Many marine fish species are experiencing population declines, but their extinction risk profiles are largely understudied in comparison to their terrestrial vertebrate counterparts. Selective extinction of marine fish species may result in rapid alteration of the structure and function of ocean ecosystems. In this study, we compiled an ecological trait dataset for 8,185 species of marine ray-finned fishes (class Actinopterygii) from FishBase and used phylogenetic generalized linear models to examine which ecological traits are associated with increased extinction risk, based on the International Union for the Conservation of Nature Red List. We also assessed which threat types may be driving these species toward greater extinction risk and whether threatened species face a greater average number of threat types than non-threatened species. We found that larger body size and/or fishes with life histories involving movement between marine, brackish, and freshwater environments are associated with elevated extinction risk. Commercial harvesting threatens the greatest number of species, followed by pollution, development, and then climate change. We also found that threatened species, on average, face a significantly greater number of threat types than non-threatened species. These results can be used by resource managers to help address the heightened extinction risk patterns we found.

A central question in the study of mass extinction is whether these events simply intensify background extinction processes and patterns versus change the driving mechanisms and associated patterns of selectivity. Over the past two decades, aided by the development of new fossil occurrence databases, selectivity patterns associated with mass extinction have become increasingly well quantified and their differences from background patterns established. In general, differences in geographic range matter less during mass extinction than during background intervals, while differences in respiratory and circulatory anatomy that may correlate with tolerance to rapid change in oxygen availability, temperature, and pH show greater evidence of selectivity during mass extinction. The recent expansion of physiological experiments on living representatives of diverse clades and the development of simple, quantitative theories linking temperature and oxygen availability to the extent of viable habitat in the oceans have enabled the use of Earth system models to link geochemical proxy constraints on environmental change with quantitative predictions of the amount and biogeography of habitat loss. Early indications are that the interaction between physiological traits and environmental change can explain substantial proportions of observed extinction selectivity for at least some mass extinction events. A remaining challenge is quantifying the effects of primary extinction resulting from the limits of physiological tolerance versus secondary extinction resulting from the loss of taxa on which a given species depended ecologically. The calibration of physiology-based models to past extinction events will enhance their value in prediction and mitigation efforts related to the current biodiversity crisis.

Studies of insect herbivory on fossilized leaves tend to focus on a few, relatively simple metrics that are agnostic to the distribution of insect damage types among host plants. More complex metrics that link particular damage types to particular host plants have the potential to address additional ecological questions, but such metrics can be biased by sampling incompleteness due to the difficulty of distinguishing the true absence of a particular interaction from the failure to detect it—a challenge that has been raised in the ecological literature. We evaluate a range of methods for characterizing the relationships between damage types and host plants by performing resampling and subsampling exercises on a variety of datasets. We found that the components of beta diversity provide a more valid, reliable, and interpretable method for comparing component communities than do bipartite network metrics and that the rarefaction of interactions represent a valid, reliable, and interpretable method for comparing compound communities. Both beta diversity and rarefaction of interactions avoid the potential pitfalls of multiple comparisons. Finally, we found that the host specificity of individual damage types is challenging to assess. Whereas bipartite network metrics are sufficiently biased by sampling incompleteness to be inappropriate for fossil herbivory data, alternatives exist that are perfectly suitable for fossil datasets with sufficient sample coverage.

Foraminifera are important components of tropical marine benthic ecosystems and their recovery pattern from the end-Permian mass extinction can yield insights into the Mesozoic history of this group. Here we report the calcareous and agglutinated foraminifera recovered from five measured stratigraphic sections on the Great Bank of Guizhou, an uppermost Permian to Upper Triassic isolated carbonate platform in the Nanpanjiang Basin, south China. The material contains >100 Triassic species, including three that are newly described (Arenovidalina weii n. sp., Meandrospira? enosi n. sp., and Spinoendotebanella lehrmanni n. gen., n. sp.), ranging from Griesbachian (Induan) to Cordevolian (Carnian) age. The species belong to the classes Miliolata, Textulariata, Fusulinata, Nodosariata, and to an unknown class housing all aragonitic forms of the orders Involutinida and Robertinida. Based on previously established conodont zones and carbon isotope chemostratigraphy, the Griesbachian (early Induan) through Illyrian (late Anisian) interval has been subdivided into 12 foraminiferal zones and two unnamed intervals devoid of foraminifera. Following the extinction at the Permian-Triassic boundary, habitable ecological niches of Griesbachian age were invaded by disaster taxa that subsequently became extinct during the Dienerian (late Induan) and left no younger descendants. The disaster taxa were replaced by Lazarus taxa with Permian origins, which were then decimated by the Smithian-Spathian (mid-Olenekian) boundary crisis. The tempo of recovery appears to have been modulated by environmental changes during the Griesbachian through Smithian that involved both climate change and expansion of anoxic ocean bottom waters. Uninterrupted and lasting recovery of benthic foraminifera did not begin until the Spathian.

