Invited Essay
The oyster enigma variations: a hypothesis of microbial calcification
- Geerat J. Vermeij
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- 08 April 2016, pp. 1-13
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Oysters, whose inner shell layer contains chambers, vesicles, and sometimes chalky deposits, often have extraordinarily thick shells of large size, prompting the idea that there is something unusual about the process of shell fPormation in these and similarly structured bivalves with the oyster syndrome. I propose the hypothesis that calcifying microbes, especially sulfate-reducing bacteria growing on organic substrates in fluid-filled shell-wall chambers, are responsible for shell calcification away from the shell-secreting mantle of the host bivalve. Other phenomena, including the formation of cameral deposits in fossil cephalopods, the cementation of molluscs and barnacles to hard substrata, the formation of a calcified intriticalx on the shell's exterior, and cementation of objects by gastropods on the shell for camouflage, may also involve calcifying bacteria. Several lines of inquiry are suggested to test these hypotheses.
Articles
Spiral growth in Nephrolepidina: evidence of “golden selection”
- Andrea Benedetti
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- 08 April 2016, pp. 151-161
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Examination of the neanic apparatuses of known populations of Nephrolepidina praemarginata, N. morgani, and N. tournoueri reveals that the equatorial chamberlets are arranged in spirals, along the direction of connection of the oblique stolons, giving the optical effect of intersecting curves. In N. praemarginata commonly 34 left- and right-oriented primary spirals occur from the first annulus to the periphery, 21 secondary spirals from the third to fifth annulus, 13 ternary spirals from the fifth to eighth annulus, following the Fibonacci sequence.
The number of the spirals increases in larger specimens and in more embracing morphotypes, and especially in trybliolepidine specimens; the secondary and ternary spirals from the investigated N. praemarginata to N. tournoueri populations tend to start from more distal annuli. An interpretative model of the spiral growth of Nephrolepidina is attempted.
The angle formed by the basal annular stolon and distal oblique stolon in equatorial chamberlets ranges from 122° in N. praemarginata to mean values close to the golden angle (137.5°) in N. tournoueri.
The increase in the Fibonacci number of spirals during the evolution of the lineage, along with the disposition of the stolons between contiguous equatorial chamberlets, provides new evidence of evolutionary selection for specimens with optimally packed chamberlets.
Natural selection favors individuals with the most regular growth, which fills the equatorial space more efficiently, thus allowing these individuals to reach the adult stage faster. We refer to this new type of selection as “golden selection.”
Featured Article
Incubation time as an important influence on egg production and distribution into clutches for sauropod dinosaurs
- Graeme D. Ruxton, Geoffrey F. Birchard, D. Charles Deeming
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- 08 April 2016, pp. 323-330
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Individual egg size and clutch size of the largest of the dinosaurs (the sauropods) are both smaller than might be expected for such large oviparous organisms. We suggest that these effects can be understood in the light of likely incubation times of sauropod eggs. Using allometric relationships from extant birds and crocodilians, we estimate that time from laying to hatching was likely to have been 65–82 days. If total predation risk varies with length of incubation time, there may be egg sizes above which the advantages of larger initial hatchling size are outweighed by the increased risk of predation during the egg stage. Also, in seasonal environments there will often be a finite limit to the period over which environmental temperatures are high enough for egg development. Thus incubation time may have been an important constraint explaining the small individual size of sauropod eggs. We further suggest that for sauropods spatial dispersal of eggs in small clutches was an adaptive strategy to mitigate this high predation risk associated with long time of exposure in the egg stage. Such a dispersive strategy brings several benefits. Thus, incubation time may also be key to explaining the surprisingly small clutch sizes.
