Phanerozoic survivors: Actinopterygian evolution through the Permo-Triassic and Triassic-Jurassic mass extinction events

Heterogeneous selectivity and morphological evolution of marine clades during the Permian-Triassic mass extinction

Morphological disparity and taxonomic diversity are distinct measures of biodiversity, typically expected to evolve synergistically. However, evidence from mass extinctions indicates that they can be decoupled, and while mass extinctions lead to a drastic loss of diversity, their impact on disparity remains unclear. Here we evaluate the dynamics of morphological disparity and extinction selectivity across the Permian-Triassic mass extinction. We developed an automated approach, termed DeepMorph, for the extraction of morphological features from fossil images using a deep learning model and applied it to a high-resolution temporal dataset encompassing 599 genera across six marine clades. Ammonoids, brachiopods and ostracods experienced a selective loss of complex and ornamented forms, while bivalves, gastropods and conodonts did not experience morphologically selective extinctions. The presence and intensity of morphological selectivity probably reflect the variations in environmental tolerance thresholds among different clades. In clades affected by selective extinctions, the intensity of diversity loss promoted the loss of morphological disparity. Conversely, under non-selective extinctions, the magnitude of diversity loss had a negligible impact on disparity. Our results highlight that the Permian-Triassic mass extinction had heterogeneous morphological selective impacts across clades, offering new insights into how mass extinctions can reshape biodiversity and ecosystem structure.

The early diversification of ray-finned fishes (Actinopterygii): hypotheses, challenges and future prospects

Actinopterygii makes up half of living vertebrate diversity, and study of fossil members during their Palaeozoic rise to dominance has a long history of descriptive work. Although research interest into Palaeozoic actinopterygians has increased in recent years, broader patterns of diversity and diversity dynamics remain critically understudied. Past studies have investigated macroevolutionary trends in Palaeozoic actinopterygians in a piecemeal fashion, variably using existing compendia of vertebrates or literature-based searches. Here, we present a comprehensive occurrence-based dataset of actinopterygians spanning the whole of the Palaeozoic. We use this to produce the first through-Palaeozoic trends in genus and species counts for Actinopterygii. Diversity through time generally tracks metrics for sampling, while major taxonomic problems pervading the Palaeozoic actinopterygian record obscure diversity trends. Many described species are concentrated in several particularly problematic 'waste-basket' genera, hiding considerable morphological and taxonomic diversity. This taxonomic confusion also feeds into a limited understanding of phylogenetic relationships. A heavy sampling bias towards Europe and North America exists in both occurrence databases and available phylogenetic matrices, with other regions underrepresented despite yielding important data. Scrutiny of the extent to which spatial biases influence the actinopterygian record is lacking, as is research on other forms of bias. Low richness in some time periods may be linked to geological biases, while the effects of taphonomic biases on Palaeozoic actinopterygians have not yet been investigated. Efforts are already underway both to redescribe poorly defined taxa and to describe taxa from underrepresented regions, helping to address taxonomic issues and accuracy of occurrence data. New methods of sampling standardisation utilising up-to-date occurrence databases will be critical in teasing apart biological changes in diversity and those resulting from bias. Lastly, continued phylogenetic work will enable the use of phylogenetic comparative methods to elucidate the origins of actinopterygian biogeography and subsequent patterns of radiation throughout their rise to dominate aquatic faunas.

A new perleidid neopterygian fish from the Early Triassic (Dienerian, Induan) of South China, with a reassessment of the relationships of Perleidiformes

Neopterygii is the largest clade of ray-finned fishes, including Teleostei, Holostei, and their closely related fossil taxa. This clade was first documented in the Early Carboniferous and underwent rapid evolutionary radiation during the Early to Middle Triassic. This article describes a new perleidid neopterygian species, Teffichthys elegans sp. nov., based on 13 well-preserved specimens from the lower Daye Formation (Dienerian, Induan) in Guizhou, China. The new species documents one of the oldest perleidids, providing insights into the early diversification of this family. The results of a phylogenetic analysis recover Teffichthys elegans sp. nov. as the sister taxon to Teffichthys madagascariensis within the Perleididae. T. elegans sp. nov. shares three derived features of Perleididae: the length of the anteroventral margin of the dermohyal nearly half the length of the anterodorsal margin of the preopercle; the anteroventral margin of the preopercle nearly equal to the anterior margin of the subopercle in length; and the anteroventral margin of the preopercle one to two times as long as the anterodorsal margin of the preopercle. It possesses diagnostic features of Teffichthys but differs from T. madagascariensis by the following features: presence of three supraorbitals; six pairs of branchiostegal rays; relatively deep anterodorsal process of subopercle; absence of spine on the posterior margin of the jugal; and pterygial formula of D26/P14, A22, C36/T39-41. The Perleidiformes are restricted to include only the Perleididae, and other previously alleged 'perleidiform' families (e.g., Hydropessidae and Gabanellidae) are excluded to maintain the monophyly of the order. Similar to many other perleidids, T. elegans sp. nov. was likely a durophagous predator with dentition combining grasping and crushing morphologies. The new finding also may indicate a relatively complex trophic structure of the Early Triassic marine ecosystem in South China.