UUID: http://zoobank.org/2a6e9061-b163-402a-9098-8765a80576b3

The typical marine animal has increased in biovolume by more than two orders of magnitude since the beginning of the Cambrian, but the causes of this trend remain unknown. We test the hypothesis that the efficiency of intra-organism oxygen delivery is a major constraint on body-size evolution in marine animals. To test this hypothesis, we compiled a dataset comprising 13,723 marine animal genera spanning the Phanerozoic. We coded each genus according to its respiratory medium, circulatory anatomy, and feeding mode. In extant genera, we find that respiratory medium and circulatory anatomy explain more of the difference in size than feeding modes. Likewise, we find that most of the Phanerozoic increase in mean biovolume is accounted for by size increase in taxa that accomplish oxygen delivery through closed circulatory systems. During the Cambrian, water-breathing animals with closed circulatory systems were smaller, on average, than contemporaries with open circulatory systems. However, genera with closed circulatory systems superseded in size genera with open circulatory systems by the Middle Ordovician, as part of their Phanerozoic-long trend of increasing size. In a regression analysis, respiratory and circulatory anatomy explain far more size variation in the living fauna than do feeding modes, even after accounting for taxonomic affinity at the class level. These findings suggest that ecological and environmental drivers of the Phanerozoic increase in the mean size of marine animals operated within strong, anatomically determined constraints.

Larger body size has long been assumed to correlate with greater risk of extinction, helping to shape body-size distributions across the tree of life, but a lack of comprehensive size data for fossil taxa has left this hypothesis untested for most higher taxa across the vast majority of evolutionary time. Here we assess the relationship between body size and extinction using a data set comprising the body sizes, stratigraphic ranges, and occurrence patterns of 9408 genera of fossil marine animals spanning eight Linnaean classes across the past 485 Myr. We find that preferential extinction of smaller-bodied genera within classes is substantially more common than expected due to chance and that there is little evidence for preferential extinction of larger-bodied genera. Using a capture–mark–recapture analysis, we find that this size bias of extinction persists even after accounting for a pervasive bias against the sampling of smaller-bodied genera within classes. The size bias in extinction also persists after including geographic range as an additional predictor of extinction, indicating that correlation between body size and geographic range does not provide a simple explanation for the association between size and extinction. Regardless of the underlying causes, the preferential extinction of smaller-bodied genera across many higher taxa and most of geologic time indicates that the selective loss of large-bodied animals is the exception, rather than the rule, in the evolution of marine animals.

The taxonomic and ecologic composition of Earth's biota has shifted dramatically through geologic time, with some clades going extinct while others diversified. Here, we derive a metric that quantifies the change in biotic composition due to extinction or origination and show that it equals the product of extinction/origination magnitude and selectivity (variation in magnitude among groups). We also define metrics that describe the extent to which a recovery (1) reinforced or reversed the effects of extinction on biotic composition and (2) changed composition in ways uncorrelated with the extinction. To demonstrate the approach, we analyzed an updated compilation of stratigraphic ranges of marine animal genera. We show that mass extinctions were not more selective than background intervals at the phylum level; rather, they tended to drive greater taxonomic change due to their higher magnitudes. Mass extinctions did not represent a separate class of events with respect to either strength of selectivity or effect. Similar observations apply to origination during recoveries from mass extinctions, and on average, extinction and origination were similarly selective and drove similar amounts of biotic change. Elevated origination during recoveries drove bursts of compositional change that varied considerably in effect. In some cases, origination partially reversed the effects of extinction, returning the biota toward the pre-extinction composition; in others, it reinforced the effects of the extinction, magnifying biotic change. Recoveries were as important as extinction events in shaping the marine biota, and their selectivity deserves systematic study alongside that of extinction.