The Generification of the Fossil Record
- Jonathan R. Hendricks, Erin E. Saupe, Corinne E. Myers, Elizabeth J. Hermsen, Warren D. Allmon
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- 08 April 2016, pp. 511-528
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Many modern paleobiological analyses are conducted at the generic level, a practice predicated on the validity of genera as meaningful proxies for species. Uncritical application of genera in such analyses, however, has led—perhaps inadvertently—to the unjustified reification of genera in an evolutionary context. While the utility of genera as proxies for species in evolutionary studies should be evaluated as an empirical issue, in practice it is increasingly assumed (rather than demonstrated) that genera are suitable proxies for species. This is problematic on both ontological and epistemological grounds. Genera are arbitrarily circumscribed, non-equivalent, often paraphyletic, and sometimes polyphyletic collections of species. They are useful tools for communication but have no theoretical or biological reality of their own and, whether monophyletic or not, cannot themselves operate in the evolutionary process. Attributes considered important for understanding macroevolution—e.g., geographic ranges, niche breadths, and taxon durations—are frequently variable among species within genera and will be inflated at the generic level, especially in species-rich genera. Consequently, the meaning(s) of results attained at the generic level may not “trickle down” in any obvious way that elucidates our understanding of evolution at the species level. Ideally, then, evolutionary studies that are actually about species should be pursued using species-level data rather than proxy data tabulated using genera. Where genera are used, greater critical attention should be focused on the degree to which attributes tabulated at the generic level reflect biological properties and processes at the species level.
Articles
Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record
- David W. Bapst
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- 08 April 2016, pp. 331-351
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Phylogeny-based approaches can be used to infer diversification dynamics and the rate and pattern of trait change. Applying these analyses to fossil data often requires time-scaling a cladogram of morphotaxon relationships. Although several time-scaling methods have been developed for this purpose, the incomplete sampling of the fossil record can distort the apparent timing of branching. It is unclear how well different time-scaling methods reconstruct the true temporal relationships or how any such inaccuracy could affect tree-based evolutionary analyses. I developed process-based simulations of the fossil record that allow the comparison of approximated time-scaled trees to true time-scaled trees. I used this simulation framework to test the effect of time-scaling methods on the fidelity of several commonly applied tree-based analyses, across a range of simulation conditions. When the fidelity of time-scaling methods differed, the stochastic “cal3” time-scaling method with ancestral assignment produced preferable results. Estimating rates and models of continuous trait evolution was particularly sensitive to bias from scenarios that forced the insertion of many short branch lengths, a bias that is not solved by any of the considered time-scaling methods in all scenarios. The cal3 method of time-scaling can be recommended as the preferred time-scaling method among those tested, but caution must be exercised because tree-based analyses are prone to easily overlooked biases.
Identification of chitin in 200-million-year-old gastropod egg capsules
- Marcin Wysokowski, Michał Zatoń, Vasilii V. Bazhenov, Thomas Behm, Andre Ehrlich, Allison L. Stelling, Martin Hog, Hermann Ehrlich
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- 08 April 2016, pp. 529-540
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Chitin occurs in a variety of invertebrates, especially in arthropod cuticles, but is rarely reported in the fossil record. Although it has been detected in fossils as old as Middle Cambrian and Silurian, the majority of records come from much younger, Cenozoic deposits. In this paper, we report the preservation of chitin in Early Jurassic neritimorph gastropod egg capsules deposited in bivalve shells from prodelta-deltafront and nearshore paleoenvironments of the Holy Cross Mountains, Poland. We used a number of analytical methods to confirm the presence of chitin preserved in these ancient fossils. This is the first record of chitin preservation in Mesozoic deposits that, interestingly, do not follow the conventional Konservat-Lagerstätten manner of preserving soft-bodied and non-biomineralized organisms. We believe that deltaic settings characterized by episodic, high input of fluvial deposits, oligohaline conditions, and oxygen-poor microenvironment within the sediment—as well as early cementation of sediment infilling the shells—were crucial for chitin preservation. The preservation of chitin in such recalcitrant structures as egg capsules and deposits that formed outside conventional Konservat-Lagerstätten conditions renders it likely similar deposits may yield promise for discoveries of similar biological macromolecules.
