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.

Bayesian analyses indicate bivalves did not drive the downfall of brachiopods following the Permian-Triassic mass extinction.

Certain times of major biotic replacement have often been interpreted as broadly competitive, mediated by innovation in the succeeding clades. A classic example was the switch from brachiopods to bivalves as major seabed organisms following the Permian-Triassic mass extinction (PTME), ~252 million years ago. This was attributed to competitive exclusion of brachiopods by the better adapted bivalves or simply to the fact that brachiopods had been hit especially hard by the PTME.

Dinosaur trackways from the Upper Cretaceous Nichkesai Formation near Mayluu Suu City, Southern Tien Shan Mountains, north-western Kyrgyzstan.

Trackways provide essential data on the biogeographic distribution, locomotion and behaviour of dinosaurs. Cretaceous dinosaur trackways are abundant in the Americas, Europe, North Africa and East Asia, but are less well documented in Central Asia despite extensive exposure of Cretaceous terrestrial sedimentary rocks in the region. Here we report the presence of bipedal, tridactyl dinosaur trackways near the city of Mayluu Suu, Jalal Abad Oblast, north-western Kyrgyzstan, the first discovery of dinosaur trace fossils within the country.

Global diversity dynamics in the fossil record are regionally heterogeneous.

Global diversity patterns in the fossil record comprise a mosaic of regional trends, underpinned by spatially non-random drivers and distorted by variation in sampling intensity through time and across space. Sampling-corrected diversity estimates from spatially-standardised fossil datasets retain their regional biogeographic nuances and avoid these biases, yet diversity-through-time arises from the interplay of origination and extinction, the processes that shape macroevolutionary history. Here we present a subsampling algorithm to eliminate spatial sampling bias, coupled with advanced probabilistic methods for estimating origination and extinction rates and a Bayesian method for estimating sampling-corrected diversity.

Does exceptional preservation distort our view of disparity in the fossil record?

How much of evolutionary history is lost because of the unevenness of the fossil record? Lagerstätten, sites which have historically yielded exceptionally preserved fossils, provide remarkable, yet distorting insights into past life. When examining macroevolutionary trends in the fossil record, they can generate an uneven sampling signal for taxonomic diversity; by comparison, their effect on morphological variety (disparity) is poorly understood. We show here that lagerstätten impact the disparity of ichthyosaurs, Mesozoic marine reptiles, by preserving higher diversity and more complete specimens.