Bivalve network reveals latitudinal selectivity gradient at the end-Cretaceous mass extinction

Reduced strength and increased variability of extinction selectivity during mass extinctions

Two of the traits most often observed to correlate with extinction risk in marine animals are geographical range and body size. However, the relative effects of these two traits on extinction risk have not been investigated systematically for either background times or during mass extinctions. To close this knowledge gap, we measure and compare extinction selectivity of geographical range and body size of genera within five classes of benthic marine animals across the Phanerozoic using capture-mark-recapture models. During background intervals, narrow geographical range is strongly associated with greater extinction probability, whereas smaller body size is more weakly associated with greater extinction probability. During mass extinctions, the association between geographical range and extinction probability is reduced in every class and fully eliminated in some, whereas the association between body size and extinction probability varies in strength and direction across classes. While geographical range is universally the stronger predictor of survival during background intervals, variation among classes during mass extinction suggests a fundamental shift in extinction processes during these global catastrophes.

Global impact and selectivity of the Cretaceous-Paleogene mass extinction among sharks, skates, and rays

The Cretaceous-Paleogene event was the last mass extinction event, yet its impact and long-term effects on species-level marine vertebrate diversity remain largely uncharacterized. We quantified elasmobranch (sharks, skates, and rays) speciation, extinction, and ecological change resulting from the end-Cretaceous event using >3200 fossil occurrences and 675 species spanning the Late Cretaceous-Paleocene interval at global scale. Elasmobranchs declined by >62% at the Cretaceous-Paleogene boundary and did not fully recover in the Paleocene. The end-Cretaceous event triggered a heterogeneous pattern of extinction, with rays and durophagous species reaching the highest levels of extinction (>72%) and sharks and nondurophagous species being less affected. Taxa with large geographic ranges and/or those restricted to high-latitude settings show higher survival. The Cretaceous-Paleogene event drastically altered the evolutionary history of marine ecosystems.

A multiscale view of the Phanerozoic fossil record reveals the three major biotic transitions

The hypothesis of the Great Evolutionary Faunas is a foundational concept of macroevolutionary research postulating that three global mega-assemblages have dominated Phanerozoic oceans following abrupt biotic transitions. Empirical estimates of this large-scale pattern depend on several methodological decisions and are based on approaches unable to capture multiscale dynamics of the underlying Earth-Life System. Combining a multilayer network representation of fossil data with a multilevel clustering that eliminates the subjectivity inherent to distance-based approaches, we demonstrate that Phanerozoic oceans sequentially harbored four global benthic mega-assemblages. Shifts in dominance patterns among these global marine mega-assemblages were abrupt (end-Cambrian 494 Ma; end-Permian 252 Ma) or protracted (mid-Cretaceous 129 Ma), and represent the three major biotic transitions in Earth’s history. Our findings suggest that gradual ecological changes associated with the Mesozoic Marine Revolution triggered a protracted biotic transition comparable in magnitude to the end-Permian transition initiated by the most severe biotic crisis of the past 500 million years. Overall, our study supports the notion that both long-term ecological changes and major geological events have played crucial roles in shaping the mega-assemblages that dominated Phanerozoic oceans.

Rojas et al. present a new multi-scale model that reveals the three major biotic transitions of the Phanerozoic fossil record. This new model supports the hypothesis that both long-term ecological changes and major geological events played crucial roles in shaping ocean mega-assemblages through the Phanerozoic.