Trends in shell fragmentation as evidence of mid-Paleozoic changes in marine predation
- Mariusz A. Salamon, Przemysław Gorzelak, Robert Niedźwiedzki, Dawid Trzęsiok, Tomasz K. Baumiller
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- 08 April 2016, pp. 14-23
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Recent observations indicate that shell fragmentation can be a useful tool in assessing crushing predation in marine communities. However, criteria for recognizing shell breakage caused by durophagous predators versus physical factors are still not well established. Here, we provide data from tumbling and aquarium experiments to argue that physical and biotic processes lead to different patterns of shell damage, specifically that angular shell fragments are good indicators of durophagous predation. Using such angular shell fragments as a predation proxy, we analyze data from 57 European Paleozoic localities spanning the Ordovician through the Mississippian. Our results reveal a significant increase in angular shell fragments (either occurring as isolated valves or present in regurgitalites) in the Mississippian. The timing of this increase is coincident with the increased diversity of crushing predators as well as marked anti-predatory changes in the architecture and mode of life of invertebrate prey observed after the end-Devonian Hangenberg extinction (359 Ma). More specifically, the observed trend in shell fragmentation constitutes strong and independent confirmation of a recently suggested end-Devonian changeover in the primary method of fish predation from shearing to crushing. These results also highlight the important effect of extinction events, not only on taxonomic diversity, but also on the nature of predator-prey interactions.
Diversification and diversity partitioning
- Michael Hautmann
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- 08 April 2016, pp. 162-176
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Model calculations predict that pathways of alpha- and beta-diversity in diversifying ecosystems notably differ depending on the relative role of competition, predation, positive effects of species' interactions, and environmental parameters. Four scenarios are discussed, in which alpha- and beta-diversity are modeled as a function of increasing gamma-diversity. The graphic illustration of this approach is herein called α-β-γ plot, in which the x-axis indicates increasing diversification rather than absolute time. In purely environmentally controlled systems, beta-diversity maintains near-maximum values throughout the diversification interval, whereas mean alpha-diversity increases linearly, with a slope being reciprocal to beta-diversity. A second scenario is based on the assumption that increasing richness will have predominantly positive effects on the addition of further species; here, alpha- and beta-diversity increase simultaneously (though not necessarily at the same rates) and without reaching a predictable upper limit. In ecosystems that are characterized by low competition between species, mean alpha-diversity asymptotically approaches a saturation level, whereas the increase in beta-diversity accelerates until alpha-diversity stagnates, and then continues to rise linearly. If competition is high, addition of species first increases beta-diversity until no further habitat contraction is possible, followed by a period in which alpha-diversity increase through adaptive divergence becomes the principal drive of diversification. Because there is a continuous transition between the late stage of the low-competition model and the early stage of the high-competition scenario, both can be combined in a single model of diversity partitioning under the premise of a diversity-dependent increase of competition. This summary model predicts three phases of diversity accumulation: (1) a niche overlap phase, (2) a habitat contraction phase, and (3) a niche differentiation phase. The models herein discussed provide a potential tool to assess the question which factors primary controlled the diversification of life over geological times.
The Probable Datum Method (PDM): a technique for estimating the age of origination or extinction of nannoplankton
- Jonathan D. Schueth, Klaus Keller, Timothy J. Bralower, Mark E. Patzkowsky
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- 08 April 2016, pp. 541-559
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Accurate interpretation of origination and extinction of fossil species is crucial to answering a variety of questions in paleontology. Fossil datums, the observed age of first or last occurrences, are subject to sampling error as a result of preservation and low abundances near range endpoints. This sampling error can cause local range offset, an age difference between the observed first or last occurrence of a species and its true origination or extinction. Here, we develop and test a new technique, the Probable Datum Method (PDM), that can be used to assess the extent of local range offset for nannofossil species. The PDM estimates the original abundance of a taxon and its probable true age of first or last occurrence. The PDM uses a model in which original abundance is related to count abundance through preservation and the counting process. This model is empirically parameterized, including an experimental determination of false positive and error rates of a nannofossil count. The model is simulated then inverted to estimate likely original abundance and true datum age from count abundance data. We first test the PDM in a positive control experiment with known parameter values. This experiment shows that the PDM is robust and returns known values accurately. Next we apply the method to the origination of nannoplankton after the Cretaceous/Paleogene boundary to test whether first occurrences were synchronous between widely spaced locations. The PDM results suggest that observed diachrony of K/Pg originations cannot be explained by the effects of local range offset; rather, in some cases they indicate truly diachronous first occurrences between localities. Although the technique was developed to analyze nannoplankton ranges, the statistical nature of the PDM, its experimentally derived parameters, and its parsimonious nature should make it applicable to many micropaleontological studies that interpret patterns of origination and extinction.