Organismal metabolic rates reflect the interaction of environmental and physiological factors. Thus, calcifying organisms that record growth history can provide insight into both the ancient environments in which they lived and their own physiology and life history. However, interpreting them requires understanding which environmental factors have the greatest influence on growth rate and the extent to which evolutionary history constrains growth rates across lineages. We integrated satellite measurements of sea-surface temperature and chlorophyll-a concentration with a database of growth coefficients, body sizes, and life spans for 692 populations of living marine bivalves in 195 species, set within the context of a new maximum-likelihood phylogeny of bivalves. We find that environmental predictors overall explain only a small proportion of variation in growth coefficient across all species; temperature is a better predictor of growth coefficient than food supply, and growth coefficient is somewhat more variable at higher summer temperatures. Growth coefficients exhibit moderate phylogenetic signal, and taxonomic membership is a stronger predictor of growth coefficient than any environmental predictor, but phylogenetic inertia cannot fully explain the disjunction between our findings and the extensive body of work demonstrating strong environmental control on growth rates within taxa. Accounting for evolutionary history is critical when considering shells as historical archives. The weak relationship between variation in food supply and variation in growth coefficient in our data set is inconsistent with the hypothesis that the increase in mean body size through the Phanerozoic was driven by increasing productivity enabling faster growth rates.

Energy availability influences natural selection on the ontogenetic histories of organisms. However, it remains unclear whether physiological controls on size remain constant throughout ontogeny or instead shift as organisms grow larger. Benthic foraminifera provide an opportunity to quantify and interpret the physicochemical controls on both initial (proloculus) and adult volumes across broad environmental gradients using first principles of cell physiology. Here, we measured proloculus and adult test dimensions of 129 modern rotaliid species from published images of holotype specimens, using holotype size to represent the maximum size of all species’ occurrences across the North American continental margin. We merged size data with mean annual temperature, dissolved oxygen concentration, particulate organic carbon flux, and seawater calcite saturation for 718 unique localities to quantify the relationship between physicochemical variables and among-species adult/proloculus size ratios. We find that correlation of community mean adult/proloculus size ratios with environmental parameters reflects covariation of adult test volume with environmental conditions. Among-species proloculus sizes do not covary identifiably with environmental conditions, consistent with the expectation that environmental constraints on organism size impose stronger selective pressures on adult forms due to lower surface area-to-volume ratios at larger sizes. Among-species adult/proloculus size ratios of foraminifera occurring in resource-limited environments are constrained by the limiting resource in addition to temperature. Identified limiting resources are food in oligotrophic waters and oxygen in oxygen minimum zones. Because among-species variations in adult/proloculus size ratios from the North American continental margin are primarily driven by the local environment’s influence on adult sizes, the evolution of foraminiferal sizes over the Phanerozoic may have been strongly influenced by changing oceanographic conditions. Furthermore, lack of correspondence between among-species proloculus sizes and environmental conditions suggests that offspring sizes in foraminifera are rarely limited by physiological constraints and are more susceptible to selection related to other aspects of fitness.

The quantity of biomass in an ecosystem is constrained by energy availability. It is less clear, however, how energy availability constrains taxonomic and functional diversity. Competing models suggest biodiversity is either resource-limited or far from any bound. We test the hypothesis that functional diversity in marine bivalve communities is constrained by energy availability, measured as particulate organic carbon (POC) flux, in the modern oceans. We find that POC flux predicts the relative prevalence of ecological modes in both the Atlantic and Pacific Oceans. Moreover, the associations of ecological modes with POC fluxes are similar between the Atlantic and Pacific despite being based on independent sets of species, indicating a direct causal relationship. We then use the relationship between POC flux and the prevalence of functional groups in the modern to test the hypothesis that the trend of increasing functional diversity in bivalves across the past 500 Myr has occurred in response to increased POC flux. We find no evidence that the earliest-appearing modes of life are preferentially associated with low-POC environments or that the mean POC flux experienced by marine bivalves has increased across geological time. To reconcile the close association between ecological mode and POC flux in the modern oceans with the lack of evidence for increasing POC fluxes across time, we propose that POC flux has not increased substantially over time but, rather, the increase in bivalve functional diversity enabled bivalves to become more abundant, to occupy a broader range of environments, and to capture a greater fraction of the total POC flux. The results here suggest at the geographic scale of oceans and through geologic time bivalve diversity was not bounded by food availability.