Biogeographical Network Analysis of Cretaceous Terrestrial Tetrapods: A Phylogeny-Based Approach

Network methods are widely used to represent and analyze biogeography. It is difficult, however, to convert occurrence data of fossil vertebrates to a biogeographical network, as most species were known from a single locality. A new method for creating a biogeographical network that can incorporate phylogenetic information is proposed in this study, which increases the number of edges in the network of fossil vertebrates and enables the application of various network methods. Using ancestral state reconstruction via maximum parsimony, the method first estimates the biogeographical regions of all internal nodes of a given phylogeny using biogeographical information on the terminal taxa. Then, each internal node in the phylogenetic tree is converted to an edge in the biogeographical network that connects the region(s), if unambiguously estimated, of its two descendants. The new method was applied to phylogenetic trees generated by a birth-death model. Under all conditions tested, an average of $CDATA[$CDATA[$>$$70% of the internal nodes in phylogenetic trees were converted into edges. Three network indices-link density, average link weight, and endemism index (EI)-were evaluated for their usefulness in comparing different biogeographical networks. The EI reflects the rate of dispersal; the other indices reflect nonbiogeographical parameters, the number of taxa and regions, which highlights the importance of evaluating network indices before applying them to biogeographical studies. Multiple Cretaceous biogeographical networks were constructed from the phylogenies of five tetrapod taxa: terrestrial crocodyliforms, terrestrial turtles, nonavian dinosaurs, avians, and pterosaurs. The networks of avians and pterosaurs showed similar topologies and a strong correlation, and unexpectedly high endemism indices. These similarities were probably a result of shared taphonomic biases (i.e., the Lagerstätten effect) for volant taxa with fragile skeletons. The crocodyliform network was partitioned into the Gondwanan and Laurasian continents. The dinosaur network was partitioned into three groups of continents: 1) North America, Asia, and Australia; 2) Europe and Africa; and 3) India, Madagascar, and South America. When Early and Late Cretaceous dinosaurs were analyzed separately, the dinosaur networks were divided into 1) North America, Asia, and Australia; and 2) Europe, Africa, India, and South America for the Early Cretaceous and 1) North America, Asia, and Europe; and 2) India, Madagascar, and South America for the Late Cretaceous. This partitioning of dinosaur and crocodyliform networks corroborates the results of previous biogeographical studies and indicates that the method introduced here can retrieve biogeographical signals from a source phylogeny when sufficient data are available for most targeted biogeographical regions.

The biogeographical imprint of mass extinctions

Mass extinctions are defined by extinction rates significantly above background levels and have had substantial consequences for the evolution of life. Geographically selective extinctions, subsequent originations and species redistributions may have changed global biogeographical structure, but quantification of this change is lacking. In order to assess quantitatively the biogeographical impact of mass extinctions, we outline time-traceable bioregions for benthic marine species across the Phanerozoic using a compositional network. Mass extinction events are visually recognizable in the geographical depiction of bioregions. The end-Permian extinction stands out with a severe reduction of provinciality. Time series of biogeographical turnover represent a novel aspect of the analysis of mass extinctions, confirming concentration of changes in the geographical distribution of benthic marine life.

Quantifying ecological impacts of mass extinctions with network analysis of fossil communities

The geologic record provides evidence of repeated diversification events and mass extinctions, which entailed benchmark changes in biodiversity and ecology. For insights into these events, we explore the fossil record of marine animal communities using a network-based approach to quantifying ecological change over time. The major radiations and mass extinctions of the Phanerozoic Eon resulted in the biggest ecological changes, as they involved the rise and decline of interrelated communities in relative dominance. Our analyses provide support for an ecological severity ranking of mass extinctions and illuminate the long-term consequences of the Ordovician radiation and Devonian mass depletion of biodiversity. Our work highlights the potential for irreversible ecosystem changes with species losses, both previously documented and predicted in the future.