Featured Article
Analysis of periodicity of extinction using the 2012 geological timescale
- Adrian L. Melott, Richard K. Bambach
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- 08 April 2016, pp. 177-196
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Analysis of two independent data sets with increased taxonomic resolution (genera rather than families) using the revised 2012 timescale reveals that an extinction periodicity first detected by Raup and Sepkoski (1984) for only the post-Paleozoic actually runs through the entire Phanerozoic. Although there is not a local peak of extinction every 27 Myr, an excess of the fraction of genus extinction by interval follows a 27-Myr timing interval and differs from a random distribution at the p ∼ 0.02 level. A 27-Myr periodicity in the spectrum of interval lengths no longer appears, removing the question of a possible artifact arising from it. Using a method originally developed in Bambach (2006) we identify 19 intervals of marked extinction intensity, including mass extinctions, spanning the last 470 Myr (and with another six present in the Cambrian) and find that ten of the 19 lie within ±3 Myr of the maxima in the spacing of the 27-Myr periodicity, which differs from a random distribution at the p = 0.004 level. These 19 intervals of marked extinction intensity also preferentially occur during decreasing diversity phases of a well-known 62-Myr periodicity in diversity (16 of 19, p = 0.002). Both periodicities appear to enhance the likelihood of increased severity of extinction, but the cause of neither periodicity is known. Variation in the strength of the many suggested causes of extinction coupled to the variation in combined effect of the two different periodicities as they shift in and out of phase is surely one of the reasons that definitive comparative study of the causes of major extinction events is so elusive.
Articles
The environmental structure of trilobite morphological disparity
- Melanie J. Hopkins
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- 08 April 2016, pp. 352-373
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Despite the mounting evidence that taxonomic diversity dynamics are patterned environmentally and that taxonomic diversity and morphological disparity are decoupled both temporally and spatially in many clades, very little work has been done to assess whether disparity is also influenced by environment. Here I investigate whether trilobite disparity shows environmental patterning through time. I used the method developed by Simpson and Harnik (2009) for estimating latitudinal, substrate, and bathymetric affinities from fossil occurrence data, downloaded from the Paleobiology Database. This method has the advantages that the biological null hypothesis is explicitly separated from the expectation due to sampling, and that the posterior probability can be used to infer degree of preference for one habitat compared to another. To measure morphology, I used a data set of outlines of the trilobite cranidium from Foote (1993). Many of the species in this data set are not represented in the Paleobiology Database in sufficient numbers to assess species-level affinity for these taxa, but species-level affinity could be estimated with high fidelity by using genus-level affinities. Results show that cranidial morphological diversity was structured by environmental preferences of the taxa but the structure was complex and changed through time. In particular, there was little differentiation in morphospace around latitudinal, substrate, or bathymetric affinity during the Cambrian. In contrast, both diversification and expansion into previously unoccupied areas of morphospace during the Ordovician were dominated by tropical, deeper-water taxa.