Holosteans contextualize the role of the teleost genome duplication in promoting the rise of evolutionary novelties in the ray-finned fish innate immune system

Over 99% of ray-finned fishes (Actinopterygii) are teleosts, a clade that comprises half of all living vertebrate species that have diversified across virtually all fresh and saltwater ecosystems. This ecological breadth raises the question of how the immunogenetic diversity required to persist under heterogeneous pathogen pressures evolved. The teleost genome duplication (TGD) has been hypothesized as the evolutionary event that provided the substrate for rapid genomic evolution and innovation. However, studies of putative teleost-specific innate immune receptors have been largely limited to comparisons either among teleosts or between teleosts and distantly related vertebrate clades such as tetrapods. Here we describe and characterize the receptor diversity of two clustered innate immune gene families in the teleost sister lineage: Holostei (bowfin and gars). Using genomic and transcriptomic data, we provide a detailed investigation of the phylogenetic history and conserved synteny of gene clusters encoding diverse immunoglobulin domain-containing proteins (DICPs) and novel immune-type receptors (NITRs). These data demonstrate an ancient linkage of DICPs to the major histocompatibility complex (MHC) and reveal an evolutionary origin of NITR variable-joining (VJ) exons that predate the TGD by at least 50 million years. Further characterizing the receptor diversity of Holostean DICPs and NITRs illuminates a sequence diversity that rivals the diversity of these innate immune receptor families in many teleosts. Taken together, our findings provide important historical context for the evolution of these gene families that challenge prevailing expectations concerning the consequences of the TGD during actinopterygiian evolution.

Niche partitioning shaped herbivore macroevolution through the early Mesozoic

The Triassic (252-201 Ma) marks a major punctuation in Earth history, when ecosystems rebuilt themselves following the devastating Permian-Triassic mass extinction. Herbivory evolved independently several times as ecosystems comprising diverse assemblages of therapsids, parareptiles and archosauromorphs rose and fell, leading to a world dominated by dinosaurs. It was assumed that dinosaurs prevailed either through long-term competitive replacement of the incumbent clades or rapidly and opportunistically following one or more extinction events. Here we use functional morphology and ecology to explore herbivore morphospace through the Triassic and Early Jurassic. We identify five main herbivore guilds (ingestion generalists, prehension specialists, durophagous specialists, shearing pulpers, and heavy oral processors), and find that herbivore clades generally avoided competition by almost exclusively occupying different guilds. Major ecosystem remodelling was triggered multiple times by external environmental challenges, and previously dominant herbivores were marginalised by newly emerging forms. Dinosaur dominance was a mix of opportunity following disaster, combined with competitive advantage in their new world.

Mesozoic mitogenome rearrangements and freshwater mussel (Bivalvia: Unionoidea) macroevolution

Using a new fossil-calibrated mitogenome-based approach, we identified macroevolutionary shifts in mitochondrial gene order among the freshwater mussels (Unionoidea). We show that the early Mesozoic divergence of the two Unionoidea clades, Margaritiferidae and Unionidae, was accompanied by a synchronous split in the gene arrangement in the female mitogenome (i.e., gene orders MF1 and UF1). Our results suggest that this macroevolutionary jump was completed within a relatively short time interval (95% HPD 201-226 Ma) that coincided with the Triassic-Jurassic mass extinction. Both gene orders have persisted within these clades for ~200 Ma. The monophyly of the so-called "problematic" Gonideinae taxa was supported by all the inferred phylogenies in this study using, for the first time, the M- and F-type mitogenomes either singly or combined. Within Gonideinae, two additional splits in the gene order (UF1 to UF2, UF2 to UF3) occurred in the Mesozoic and have persisted for ~150 and ~100 Ma, respectively. Finally, the mitogenomic results suggest ancient connections between freshwater basins of East Asia and Europe near the Cretaceous-Paleogene boundary, probably via a continuous paleo-river system or along the Tethys coastal line, which are well supported by at least three independent but almost synchronous divergence events.

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. Elsewhere in the fossil record, undersampled diversity and more fragmentary specimens produce spurious results. We identify a novel effect, that a taxon moves towards the centroid of a Generalized Euclidean dataset as its proportion of missing data increases. We term this effect 'centroid slippage', as a disparity-based analogue of phylogenetic stemward slippage. Our results suggest that uneven sampling presents issues for our view of disparity in the fossil record, but that this is also dependent on the methodology used, especially true with widely used Generalized Euclidean distances. Mitigation of missing cladistic data is possible by phylogenetic gap filling, and heterogeneous effects of lagerstätten on disparity may be accounted for by understanding the factors affecting their spatio-temporal distribution.

Two pulses of morphological diversification in Pacific pelagic fishes following the Cretaceous-Palaeogene mass extinction

Molecular phylogenies suggest some major radiations of open-ocean fish clades occurred roughly coincident with the Cretaceous-Palaeogene (K/Pg) boundary, however the timing and nature of this diversification is poorly constrained. Here, we investigate evolutionary patterns in ray-finned fishes across the K/Pg mass extinction 66 million years ago (Ma), using microfossils (isolated teeth) preserved in a South Pacific sediment core spanning 72-43 Ma. Our record does not show significant turnover of fish tooth morphotypes at the K/Pg boundary: only two of 48 Cretaceous tooth morphotypes disappear at the event in the South Pacific, a rate no different from background extinction. Capture-mark-recapture analysis finds two pulses of origination in fish tooth morphotypes following the mass extinction. The first pulse, at approximately 64 Ma, included short-lived teeth, as well as forms that contribute to an expansion into novel morphospace. A second pulse, centred at approximately 58 Ma, produced morphotype novelty in a different region of morphospace from the first pulse, and contributed significantly to Eocene tooth morphospace occupation. There was no significant increase in origination rates or expansion into novel morphospace during the early or middle Eocene, despite a near 10-fold increase in tooth abundance during that interval. Our results suggest that while the K/Pg event had a minor impact on fish diversity in terms of extinction, the removal of the few dominant Cretaceous morphotypes triggered a sequence of origination events allowing fishes to rapidly diversify morphologically, setting the stage for exceptional levels of ray-finned fish diversity in the Cenozoic.