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Estimating speciation and extinction rates is essential for understanding past and present biodiversity, but is challenging given the incompleteness of the rock and fossil records. Interest in this topic has led to a divergent suite of independent methods—paleontological estimates based on sampled stratigraphic ranges and phylogenetic estimates based on the observed branching times in a given phylogeny of living species. The fossilized birth–death (FBD) process is a model that explicitly recognizes that the branching events in a phylogenetic tree and sampled fossils were generated by the same underlying diversification process. A crucial advantage of this model is that it incorporates the possibility that some species may never be sampled. Here, we present an FBD model that estimates tree-wide diversification rates from stratigraphic range data when the underlying phylogeny of the fossil taxa may be unknown. The model can be applied when only occurrence data for taxonomically identified fossils are available, but still accounts for the incomplete phylogenetic structure of the data. We tested this new model using simulations and focused on how inferences are impacted by incomplete fossil recovery. We compared our approach with a phylogenetic model that does not incorporate incomplete species sampling and to three fossil-based alternatives for estimating diversification rates, including the widely implemented boundary-crosser and three-timer methods. The results of our simulations demonstrate that estimates under the FBD model are robust and more accurate than the alternative methods, particularly when fossil data are sparse, as the FBD model incorporates incomplete species sampling explicitly.
The choice of measures used to estimate the richness of species, genera, or higher taxa is a crucial matter in paleobiology and ecology. This paper evaluates four methods called shareholder quorum subsampling, true richness estimated using a Poisson sampling model (TRiPS), squares, and the corrected first-order jackknife (cJ1). Quorum subsampling interpolates to produce a relative richness estimate, while the other three extrapolate to the size of the overall species pool. Here I use routine ecological data to show that squares and cJ1 pass several basic validation tests, but TRiPS does not. First, TRiPS estimates are insensitive to the shape of abundance distributions, being entirely predicted by total counts of species and of individuals regardless of the details. Furthermore, TRiPS tends not to extrapolate at all when sampling is moderate or intense. Second, all three extrapolators yield lower values when they work with small uniform subsamples of large raw inventories. The third test is a split-analyze-and-sum analysis: each inventory is divided between the most common and least common halves of the abundance distribution, the methods are applied to the half-inventories, and the estimates are summed. Squares and cJ1 perform well here, but TRiPS does not extrapolate as long as the full inventories are reasonably well-sampled. It is otherwise not particularly accurate. The extrapolators are largely insensitive to the influence of abundance distribution evenness, as quantified using Pielou's J and a new index called the ratio of means. Quorum subsampling generally performs well, but it stumbles on the split-analyze-and-sum test and is confounded somewhat by evenness.
One of the most remarkable differences between Paleogene penguins and their living relatives is the shape and length of their beaks. Many of the Eocene and Oligocene penguins have a thin and elongated spear-like bill, which contrasts with the proportionally shorter and more robust bill of most living species. These differences suggest an important shift in their feeding strategies. This study explores the morphological disparity on the skull of penguins, emphasizing bill morphology and it relationship with feeding habits. For this, the skulls of 118 species of aquatic birds, including 21 fossil and living penguins, were analyzed using two-dimensional geometric morphometric. The results show that, unlike what has been reported for modern birds overall, in penguins and Aequornithes, bill elongation is related to a reduction of the braincase. The discriminant analysis shows that there are significant differences between penguins that feed near or far from the coast and between those that consume nectonic and planktonic prey, identifying Madrynornis as the only extinct form with a possibly planktonic diet. Additionally, it is clear that Paleogene penguins occupy a region of morphospace unexplored by most diving birds, with the western grebe being their closest modern analogue. This is consistent with the hypothesis that giant penguins hunted by harpooning and not by biting as living forms do, signaling a significant change in the habits of those birds leading to the emergence of their crown group.
The Cenozoic genus Terebratula seems to be an exception to the post-Permian trend in brachiopod retreat to offshore habitats, because it was species rich and numerically abundant in warm-temperate shallow-water environments in the Mediterranean and the Paratethys realms. This was so despite the general dominance of bivalves and the pervasive bioturbation and predation pressure during the Neogene. Terebratula, however, went extinct in the Calabrian (Pleistocene). The optimal environmental conditions for Terebratula during its prime are poorly known. The Águilas Basin (SE Spain) is an ideal study area to investigate the habitat of Terebratula, because shell beds of this brachiopod occur there cyclically in early Pliocene deposits. We evaluate the paleoecological boundary conditions controlling the distribution of Terebratula by estimating its environmental tolerances using benthic and planktic foraminiferal and nannoplanktic assemblages and oxygen isotopes of the secondary layer brachiopod calcite. Our results suggest that Terebratula in the Águilas Basin favored oligotrophic to mesotrophic, well-oxygenated environments at water depths of 60–90 m. Planktic foraminiferal assemblages and oxygen isotopes point to sea-surface temperatures between ~16°C and 22°C, and bottom-water temperatures between 17°C and 24°C. The analyzed proxies indicate that Terebratula tolerated local variations in water depth, bottom temperature, oxygenation, productivity, and organic enrichment. Terebratula was probably excluded by grazing pressure from well-lit environments and preferentially occupied sediment-starved, current-swept upper offshore habitats where coralline red algae were absent. Narrow temperature ranges of Terebratula species might have been a disadvantage during the high-amplitude seawater temperature fluctuations that started about 1 Ma, when the genus went extinct.