Paleoecology of the K-Pg mass extinction survivor Guembelitria (Cushman): isotopic evidence from pristine foraminifera from Brazos River, Texas (Maastrichtian)
- Sarit Ashckenazi-Polivoda, Carmi Rak, Ahuva Almogi-Labin, Berner Zsolt, Ofer Ovadia, Sigal Abramovich
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- 08 April 2016, pp. 24-33
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The late Maastrichtian sediments of the Mullinax-1 and Mullinax-3 boreholes from Brazos River, Texas, offer pristine material. These cores are prime candidates for providing an extraordinary window into the ecology of Guembelitria, a key genus in the K/Pg mass extinction event, as well as information on the habitats of other neritic species. Stable oxygen and carbon isotope analyses were performed on six planktic species (Guembelitria cretacea, Globigerinelloides asper, Heterohelix globulosa, Paraspiroplecta navarroensis, Pseudoguembelina costulata, Rugoglobigerina rugosa) and three benthic genera (Gavelinella, Cibicides, and Lenticulina). Our records support the contention that Guembelitria was fully planktic, as indicated by its δ18O values, which overlap the other planktic species, despite its possible origin from a tychopelagic benthic ancestor. However, Guembelitria is distinctly ranked very low in δ13C values, which overlap the benthic records. The anomalously low δ13C values of Guembelitria may represent an isotopic disequilibrium due to fast shell growth, like in its modern analogue Gallitellia vivans. Another explanation may be that these values are attributable to a neustonic life mode in the uppermost part of the oceans, where photosynthesis is inhibited by high UV and the near absence of nutrients. Because these waters are not photosynthetically depleted, calcification using carbon directly from these waters should yield δ13C values consistent with those found in Guembelitria. The ecological strategy that Guembelitria species used to deal with the nutrient-poor surface-water environments was an opportunistic blooming during stressful times of Maastrichtian global warming events and later during the K-Pg catastrophe.
Ecological fidelity of functional traits based on species presence-absence in a modern mammalian bone assemblage (Amboseli, Kenya)
- Joshua H. Miller, Anna K. Behrensmeyer, Andrew Du, S. Kathleen Lyons, David Patterson, Anikó Tóth, Amelia Villaseñor, Erustus Kanga, Denné Reed
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- 08 April 2016, pp. 560-583
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Comparisons between modern death assemblages and their source communities have demonstrated fidelity to species diversity across a variety of environments and taxonomic groups. However, differential species preservation and collection (including body-size bias) in both modern and fossil death assemblages may still skew the representation of other important ecological characteristics. Here, we move beyond live-dead taxonomic fidelity and focus on the recovery of functional ecology (how species interact with their ecosystem) at the community level for a diverse non-volant mammal community (87 species; Amboseli, Kenya). We use published literature to characterize species, using four functional traits and their associated categorical attributes (i) dietary mode (11 attributes; e.g., browser, grazer), (ii) preferred feeding habitat (16 attributes; e.g., grassland, woodland), (iii) preferred sheltering habitat (17 attributes; e.g., grassland, underground cavity), and (iv) activity time (7 attributes; e.g., diurnal, nocturnal, nocturnally dominated crepuscular). For each functional ecological trait we compare the death assemblage's recovered richness and abundance structure of constituent functional attributes with those of the source community, using Jaccard similarity, Spearman's rho, and the Probability of Interspecific Encounter (evenness). We use Monte Carlo simulations to evaluate whether these empirical comparisons are significantly different from expectations calculated from randomized sampling of species from the source community. Results indicate that although the Amboseli death assemblage is significantly overrepresented by large-bodied species relative to the Amboseli source community, it captures many functional dimensions of the ecosystem within expectations of a randomized collection of species. Additional resampling simulations and logistic regressions further illustrate that the size bias inherent to the Amboseli death assemblage is not a major driver of deviations between the functional ecological properties of the death assemblage and its source community. Finally, the Amboseli death assemblage also enhances our understanding of the mammal community by adding nine species and two functional attributes previously unknown from the ecosystem.
