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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. 

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. 

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. 

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. 

Abstract Evolvability is best addressed from a multi-level, macroevolutionary perspective through a comparative approach that tests for among-clade differences in phenotypic diversification in response to an opportunity, such as encountered after a mass extinction, entering a new adaptive zone, or entering a new geographic area. Analyzing the dynamics of clades under similar environmental conditions can (partially) factor out shared external drivers to recognize intrinsic differences in evolvability, aiming for a macroevolutionary analog of a common-garden experiment. Analyses will be most powerful when integrating neontological and paleontological data: determining differences among extant populations that can be hypothesized to generate large-scale, long-term contrasts in evolvability among clades; or observing large-scale differences among clade histories that can by hypothesized to reflect contrasts in genetics and development observed directly in extant populations. However, many comparative analyses can be informative on their own, as explored in this overview. Differences in clade-level evolvability can be visualized in diversity-disparity plots, which can quantify positive and negative departures of phenotypic productivity from stochastic expectations scaled to taxonomic diversification. Factors that evidently can promote evolvability include modularity—when selection aligns with modular structure or with morphological integration patterns; pronounced ontogenetic changes in morphology, as in allometry or multiphase life cycles; genome size; and a variety of evolutionary novelties, which can also be evaluated using macroevolutionary lags between the acquisition of a trait and phenotypic diversification, and dead-clade-walking patterns that may signal a loss of evolvability when extrinsic factors can be excluded. High speciation rates may indirectly foster phenotypic evolvability, and vice versa. Mechanisms are controversial, but clade evolvability may be higher in the Cambrian, and possibly early in the history of clades at other times; in the tropics; and, for marine organisms, in shallow-water disturbed habitats. 

1. Unravelling why species richness shows such dramatic spatial variation is an ongoing challenge. Common to many theories is that increasing species richness (e.g. with latitude) requires a compensatory trade-off on an axis of species' ecology. Spatial variation in species richness may also affect genetic diversity if large numbers of coexisting, related species result in smaller population sizes. 2. Here, we test whether increasing species richness results in differential occupation of morphospace by the constituent species, or decreases species' genetic diversity. We test for two potential mechanisms of morphological accommodation: denser packing in ecomorphological space, and expansion of the space. We then test whether species differ in their nucleotide diversity depending on allopatry or sympatry with relatives, indicative of potential genetic consequences of coexistence that would reduce genetic diversity in sympatry. We ask these questions in a spatially explicit framework, using a global database of avian functional trait measurements in combination with >120,000 sequences downloaded from GenBank. 3. We find that higher species richness within families is not systematically correlated with either packing in morphological space or overdispersion but, at the Class level, we find a general positive relationship between packing and species richness, but that points sampled in the tropics have comparatively greater packing than temperate ones relative to their species richness. We find limited evidence that geographical co-occurrence with closely related species or tropical distributions decreases nucleotide diversity of nuclear genes; however, this requires further analysis. 4. Our results suggest that avian families can accumulate species regionally with minimal tradeoffs or cost, implying that external biotic factors do not limit species richness. 

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.