Mass extinctions documented by the fossil record provide critical benchmarks for assessing changes through time in biodiversity and ecology. Efforts to compare biotic crises of the past and present, however, encounter difficulty because taxonomic and ecological changes are decoupled, and although various metrics exist for describing taxonomic turnover, no methods have yet been proposed to quantify the ecological impacts of extinction events. To address this issue, we apply a network-based approach to exploring the evolution of marine animal communities over the Phanerozoic Eon. Network analysis of fossil co-occurrence data enables us to identify nonrandom associations of interrelated paleocommunities. These associations, or evolutionary paleocommunities, dominated total diversity during successive intervals of relative community stasis. Community turnover occurred largely during mass extinctions and radiations, when ecological reorganization resulted in the decline of one association and the rise of another. Altogether, we identify five evolutionary paleocommunities at the generic and familial levels in addition to three ordinal associations that correspond to Sepkoski’s Cambrian, Paleozoic, and Modern evolutionary faunas. In this context, we quantify magnitudes of ecological change by measuring shifts in the representation of evolutionary paleocommunities over geologic time. Our work shows that the Great Ordovician Biodiversification Event had the largest effect on ecology, followed in descending order by the Permian–Triassic, Cretaceous–Paleogene, Devonian, and Triassic–Jurassic mass extinctions. Despite its taxonomic severity, the Ordovician extinction did not strongly affect co-occurrences of taxa, affirming its limited ecological impact. Network paleoecology offers promising approaches to exploring ecological consequences of extinctions and radiations.

Contrasting responses of functional diversity to major losses in taxonomic diversity

Taxonomic diversity of benthic marine invertebrate shelf species declines at present by nearly an order of magnitude from the tropics to the poles in each hemisphere along the latitudinal diversity gradient (LDG), most steeply along the western Pacific where shallow-sea diversity is at its tropical maximum. In the Bivalvia, a model system for macroevolution and macroecology, this taxonomic trend is accompanied by a decline in the number of functional groups and an increase in the evenness of taxa distributed among those groups, with maximum functional evenness (FE) in polar waters of both hemispheres. In contrast, analyses of this model system across the two era-defining events of the Phanerozoic, the Permian-Triassic and Cretaceous-Paleogene mass extinctions, show only minor declines in functional richness despite high extinction intensities, resulting in a rise in FE owing to the persistence of functional groups. We hypothesize that the spatial decline of taxonomic diversity and increase in FE along the present-day LDG primarily reflect diversity-dependent factors, whereas retention of almost all functional groups through the two mass extinctions suggests the operation of diversity-independent factors. Comparative analyses of different aspects of biodiversity thus reveal strongly contrasting biological consequences of similarly severe declines in taxonomic diversity and can help predict the consequences for functional diversity among different drivers of past, present, and future biodiversity loss.

Aquatic urban ecology at the scale of a capital: community structure and interactions in street gutters

In most cities, streets are designed for collecting and transporting dirt, litter, debris, storm water and other wastes as a municipal sanitation system. Microbial mats can develop on street surfaces and form microbial communities that have never been described. Here, we performed the first molecular inventory of the street gutter-associated eukaryotes across the entire French capital of Paris and the non-potable waters sources. We found that the 5782 OTUs (operational taxonomic units) present in the street gutters which are dominated by diatoms (photoautotrophs), fungi (heterotrophs), Alveolata and Rhizaria, includes parasites, consumers of phototrophs and epibionts that may regulate the dynamics of gutter mat microbial communities. Network analyses demonstrated that street microbiome present many species restricted to gutters, and an overlapping composition between the water sources used for street cleaning (for example, intra-urban aquatic networks and the associated rivers) and the gutters. We propose that street gutters, which can cover a significant surface area of cities worldwide, potentially have important ecological roles in the remediation of pollutants or downstream wastewater treatments, might also be a niche for growth and dissemination of putative parasite and pathogens.