Accurate and precise estimates of origination and extinction rates
- John Alroy
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- 08 April 2016, pp. 374-397
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Paleobiologists have used many different methods for estimating rates of origination and extinction. Unfortunately, all equations that consider entire age ranges are distorted by the Pull of the Recent, the Signor-Lipps effect, and simple edge effects. Attention has been paid recently to an equation of Foote's that considers counts of taxa either crossing the bottom and top of an interval or crossing one boundary but not the other. This generalized boundary-crosser (BC) method has important advantages but is still potentially subject to the major biases. The only published equation that circumvents all of them is the three-timer (3T) log ratio, which does so by focusing on a four-interval moving window. Although it is highly accurate it is noisy when turnover rates are very high or sampling is very poor. More precise values are yielded by a newly derived equation that uses the same counts. However, it also considers taxa sampled in a window's first and fourth intervals but missing from the third (i.e., gap-fillers). Simulations show that the 3T, gap-filler (GF), and BC equations yield identical values when sampling and turnover are uniform through time. When applied to Phanerozoic-scale marine animal data, 3T and GF agree well but the BC rates are systematically lower. The apparent reason is that (1) long-ranging but infrequently sampled genera are less likely to be split up by taxonomists and (2) the BC equation overweights taxa with long ranges. Thus, BC rates pertain more to rare genera that are likely to represent large clades whereas GF rates pertain more to actual species-level patterns. Given these results, all published turnover rates based either on genus-level data or on age ranges must be reconsidered because they may reflect taxonomic practices more strongly than the species-level dynamics of interest to biologists.
Diversification of mammals from the Miocene of Spain
- M. Soledad Domingo, Catherine Badgley, Beatriz Azanza, Daniel DeMiguel, M. Teresa Alberdi
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- 08 April 2016, pp. 197-221
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The mammalian fossil record of Spain is long and taxonomically well resolved, offering the most complete record of faunal change for the Neogene of Europe. We evaluated changes in diversification, composition, trophic structure, and size structure of large mammals over the middle and late Miocene with methods applied to this record for the first time, including ordination of fossil localities to improve temporal resolution and estimation of confidence intervals on taxa temporal ranges. By contrast, analysis within the traditional Mammal Neogene (MN) biochronology obscures important aspects of diversification. We used inferred temporal ranges of species and evaluated per capita rates of origination, extinction, diversification, and turnover over 0.5-Myr time intervals.
Three periods of significant faunal change occurred between 12.0 and 5.5 Ma: (1) From 12.0 to 10.5 Ma, elevated origination rates led to an increase in diversity without significant change in ecological structure. Immigrants and geographic-range shifts of species to lower latitudes during an interval of global cooling contributed to these faunal changes. (2) From 9.5 to 7.5 Ma, high extinction rates followed by high origination rates coincided with significant changes in taxonomic composition and ecological structure. These changes represent the Vallesian Crisis, with replacement of a fauna of forest affinities (with frugivores and browsers) by a fauna of open woodlands (with grazers and mixed feeders). (3) From 6.5 to 5.5 Ma, high extinction rates reduced diversity without substantial changes in ecological structure, and large mammal faunas became highly endemic across the northern Mediterranean region. This interval includes the Messinian Salinity Crisis, the desiccation of the Mediterranean basin. Extinction may have been caused by geographic isolation and aridification, with evolution of endemic lineages giving rise to new species in the early Pliocene. These distinct macroevolutionary patterns of faunal change correspond to different geographic scales of inferred climatic and tectonic drivers.
