism (as reflected by convergence among distantly related taxa) and contingency (as reflected by the endoliths that remain close to the disparate morphologies of their source clades) underlie the occupation of endolith morphospace. 

Both the Cambrian explosion, more than half a billion years ago, and its Ordovician aftermath some 35 Myr later, are often framed as episodes of widespread ecological opportunity, but not all clades originating during this interval showed prolific rises in morphological or functional disparity. In a direct analysis of functional disparity, instead of the more commonly used proxy of morphological disparity, we find that ecological functions of Class Bivalvia arose concordantly with and even lagged behind taxonomic diversification, rather than the early-burst pattern expected for clades originating in supposedly open ecological landscapes. Unlike several other clades originating in the Cambrian explosion, the bivalves' belated acquisition of key anatomical novelties imposed a macroevolutionary lag, and even when those novelties evolved in the Early Ordovician, functional disparity never surpassed taxonomic diversity. Beyond this early period of animal evolution, the founding and subsequent diversification of new major clades and their functions might be expected to follow the pattern of the early bivalves—one where interactions between highly dynamic environmental and biotic landscapes and evolutionary contingencies need not promote prolific functional innovation. 

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. 

Modular evolution, the relatively independent evolution of body parts, may promote high morphological disparity in a clade. Conversely, integrated evolution via stronger covariation of parts may limit disparity. However, integration can also promote high disparity by channelling morphological evolution along lines of least resistance—a process that may be particularly important in the accumulation of disparity in the many invertebrate systems having accretionary growth. We use a time-calibrated phylogenetic hypothesis and high-density, three-dimensional semilandmarking to analyse the relationship between modularity, integration and disparity in the most diverse extant bivalve family: the Veneridae. In general, venerids have a simple, two-module parcellation of their body that is divided into features of the calcium carbonate shell and features of the internal soft anatomy. This division falls more along developmental than functional lines when placed in the context of bivalve anatomy and biomechanics. The venerid body is tightly integrated in absolute terms, but disparity appears to increase with modularity strength among subclades and ecologies. Thus, shifts towards more mosaic evolution beget higher morphological variance in this speciose family. 

Analyses of evolutionary dynamics depend on how phylogenetic data are time-scaled. Most analyses of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. This contrasts with budding, where nodes are calibrated using the younger first occurrence. Here, we use the extensive fossil record of bivalve molluscs for a large-scale evaluation of how branching models affect macroevolutionary analyses. We time-calibrated 91% of nodes, ranging in age from 2.59 to 485 Ma, in a phylogeny of 97 extant bivalve families. Allowing budding-based calibrations minimizes conflict between the tree and observed fossil record, and reduces the summed duration of inferred ‘ghost lineages’ from 6.76 billion years (Gyr; bifurcating model) to 1.00 Gyr (budding). Adding 31 extinct paraphyletic families raises ghost lineage totals to 7.86 Gyr (bifurcating) and 1.92 Gyr (budding), but incorporates more information to date divergences between lineages. Macroevolutionary analyses under a bifurcating model conflict with other palaeontological evidence on the magnitude of the end-Palaeozoic extinction, and strongly reduce Cenozoic diversification. Consideration of different branching models is essential when node-calibrating phylogenies, and for a major clade with a robust fossil record, a budding model appears more appropriate. 

Abstract The Veneridae are the most speciose modern family of bivalves, and one of the most morphologically conservative and homoplastic, making subfamily- and sometimes even genus-level classification difficult. The widespread Cretaceous genus Legumen Conrad, 1858 is currently placed in the subfamily Tapetinae of the Veneridae, although it more closely resembles the Solenoida (razor clams, Pharidae and Solenidae) in general shell form. Here we provide high-resolution images of the Legumen hinge for the first time. We confirm from hinge morphology that Legumen belongs in Veneridae, but it should be referred to incertae subfamiliae, rather than retained in the Tapetinae, particularly in light of the incomplete and unstable understanding of venerid systematics. Legumen represents a unique hinge dentition and a shell form—and associated life habit—that is absent in the modern Veneridae despite their taxonomic diversity. Veneridae are hyperdiverse in the modern fauna, but strikingly ‘under-disparate,’ having lost forms while gaining species in the long recovery from the end-Cretaceous extinction.