Mass extinctions drove increased global faunal cosmopolitanism on the supercontinent Pangaea

Mass extinctions have profoundly impacted the evolution of life through not only reducing taxonomic diversity but also reshaping ecosystems and biogeographic patterns. In particular, they are considered to have driven increased biogeographic cosmopolitanism, but quantitative tests of this hypothesis are rare and have not explicitly incorporated information on evolutionary relationships. Here we quantify faunal cosmopolitanism using a phylogenetic network approach for 891 terrestrial vertebrate species spanning the late Permian through Early Jurassic. This key interval witnessed the Permian–Triassic and Triassic–Jurassic mass extinctions, the onset of fragmentation of the supercontinent Pangaea, and the origins of dinosaurs and many modern vertebrate groups. Our results recover significant increases in global faunal cosmopolitanism following both mass extinctions, driven mainly by new, widespread taxa, leading to homogenous ‘disaster faunas’. Cosmopolitanism subsequently declines in post-recovery communities. These shared patterns in both biotic crises suggest that mass extinctions have predictable influences on animal distribution and may shed light on biodiversity loss in extant ecosystems.

Mass extinctions are thought to produce ‘disaster faunas’, communities dominated by a small number of widespread species. Here, Button et al. develop a phylogenetic network approach to test this hypothesis and find that mass extinctions did increase faunal cosmopolitanism across Pangaea during the late Palaeozoic and early Mesozoic.

Life in the Aftermath of Mass Extinctions

The vast majority of species that have ever lived went extinct sometime other than during one of the great mass extinction events. In spite of this, mass extinctions are thought to have outsized effects on the evolutionary history of life. While part of this effect is certainly due to the extinction itself, I here consider how the aftermaths of mass extinctions might contribute to the evolutionary importance of such events. Following the mass loss of taxa from the fossil record are prolonged intervals of ecological upheaval that create a selective regime unique to those times. The pacing and duration of ecosystem change during extinction aftermaths suggests strong ties between the biosphere and geosphere, and a previously undescribed macroevolutionary driver - earth system succession. Earth system succession occurs when global environmental or biotic change, as occurs across extinction boundaries, pushes the biosphere and geosphere out of equilibrium. As species and ecosystems re-evolve in the aftermath, they change global biogeochemical cycles - and in turn, species and ecosystems - over timescales typical of the geosphere, often many thousands to millions of years. Earth system succession provides a general explanation for the pattern and timing of ecological and evolutionary change in the fossil record. Importantly, it also suggests that a speed limit might exist for the pace of global biotic change after massive disturbance - a limit set by geosphere-biosphere interactions. For mass extinctions, earth system succession may drive the ever-changing ecological stage on which species evolve, restructuring ecosystems and setting long-term evolutionary trajectories as they do.

Expected time-invariant effects of biological traits on mammal species duration

Determining which biological traits influence differences in extinction risk is vital for understanding the differential diversification of life and for making predictions about species' vulnerability to anthropogenic impacts. Here I present a hierarchical Bayesian survival model of North American Cenozoic mammal species durations in relation to species-level ecological factors, time of origination, and phylogenetic relationships. I find support for the survival of the unspecialized as a time-invariant generalization of trait-based extinction risk. Furthermore, I find that phylogenetic and temporal effects are both substantial factors associated with differences in species durations. Finally, I find that the estimated effects of these factors are partially incongruous with how these factors are correlated with extinction risk of the extant species. These findings parallel previous observations that background extinction is a poor predictor of mass extinction events and suggest that attention should be focused on mass extinctions to gain insight into modern species loss.

A network approach for identifying and delimiting biogeographical regions

Biogeographical regions (geographically distinct assemblages of species and communities) constitute a cornerstone for ecology, biogeography, evolution and conservation biology. Species turnover measures are often used to quantify spatial biodiversity patterns, but algorithms based on similarity can be sensitive to common sampling biases in species distribution data. Here we apply a community detection approach from network theory that incorporates complex, higher-order presence-absence patterns. We demonstrate the performance of the method by applying it to all amphibian species in the world (c. 6,100 species), all vascular plant species of the USA (c. 17,600) and a hypothetical data set containing a zone of biotic transition. In comparison with current methods, our approach tackles the challenges posed by transition zones and succeeds in retrieving a larger number of commonly recognized biogeographical regions. This method can be applied to generate objective, data-derived identification and delimitation of the world's biogeographical regions.