Effects of a high-risk environment on edge-drilling behavior: inference from Recent bivalves from the Red Sea
- Devapriya Chattopadhyay, Martin Zuschin, Adam Tomašových
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- 08 April 2016, pp. 34-49
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Edge-drilling is an unusual predation pattern in which a predatory gastropod drills a hole on the commissure between the valves of a bivalve. Although it is faster than wall drilling, it involves the potential risk of amputating the drilling organ. We therefore hypothesize that this risky strategy is advantageous only in environments where predators face high competition or predation pressure while feeding. The high frequency of edge-drilling (EDF, relative to the total number of drilled valves) in a diverse Recent bivalve assemblage from the Red Sea enables us to test this hypothesis, predicting (1) a low EDF in infaunal groups, (2) a high EDF in bivalves with elongated shape, (3) high incidence of edge-drilling in groups showing a high wall-drilling frequency, and (4) high EDF in shallow habitats. We evaluate these predictions based on >15,000 bivalve specimens. Among ecological attributes, we found substrate affinity and predation intensity of a species to be good predictors of edge-drilling incidence. Infaunal taxa with high length/width ratio have a low EDF, in accordance with our predictions. Predation intensity is also a significant predictor of edge-drilling; groups with high predation intensity show higher incidence of edge-drilling, confirming our prediction. Although water depth fails to show any significant effect on EDF, this analysis generally supports the high-risk hypothesis of edge-drilling incidence because shallow depths have considerable microhabitat variability. Classically the drill hole site selection has often been linked to predatory behavior. Our study indicates that prey attributes are also crucial in dictating the behavioral traits of a driller such as site selection. This calls for considering such details of the prey to fully understand predation in modern and fossil habitats. Moreover, this perspective is important for tackling the longstanding riddle of the limited temporal and spatial distribution of edge-drilling.
Heterochrony, dental ontogenetic diversity, and the circumvention of constraints in marsupial mammals and extinct relatives
- Analía M. Forasiepi, Marcelo R. Sánchez-Villagra
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- 08 April 2016, pp. 222-237
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In marsupial mammals and their extinct relatives—collectively, metatherians—only the last premolar is replaced, but the timing of dental eruption is variable within the group. Our knowledge of fossils metatherians is limited, but is critical to understanding several aspects of the evolution and morphological diversification of this clade. We analyzed the sequence of eruption of 76 specimens of metatherians, including Sparassodonta, an extinct clade of specialized carnivores from South America. In Sparassodonta (1) the P3/p3 erupt simultaneously, in common with some didelphids (in other didelphids, p3 erupts before P3, whereas in the remaining didelphids, some peramelids, one caenolestid, and Pucadelphys this order is reversed); (2) the upper and lower molars at the same locus erupt more in synchrony than in other carnivorous metatherians in which the lower molars clearly precede the upper equivalents; (3) the upper canine in thylacosmilids and proborhyaenids is hypselodont; (4) species with similar molar morphologies have different morphologies of the deciduous premolars, suggesting diverse diets among the juveniles of different taxa; (5) deciduous teeth are functional for a long period of time, with thylacosmilids even retaining a functional DP3 in the permanent dentition. The retention of the DP3 and the hypertrophied and hypselodont upper canine of thylacosmilids represent clear heterochronic shifts. Specializations in the timing of dental eruption and in the deciduous tooth shape of sparassodonts are evolutionary mechanisms that circumvent constraints imposed by the metatherian replacement pattern and increase morphological disparity during ontogeny.
A simple Bayesian method of inferring extinction
- John Alroy
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- Published online by Cambridge University Press:
- 08 April 2016, pp. 584-607
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Determining whether a species has gone extinct is a central problem in both paleobiology and conservation biology. Past literature has mostly employed equations that yield confidence intervals around the endpoints of temporal ranges. These frequentist methods calculate the chance of not having seen a species lately given that it is still alive (a conditional probability). However, any reasonable person would instead want to know the chance that a species is extinct given that it has not been seen (the posterior probability). Here, I present a simple Bayesian equation that estimates posteriors. It uninterestingly assumes that the sampling probability equals the frequency of sightings within the range. It interestingly sets the prior probability of going extinct during any one time interval (E) by assuming that extinction is an exponential decay process and there is a 50% chance a species has gone extinct by the end of its observed range. The range is first adjusted for undersampling by using a routine equation. Bayes' theorem is then used to compute the posterior for interval 1 (ε1), which becomes the prior for interval 2. The following posterior ε2 again incorporates E because extinction might have happened instead during interval 2. The posteriors are called “creeping-shadow-of-a-doubt values” to emphasize the uniquely iterative nature of the calculation. Simulations show that the method is highly accurate and precise given moderate to high sampling probabilities and otherwise conservative, robust to random variation in sampling, and able to detect extinction pulses after a short lag. Improving the method by having it consider clustering of sightings makes it highly resilient to trends in sampling. Example calculations involving recently extinct Costa Rican frogs and Maastrichtian ammonites show that the method helps to evaluate the status of critically endangered species and identify species likely to have gone extinct below some stratigraphic horizon.
