Post-extinction recovery of the Phanerozoic oceans and biodiversity hotspots

Late Cretaceous ammonoids show that drivers of diversification are regionally heterogeneous

Palaeontologists have long sought to explain the diversification of individual clades to whole biotas at global scales. Advances in our understanding of the spatial distribution of the fossil record through geological time, however, has demonstrated that global trends in biodiversity were a mosaic of regionally heterogeneous diversification processes. Drivers of diversification must presumably have also displayed regional variation to produce the spatial disparities observed in past taxonomic richness. Here, we analyse the fossil record of ammonoids, pelagic shelled cephalopods, through the Late Cretaceous, characterised by some palaeontologists as an interval of biotic decline prior to their total extinction at the Cretaceous-Paleogene boundary. We regionally subdivide this record to eliminate the impacts of spatial sampling biases and infer regional origination and extinction rates corrected for temporal sampling biases using Bayesian methods. We then model these rates using biotic and abiotic drivers commonly inferred to influence diversification. Ammonoid diversification dynamics and responses to this common set of diversity drivers were regionally heterogeneous, do not support ecological decline, and demonstrate that their global diversification signal is influenced by spatial disparities in sampling effort. These results call into question the feasibility of seeking drivers of diversity at global scales in the fossil record.

DeepDive: estimating global biodiversity patterns through time using deep learning

Understanding how biodiversity has changed through time is a central goal of evolutionary biology. However, estimates of past biodiversity are challenged by the inherent incompleteness of the fossil record, even when state-of-the-art statistical methods are applied to adjust estimates while correcting for sampling biases. Here we develop an approach based on stochastic simulations of biodiversity and a deep learning model to infer richness at global or regional scales through time while incorporating spatial, temporal and taxonomic sampling variation. Our method outperforms alternative approaches across simulated datasets, especially at large spatial scales, providing robust palaeodiversity estimates under a wide range of preservation scenarios. We apply our method on two empirical datasets of different taxonomic and temporal scope: the Permian-Triassic record of marine animals and the Cenozoic evolution of proboscideans. Our estimates provide a revised quantitative assessment of two mass extinctions in the marine record and reveal rapid diversification of proboscideans following their expansion out of Africa and a >70% diversity drop in the Pleistocene.

Landscape dynamics and the Phanerozoic diversification of the biosphere

The long-term diversification of the biosphere responds to changes in the physical environment. Yet, over the continents, the nearly monotonic expansion of life started later in the early part of the Phanerozoic eon1 than the expansion in the marine realm, where instead the number of genera waxed and waned over time2. A comprehensive evaluation of the changes in the geodynamic and climatic forcing fails to provide a unified theory for the long-term pattern of evolution of life on Earth. Here we couple climate and plate tectonics models to numerically reconstruct the evolution of the Earth's landscape over the entire Phanerozoic eon, which we then compare to palaeo-diversity datasets from marine animal and land plant genera. Our results indicate that biodiversity is strongly reliant on landscape dynamics, which at all times determine the carrying capacity of both the continental domain and the oceanic domain. In the oceans, diversity closely adjusted to the riverine sedimentary flux that provides nutrients for primary production. On land, plant expansion was hampered by poor edaphic conditions until widespread endorheic basins resurfaced continents with a sedimentary cover that facilitated the development of soil-dependent rooted flora, and the increasing variety of the landscape additionally promoted their development.

Impact of global climate cooling on Ordovician marine biodiversity

Global cooling has been proposed as a driver of the Great Ordovician Biodiversification Event, the largest radiation of Phanerozoic marine animal Life. Yet, mechanistic understanding of the underlying pathways is lacking and other possible causes are debated. Here we couple a global climate model with a macroecological model to reconstruct global biodiversity patterns during the Ordovician. In our simulations, an inverted latitudinal biodiversity gradient characterizes the late Cambrian and Early Ordovician when climate was much warmer than today. During the Mid-Late Ordovician, climate cooling simultaneously permits the development of a modern latitudinal biodiversity gradient and an increase in global biodiversity. This increase is a consequence of the ecophysiological limitations to marine Life and is robust to uncertainties in both proxy-derived temperature reconstructions and organism physiology. First-order model-data agreement suggests that the most conspicuous rise in biodiversity over Earth's history - the Great Ordovician Biodiversification Event - was primarily driven by global cooling.

Why the Early Paleozoic was intrinsically prone to marine extinction

The geological record of marine animal biodiversity reflects the interplay between changing rates of speciation versus extinction. Compared to mass extinctions, background extinctions have received little attention. To disentangle the different contributions of global climate state, continental configuration, and atmospheric oxygen concentration (pO2) to variations in background extinction rates, we drive an animal physiological model with the environmental outputs from an Earth system model across intervals spanning the past 541 million years. We find that climate and continental configuration combined to make extinction susceptibility an order of magnitude higher during the Early Paleozoic than during the rest of the Phanerozoic, consistent with extinction rates derived from paleontological databases. The high extinction susceptibility arises in the model from the limited geographical range of marine organisms. It stands even when assuming present-day pO2, suggesting that increasing oxygenation through the Paleozoic is not necessary to explain why extinction rates apparently declined with time.

Increases in reef size, habitat and metacommunity complexity associated with Cambrian radiation oxygenation pulses

Oxygenation during the Cambrian Radiation progressed via a series of short-lived pulses. However, the metazoan biotic response to this episodic oxygenation has not been quantified, nor have the causal evolutionary processes been constrained. Here we present ecological analyses of Cambrian archaeocyath sponge reef communities on the Siberian Platform (525-514 Ma). During the oxic pulse at ~521-519 Ma, we quantify reef habitat expansion coupled to an increase in reef size and metacommunity complexity, from individual within-community reactions to their local environment, to ecologically complex synchronous community-wide response, accompanied by an increase in rates of origination. Subsequently, reef and archaeocyath body size are reduced in association with increased rates of extinction due to inferred expanded marine anoxia (~519-516.5 Ma). A later oxic pulse at ~515 Ma shows further reef habitat expansion, increased archaeocyath body size and diversity, but weaker community-wide environmental responses. These metrics confirm that oxygenation events created temporary pulses of evolutionary diversification and enhanced ecosystem complexity, potentially via the expansion of habitable space, and increased archaeocyath individual and reef longevity in turn leading to niche differentiation. Most notably, we show that progression towards increasing biodiversity and ecosystem complexity was episodic and discontinuous, rather than linear, during the Cambrian Radiation.

Diversity dependence is a ubiquitous phenomenon across Phanerozoic oceans

Biodiversity on Earth is shaped by abiotic perturbations and rapid diversifications. At the same time, there are arguments that biodiversity is bounded and regulated via biotic interactions. Evaluating the role and relative strength of diversity regulation is crucial for interpreting the ongoing biodiversity changes. We have analyzed Phanerozoic fossil record using public databases and new approaches for identifying the causal dependence of origination and extinction rates on environmental variables and standing diversity. While the effect of environmental factors on origination and extinction rates is variable and taxon specific, the diversity dependence of the rates is almost universal across the studied taxa. Origination rates are dependent on instantaneous diversity levels, while extinction rates reveal delayed diversity dependence. Although precise mechanisms of diversity dependence may be complex and difficult to recover, global regulation of diversity via negative diversity dependence of lineage diversification seems to be a common feature of the biosphere, with profound consequences for understanding current biodiversity crisis.