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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. 

Abstract Mass extinctions are natural experiments on the short- and long-term consequences of pushing biotas past breaking points, often with lasting effects on the structure and function of biodiversity. General properties of mass extinctions—exceptionally severe, taxonomically broad, global losses of taxa—are starting to come into focus through comparisons among dimensions of biodiversity, including morphological, functional, and phylogenetic diversity. Notably, functional diversity tends to persist despite severe losses of taxonomic diversity, whereas taxic and morphological losses may or may not be coupled. One of the biggest challenges in synthesizing and extracting general consequences of these events has been that they are often driven by multiple, interacting pressures, and the taxa and their traits vary among events, making it difficult to link single stressors to specific traits. Ongoing improvements in the taxonomic and stratigraphic resolution of these events for multiple clades will sharpen tests for selectivity and help to isolate hitchhiking effects, whereby organismal traits are carried by differential survival or extinction of taxa owing to other organismal or higher-level attributes, such as geographic-range size. Direct comparative analyses across multiple extinction events will also clarify the impacts of particular drivers on taxa, functional traits, and morphologies. It is not just the extinction filter that deserves attention, as the longer-term impact of extinctions derives in part from their ensuing rebounds. More work is needed to uncover the biotic and abiotic circumstances that spur some clades into re-diversification while relegating others to marginal shares of biodiversity. Combined insights from mass extinction filters and their rebounds bring a macroevolutionary view to approaching the biodiversity crisis in the Anthropocene, helping to pinpoint the clades, functional groups, and morphologies most vulnerable to extinction and failed rebounds. 

Abstract Many of the most dramatic patterns in biological diversity are created by “Perfect Storms” —rare combinations of mutually reinforcing factors that push origination, extinction, or diversity accommodation to extremes. These patterns include the strongest diversification events (e.g. the Cambrian Explosion of animal body plans), the proliferation of hyperdiverse clades (e.g. insects, angiosperms), the richest biodiversity hotspots (e.g. the New World Tropical Montane regions and the ocean's greatest diversity pump, the tropical West Pacific), and the most severe extinction events (e.g. the Big Five mass extinctions of the Phanerozoic). Human impacts on the modern biota are also a Perfect Storm, and both mitigation and restoration strategies should be framed accordingly, drawing on biodiversity's responses to multi-driver processes in the geologic past. This approach necessarily weighs contributing factors, identifying their often non-linear and time-dependent interactions, instead of searching for unitary causes. 

Abstract Marine bivalves are important components of ecosystems and exploited by humans for food across the world, but the intrinsic vulnerability of exploited bivalve species to global changes is poorly known. Here, we expand the list of shallow-marine bivalves known to be exploited worldwide, with 720 exploited bivalve species added beyond the 81 in the United Nations FAO Production Database, and investigate their diversity, distribution and extinction vulnerability using a metric based on ecological traits and evolutionary history. The added species shift the richness hotspot of exploited species from the northeast Atlantic to the west Pacific, with 55% of bivalve families being exploited, concentrated mostly in two major clades but all major body plans. We find that exploited species tend to be larger in size, occur in shallower waters, and have larger geographic and thermal ranges—the last two traits are known to confer extinction-resistance in marine bivalves. However, exploited bivalve species in certain regions such as the tropical east Atlantic and the temperate northeast and southeast Pacific, are among those with high intrinsic vulnerability and are a large fraction of regional faunal diversity. Our results pinpoint regional faunas and specific taxa of likely concern for management and conservation. 

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. 

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. 

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. 

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.