Diversity and species abundance patterns of the Early Cambrian (Series 2, Stage 3) Chengjiang Biota from China
- Fangchen Zhao, Jean-Bernard Caron, David J. Bottjer, Shixue Hu, Zongjun Yin, Maoyan Zhu
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- 08 April 2016, pp. 50-69
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Lagerstätten from the Precambrian–Cambrian transition have traditionally been a relatively untapped resource for understanding the paleoecology of the “Cambrian explosion.” This quantitative paleoecological study is based on 10,238 fossil specimens belonging to 100 animal species, 11 phyla, and 15 ecological categories from the lower Cambrian (Series 2, Stage 3) Chengjiang biota (Mafang locality near Haikou, Yunnan Province, China). Fossils were systematically collected within a 2.5-meter-thick sequence divided into ten stratigraphic intervals. Each interval represents an induced time-averaged assemblage of various event (obrution) beds of unknown duration. Overall, the different fossil assemblages are taxonomically and ecologically similar, suggesting the presence of a single community type recurring throughout the Mafang section. The Mafang community is dominated by epibenthic vagile hunters or scavengers, sessile suspension feeders, and infaunal vagile hunters or scavengers represented primarily by arthropods, brachiopods, and priapulids, respectively. Most species have low abundance and low occurrence frequencies, whereas a few species are numerically abundant and occur frequently. Overall, in structure and ecology the Mafang community is comparable to the Middle Cambrian (Series 3, Stage 5) Burgess Shale biota (Walcott Quarry, Yoho National Park, British Columbia, Canada). This suggests that, despite variations in species identity within taxonomic and ecological groups, the structure and ecology of Cambrian Burgess Shale-type communities remained relatively stable until at least the Middle Cambrian (Series 3, Stage 5) in subtidal to relatively deep-water offshore settings in siliciclastic soft-substrate environments.
Differential drivers of benthic foraminiferal and molluscan community composition from a multivariate record of early Miocene environmental change
- Christina L. Belanger, Marites Villarosa Garcia
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- Published online by Cambridge University Press:
- 08 April 2016, pp. 398-416
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Climate changes are multivariate in nature, and disentangling the proximal drivers of biotic responses to paleoclimate events requires time series of multiple environmental proxies. We reconstruct a multivariate time series of local environmental change for the early Miocene Newport Member of the Astoria Formation (20.26–18 Ma), using proxies for temperature (δ18O), productivity (δ13C), organic carbon flux (Δδ13C), oxygenation (δ15N), and sedimentary grain size (% mud). Our data suggest increases in productivity and declines in oxygenation on the Oregon shelf during this interval of global warming. We evaluate the association of individual environmental factors, and combinations of factors, with changes in faunal composition observed in benthic foraminiferal and molluscan communities collected from the exact same sediments as the environmental data. The δ15N values are the most parsimonious correlates with major changes in foraminiferal composition, whereas molluscan composition is most closely related to δ13C values, suggesting that different components of the environment are influencing each group. When the proxies that have the best supported relationships with the faunal gradients are removed from the analyses to simulate the absence of those proxy data, significant relationships between the faunal gradients and the remaining environmental proxies can still be found. This suggests that environmental drivers can be incorrectly attributed to faunal changes when key proxy data are missing. Paleoecological studies of biotic response that test multiple environmental drivers for multiple taxonomic groups are powerful tools for identifying the ecological consequences of past warming events and the regional drivers of ecological changes.