Spatially extensive internal layers have been traced in airborne radio-echo sounding (RES) data collected over Greenland during the late 1990s. By linking internal layers within individual flight-lines at crossover points, it is possible to identify spatially continuous layers that are interpreted as isochronous surfaces. Several of the survey lines pass over the GRIP core site, and this allows us to use the published GRIP age–depth relationship to accurately date these surfaces. Two layers, with ages of 3891 and 6956 years BP, have been traced over a large part of North Greenland. Accurately dated and spatially continuous isochrones are valuable for both assimilation within, and verification of, numerical models. For example, comparison of isochronous surfaces from a numerical simulation with those layers observed in RES data can be used to inform the choice of parameters (e.g. rheology) and climate history used to force a numerical model. To demonstrate the potential of the RES data, two layers for North Greenland were used to determine palaeo-accumulation rates. The inversion from layer depth to accumulation rate requires a three-dimensional velocity field. This velocity field is constructed by combining a two-dimensional balance-velocity field with an assumed vertical structure for the horizontal velocity. The isochronous-layer derived accumulation rates were compared with the Bales and others (2001) rates. A larger east–west gradient was found across the central ice divide for the derived accumulation rate, suggesting a trend in the Holocene accumulation rates for this region. The layers were also compared with isochronous surfaces derived from simulations of a three-dimensional thermodynamic ice-sheet model. Using the isochronous-layer derived accumulation rates to force the model improved the match between modelled and observed layers.

The sizes and shapes of marine organisms often vary systematically across latitude and water depth, but the environmental factors that mediate these gradients in morphology remain incompletely understood. A key challenge is isolating the individual contributions of many, often correlated, environmental variables of potential biological significance. Benthic foraminifera, a diverse group of rhizarian protists that inhabit nearly all marine environments, provide an unparalleled opportunity to test statistically among the various potential controls on size and volume–to–surface area ratio. Here, we use 7035 occurrences of 541 species of Rotallid foraminifera across 946 localities spanning more than 60 degrees of latitude and 1600 m of water depth around the North American continental margin to assess the relative influences of temperature, oxygen availability, carbonate saturation, and particulate organic carbon flux on their test volume and volume–to–surface area ratio. For the North American data set as a whole, the best model includes temperature and dissolved oxygen concentration as predictors. This model also applies to data from the Pacific continental margin in isolation, but only temperature is included in the best model for the Atlantic. Because these findings are consistent with predictions from the first principles of cell physiology, we interpret these statistical associations as the expressions of physiological selective pressures on test size and shape from the physical environment. Regarding existing records of temporal variation in foraminiferal test size across geological time in light of these findings suggests that the importance of temperature variation on the evolution of test volume and volume–to–surface area ratio may be underappreciated. In particular, warming may have played as important a role as reduced oxygen availability in causing test size reduction during past episodes of environmental crisis and is expected to inflict metabolic stress on benthic foraminifera over the next century due to anthropogenic climate change.

Determining which biological traits affect taxonomic durations is critical for explaining macroevolutionary patterns. Two approaches are commonly used to investigate the associations between traits and durations and/or extinction and origination rates: analyses of taxonomic occurrence patterns in the fossil record and comparative phylogenetic analyses, predominantly of extant taxa. By capitalizing upon the empirical record of past extinctions, paleontological data avoid some of the limitations of existing methods for inferring extinction and origination rates from molecular phylogenies. However, most paleontological studies of extinction selectivity have ignored phylogenetic relationships because there is a dearth of phylogenetic hypotheses for diverse non-vertebrate higher taxa in the fossil record. This omission inflates the degrees of freedom in statistical analyses and leaves open the possibility that observed associations are indirect, reflecting shared evolutionary history rather than the direct influence of particular traits on durations. Here we investigate global patterns of extinction selectivity in Devonian terebratulide brachiopods and compare the results of taxonomic vs. phylogenetic approaches. Regression models that assume independence among taxa provide support for a positive association between geographic range size and genus duration but do not indicate an association between body size and genus duration. Brownian motion models of trait evolution identify significant similarities in body size, range size, and duration among closely related terebratulide genera. We use phylogenetic regression to account for shared evolutionary history and find support for a significant positive association between range size and duration among terebratulides that is also phylogenetically structured. The estimated range size–duration relationship is moderately weaker in the phylogenetic analysis due to the down-weighting of closely related genera that were both broadly distributed and long lived; however, this change in slope is not statistically significant. These results provide evidence for the phylogenetic conservatism of organismal and emergent traits, yet also the general phylogenetic independence of the relationship between range size and duration.

