Prolonged Permian Triassic ecological crisis recorded by molluscan dominance in Late Permian offshore assemblages

Multi-omic insights into the formation and evolution of a novel shell microstructure in oysters

BACKGROUND

Molluscan shell, composed of a diverse range of architectures and microstructures, is a classic model system to study the relationships between molecular evolution and biomineralized structure formation. The shells of oysters differ from those of other molluscs by possessing a novel microstructure, chalky calcite, which facilitates adaptation to the sessile lifestyle. However, the genetic basis and evolutionary origin of this adaptive innovation remain largely unexplored.

RESULTS

We report the first whole-genome assembly and shell proteomes of the Iwagaki oyster Crassostrea nippona. Multi-omic integrative analyses revealed that independently expanded and co-opted tyrosinase, peroxidase, TIMP genes may contribute to the chalky layer formation in oysters. Comparisons with other molluscan shell proteomes imply that von Willebrand factor type A and chitin-binding domains are basic members of molluscan biomineralization toolkit. Genome-wide identification and analyses of these two domains in 19 metazoans enabled us to propose that the well-known Pif may share a common origin in the last common ancestor of Bilateria. Furthermore, Pif and LamG3 genes acquire new genetic function for shell mineralization in bivalves and the chalky calcite formation in oysters likely through a combination of gene duplication and domain reorganization.

CONCLUSIONS

The spatial expression of SMP genes in the mantle and molecular evolution of Pif are potentially involved in regulation of the chalky calcite deposition, thereby shaping the high plasticity of the oyster shell to adapt to a sessile lifestyle. This study further highlights neo-functionalization as a crucial mechanism for the diversification of shell mineralization and microstructures in molluscs, which may be applied more widely for studies on the evolution of metazoan biomineralization.

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. The brachiopod-bivalve switch is emblematic of the global turnover of marine faunas from Palaeozoic-type to Modern-type triggered by the PTME. Here, using Bayesian analyses, we find that unexpectedly the two clades displayed similar large-scale trends of diversification before the Jurassic. Insight from a multivariate birth-death model shows that the extinction of major brachiopod clades during the PTME set the stage for the brachiopod-bivalve switch, with differential responses to high ocean temperatures post-extinction further facilitating their displacement by bivalves. Our study strengthens evidence that brachiopods and bivalves were not competitors over macroevolutionary time scales, with extinction events and environmental stresses shaping their divergent fates.

The stability and collapse of marine ecosystems during the Permian-Triassic mass extinction

The history of Earth's biodiversity is punctuated episodically by mass extinctions. These are characterized by major declines of taxon richness, but the accompanying ecological collapse has rarely been evaluated quantitatively. The Permian-Triassic mass extinction (PTME; ∼252 mya), as the greatest known extinction, permanently altered marine ecosystems and paved the way for the transition from Paleozoic to Mesozoic evolutionary faunas. Thus, the PTME offers a window into the relationship between taxon richness and ecological dynamics of ecosystems during a severe extinction. However, the accompanying ecological collapse through the PTME has not been evaluated in detail. Here, using food-web models and a marine paleocommunity dataset spanning the PTME, we show that after the first extinction phase, community stability decreased only slightly despite the loss of more than half of taxonomic diversity, while community stability significantly decreased in the second phase. Thus, taxonomic and ecological changes were unequivocally decoupled, with species richness declining severely ∼61 ka earlier than the collapse of marine ecosystem stability, implying that in major catastrophes, a biodiversity crash may be the harbinger of a more devastating ecosystem collapse.

Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens

The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species (Chryseobacterium arachidiradicis, Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae) to the genus Epilithonimonas and eleven (Chryseobacterium anthropi, Chryseobacterium antarcticum, Chryseobacterium carnis, Chryseobacterium chaponense, Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum, Chryseobacterium palustre, Chryseobacterium solincola, Chryseobacterium treverense and Chryseobacterium yonginense) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.

The two phases of the Cambrian Explosion

The dynamics of how metazoan phyla appeared and evolved – known as the Cambrian Explosion – remains elusive. We present a quantitative analysis of the temporal distribution (based on occurrence data of fossil species sampled in each time interval) of lophotrochozoan skeletal species (n = 430) from the terminal Ediacaran to Cambrian Stage 5 (~545 – ~505 Million years ago (Ma)) of the Siberian Platform, Russia. We use morphological traits to distinguish between stem and crown groups. Possible skeletal stem group lophophorates, brachiopods, and molluscs (n = 354) appear in the terminal Ediacaran (~542 Ma) and diversify during the early Cambrian Terreneuvian and again in Stage 2, but were devastated during the early Cambrian Stage 4 Sinsk extinction event (~513 Ma) never to recover previous diversity. Inferred crown group brachiopod and mollusc species (n = 76) do not appear until the Fortunian, ~537 Ma, radiate in the early Cambrian Stage 3 (~522 Ma), and with minimal loss of diversity at the Sinsk Event, continued to diversify into the Ordovician. The Sinsk Event also removed other probable stem groups, such as archaeocyath sponges. Notably, this diversification starts before, and extends across the Ediacaran/Cambrian boundary and the Basal Cambrian Carbon Isotope Excursion (BACE) interval (~541 to ~540 Ma), ascribed to a possible global perturbation of the carbon cycle. We therefore propose two phases of the Cambrian Explosion separated by the Sinsk extinction event, the first dominated by stem groups of phyla from the late Ediacaran, ~542 Ma, to early Cambrian stage 4, ~513 Ma, and the second marked by radiating bilaterian crown group species of phyla from ~513 Ma and extending to the Ordovician Radiation.