Marine bryozoans have been members of benthic skeletal faunas since the Ordovician. These small suspension feeders collect particles in the range of 10 to 100 μm. Specific details of their feeding depend on the morphology of the feeding apparatus, which may be reflected in skeletal characters. While several studies have described the link between the skeletal and soft-body traits of gymnolaemate bryozoans, stenolaemates have received less attention. To fill this gap, we conducted a detailed analysis of morphometry within and across species and attempted to develop robust predictive models that can be used to infer the soft-body morphology from skeletal data. This, in turn, will help with extracting data on ecology of Paleozoic communities of suspension feeders from the extensive bryozoan fossil record. Characters of polypide morphology among New Zealand cyclostomates (single Recent order in Stenolaemata) displayed staggering variability and almost without exception were not connected to skeletal characters at the species level. When this variability is reduced to its central tendency, interspecific trends are more apparent. The relationship is positive, linear, and moderately strong, but the resulting models have wide predictive intervals (plus/minus hundreds of micrometers). A precise estimate of the characters of the feeding apparatus of modern, and especially fossil, stenolaemates may be difficult to attain, at least on the basis of the skeletal traits used here.
The seemingly aberrant coiling of heteromorphic ammonoids suggests that they underwent more significant changes in hydrostatic properties throughout ontogeny than their planispiral counterparts. Such changes may have been responses to different selective pressures at different life stages. The hydrostatic properties of three species of Didymoceras (D. stevensoni, D. nebrascense, and D. cheyennense) were investigated by creating virtual 3D models at several stages during growth. These models were used to compute the conditions for neutral buoyancy, hydrostatic stability, orientation during life, and thrust angles (efficiency of directional movement). These properties suggest that Didymoceras and similar heteromorphs lived low-energy lifestyles with the ability to hover above the seafloor. The resultant static orientations yielded a downward-facing aperture in the hatchling and a horizontally facing aperture throughout most of the juvenile stage, before terminating in an upward direction at maturity. Relatively high hydrostatic stabilities would not have permitted the orientation of Didymoceras to be considerably modified with active locomotion. During the helical phase, Didymoceras would have been poorly suited for horizontal movement, yet equipped to pirouette about the vertical axis. Two stages throughout growth, however, would have enhanced lateral mobility: a juvenile stage just after the formation of the first bend in the shell and the terminal stage after completion of the U-shaped hook. These two more mobile phases in ontogeny may have improved juvenile dispersal potential and mate acquisition during adulthood, respectively. In general, life orientation and hydrostatic stability change more wildly for these aberrantly coiled ammonoids than their planispiral counterparts.
Site-selectivity analysis of drilling predation traces may provide useful behavioral information concerning a predator interacting with its prey. However, traditional approaches exclude some spatial information (i.e., oversimplified trace position) and are dependent on the scale of analysis (e.g., arbitrary grid system used to divide the prey skeleton into sectors). Here we introduce the spatial point pattern analysis of traces (SPPAT), an approach for visualizing and quantifying the distribution of traces on shelled invertebrate prey, which includes improved collection of spatial information inherent to drillhole location (morphometric-based estimation), improved visualization of spatial trends (kernel density and hotspot mapping), and distance-based statistics for hypothesis testing (K-, L-, and pair correlation functions). We illustrate the SPPAT approach through case studies of fossil samples, modern beach-collected samples, and laboratory feeding trials of naticid gastropod predation on bivalve prey. Overall results show that kernel density and hotspot maps enable visualization of subtle variations in regions of the shell with higher density of predation traces, which can be combined with the maximum clustering distance metric to generate hypotheses on predatory behavior and anti-predatory responses of prey across time and geographic space. Distance-based statistics also capture the major features in the distribution of traces across the prey skeleton, including aggregated and segregated clusters, likely associated with different combinations of two modes of drilling predation, edge and wall drilling. The SPPAT approach is transferable to other paleoecologic and taphonomic data such as encrustation and bioerosion, allowing for standardized investigation of a wide range of biotic interactions.
A recent study by Saulsbury and colleagues assessed factors influencing growth coefficients in bivalves. Like many macroevolutionary studies that cover a wide range of taxa and environments, this study fails to account for important heterogeneity among taxa and among environments. Rankings of factors depend on the range of values sampled, patterns of allocation of energy to various competing functions, and whether taxa in any given clade are uniform in their growth coefficients. Heterogeneity is universal and must be taken into account in large-scale analyses.