Delayed biotic recovery from the end-Permian mass extinction has long been interpreted to result from environmental inhibition. Recently, evidence of more rapid recovery has begun to emerge, suggesting the role of environmental inhibition was previously overestimated. However, there have been few high-resolution taxonomic and ecological studies spanning the full Early and Middle Triassic recovery interval, leaving the precise pattern of recovery and underlying mechanisms poorly constrained. In this study, we document Early and Middle Triassic trends in taxonomic diversity, assemblage evenness, and size distribution of benthic foraminifers on an exceptionally exposed carbonate platform in south China. We observe gradual increases in all metrics through Early Triassic and earliest Middle Triassic time, with stable values reached early in the Anisian. There is little support in our data set for a substantial Early Triassic lag interval during the recovery of foraminifers or for a stepwise recovery pattern. The recovery pattern of foraminifers on the GBG corresponds well with available global data for this taxon and appears to parallel that of many benthic invertebrate clades. Early Triassic diversity increase in foraminifers was more gradual than in ammonoids and conodonts. However, foraminifers continued to increase in diversity, size, and evenness into Middle Triassic time, whereas diversity of ammonoids and conodonts declined. These contrasts suggest decoupling of recovery between benthic and pelagic environments; it is unclear whether these discrepancies reflect inherent contrasts in their evolutionary dynamics or the differential impact of Early Triassic ocean anoxia or associated environmental parameters on benthic ecosystems.

The recognition that past catastrophic events may have caused the simultaneous extinction of many taxa has prompted the development of statistical tests to determine the compatibility of the fossil record with such scenarios. Statistical tests necessitate simplifying assumptions, the most significant of which are continuous (as opposed to discrete) data in the sampling of the fossil record and random distribution of fossil occurrences because constant preservation potential and collecting intensity of fossils are assumed. The assumption of random distribution of fossil occurrences has been addressed quantitatively, but the continuity of data has not. The assumption of continuous data is not trivial, for although collecting may appear continuous, the resulting data are never strictly continuous because the stratigraphic positions of fossils are known with limited precision. For one test of simultaneous extinction, simulations demonstrate that the data behave in a less continuous manner as the occurrence rate increases, decreasing the reliability of the test at higher occurrence rates. Out of mathematical simplicity, nearly all tests use simultaneous extinction as the null hypothesis. However, even under ideal sampling circumstances, gradual extinctions that occurred over a sufficiently short stratigraphic interval are likely to be statistically indistinguishable from extinction occurring at a single horizon. Therefore, a range of gradual extinction scenarios will also be compatible with the fossil record even if the null hypothesis is not rejected. Because direct tests of gradual extinction scenarios have not yet been developed, simulations were used to determine the probability that an extinction occurring over a given stratigraphic distance with a given number of taxa will be statistically indistinguishable from extinction at a single horizon. The simulation results allow the test results to be used to define a range of extinction scenarios compatible with the fossil record. Finally, the simulation results were applied to two Late Cretaceous ammonite data sets. Although both data sets sufficiently approximate continuous sampling for the use of statistical tests, the method shows that the data are not always sufficient to rule out either stratigraphically simultaneous extinction or a literal reading of extinction rate as representing gradual or episodic extinction.

Extinction risk is inversely related to genus age (time since first appearance) in most intervals of the Phanerozoic marine fossil record, in apparent contradiction to the macroevolutionary Red Queen's Hypothesis, which posits that extinction risk is independent of taxon age. Age-dependent increases in the mean species richness and geographic range of genera have been invoked to reconcile this genus-level observation with the presumed prevalence of Red Queen dynamics at the species level. Here we test these explanations with data from the Paleobiology Database. Multiple logistic regression demonstrates that the association of extinction risk with genus age is not adequately explained by species richness or geographic range: there is a residual association between age and extinction risk even when range and richness effects are accounted for. Throughout most of the Phanerozoic the age selectivity gradient is highest among the youngest age cohorts, whereas there is no association between age and extinction risk among older age cohorts. Some of the apparent age selectivity of extinction in the global fauna is attributable to differences in extinction rate among taxonomic groups, but extinction risk declines with genus age even within most taxonomic orders. Notable exceptions to this pattern include the Cambrian-Ordovician, latest Permian, Triassic, and Paleocene intervals. The association of age with extinction risk could reflect sampling heterogeneity or taxonomic practice more than biological reality, but at present it is difficult to evaluate or correct for such biases. Alternatively, the pattern may reflect consistent extinction selectivity on some as-yet unidentified covariate of genus age. Although this latter explanation is not compatible with a Red Queen model if most genus extinctions have resulted from biological interactions, it may be applicable if most genus extinctions have instead been caused by recurrent physical disturbances that repeatedly impose similar selective pressures.