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.

Organism activity levels predict marine invertebrate survival during ancient global change extinctions

Multistressor global change, the combined influence of ocean warming, acidification, and deoxygenation, poses a serious threat to marine organisms. Experimental studies imply that organisms with higher levels of activity should be more resilient, but testing this prediction and understanding organism vulnerability at a global scale, over evolutionary timescales, and in natural ecosystems remain challenging. The fossil record, which contains multiple extinctions triggered by multistressor global change, is ideally suited for testing hypotheses at broad geographic, taxonomic, and temporal scales. Here, I assess the importance of activity level for survival of well-skeletonized benthic marine invertebrates over a 100-million-year-long interval (Permian to Jurassic periods) containing four global change extinctions, including the end-Permian and end-Triassic mass extinctions. More active organisms, based on a semiquantitative score incorporating feeding and motility, were significantly more likely to survive during three of the four extinction events (Guadalupian, end-Permian, and end-Triassic). In contrast, activity was not an important control on survival during nonextinction intervals. Both the end-Permian and end-Triassic mass extinctions also triggered abrupt shifts to increased dominance by more active organisms. Although mean activity gradually returned toward pre-extinction values, the net result was a permanent ratcheting of ecosystem-wide activity to higher levels. Selectivity patterns during ancient global change extinctions confirm the hypothesis that higher activity, a proxy for respiratory physiology, is a fundamental control on survival, although the roles of specific physiological traits (such as extracellular pCO₂ or aerobic scope) cannot be distinguished. Modern marine ecosystems are dominated by more active organisms, in part because of selectivity ratcheting during these ancient extinctions, so on average may be less vulnerable to global change stressors than ancient counterparts. However, ancient extinctions demonstrate that even active organisms can suffer major extinction when the intensity of environmental disruption is intense.

Subsequent biotic crises delayed marine recovery following the late Permian mass extinction event in northern Italy

The late Permian mass extinction event was the largest biotic crisis of the Phanerozoic and has the longest recovery interval of any extinction event. It has been hypothesised that subsequent carbon isotope perturbations during the Early Triassic are associated with biotic crises that impeded benthic recovery. We test this hypothesis by undertaking the highest-resolution study yet made of the rock and fossil records of the entire Werfen Formation, Italy. Here, we show that elevated extinction rates were recorded not only in the Dienerian, as previously recognised, but also around the Smithian/Spathian boundary. Functional richness increases across the Smithian/Spathian boundary associated with elevated origination rates in the lower Spathian. The taxonomic and functional composition of benthic faunas only recorded two significant changes: (1) reduced heterogeneity in the Dienerian, and (2) and a faunal turnover across the Smithian/Spathian boundary. The elevated extinctions and compositional shifts in the Dienerian and across the Smithian/Spathian boundary are associated with a negative and positive isotope excursion, respectively, which supports the hypothesis that subsequent biotic crises are associated with carbon isotope shifts. The Spathian fauna represents a more advanced ecological state, not recognised in the previous members of the Werfen Formation, with increased habitat differentiation, a shift in the dominant modes of life, appearance of stenohaline taxa and the occupation of the erect and infaunal tiers. In addition to subsequent biotic crises delaying the recovery, therefore, persistent environmental stress limited the ecological complexity of benthic recovery prior to the Spathian.

Ecological interactions on macroevolutionary time scales: clams and brachiopods are more than ships that pass in the night

Competition among organisms has ecological and evolutionary consequences. However, whether the consequences of competition are manifested and measureable on macroevolutionary time scales is equivocal. Marine bivalves and brachiopods have overlapping niches such that competition for food and space may occur. Moreover, there is a long-standing debate over whether bivalves outcompeted brachiopods evolutionarily, because brachiopod diversity declined through time while bivalve diversity increased. To answer this question, we estimate the origination and extinction dynamics of fossil marine bivalve and brachiopod genera from the Ordovician through to the Recent while simultaneously accounting for incomplete sampling. Then, using stochastic differential equations, we assess statistical relationships among diversification and sampling dynamics of brachiopods and bivalves and five paleoenvironmental proxies. None of these potential environmental drivers had any detectable influence on brachiopod or bivalve diversification. In contrast, elevated bivalve extinction rates causally increased brachiopod origination rates, suggesting that bivalves have suppressed brachiopod evolution.