An early Miocene extinction in pelagic sharks

The Micropaleoecology Framework: Evaluating Biotic Responses to Global Change Through Paleoproxy, Microfossil, and Ecological Data Integration

The microfossil record contains abundant, diverse, and well-preserved fossils spanning multiple trophic levels from primary producers to apex predators. In addition, microfossils often constitute and are preserved in high abundances alongside continuous high-resolution geochemical proxy records. These characteristics mean that microfossils can provide valuable context for understanding the modern climate and biodiversity crises by allowing for the interrogation of spatiotemporal scales well beyond what is available in neo-ecological research. Here, we formalize a research framework of "micropaleoecology," which builds on a holistic understanding of global change from the environment to ecosystem level. Location: Global. Time period: Neoproterozoic-Phanerozoic. Taxa studied: Fossilizing organisms/molecules. Our framework seeks to integrate geochemical proxy records with microfossil records and metrics, and draws on mechanistic models and systems-level statistical analyses to integrate disparate records. Using multiple proxies and mechanistic mathematical frameworks extends analysis beyond traditional correlation-based studies of paleoecological associations and builds a greater understanding of past ecosystem dynamics. The goal of micropaleoecology is to investigate how environmental changes impact the component and emergent properties of ecosystems through the integration of multi-trophic level body fossil records (primarily using microfossils, and incorporating additional macrofossil data where possible) with contemporaneous environmental (biogeochemical, geochemical, and sedimentological) records. Micropaleoecology, with its focus on integrating ecological metrics within the context of paleontological records, facilitates a deeper understanding of the response of ecosystems across time and space to better prepare for a future Earth under threat from anthropogenic climate change.

Can denticle morphology help identify southeastern Australian elasmobranchs?

Elasmobranchs are covered in scale-like structures called dermal denticles, comprising dentine and enameloid. These structures vary across the body of an individual and between species, and are frequently shed and preserved in marine sediments. With a good understanding of denticle morphology, current and historical elasmobranch diversity and abundance might be assessed from sediment samples. Here, replicate samples of denticles from the bodies of several known (deceased) shark species were collected and characterized for morphology before being assigned morphotypes. These data were used to expand the established literature describing denticles and to investigate intra- and interspecific variability, with the aim of increasing the viability of using sediment samples to assess elasmobranch diversity and abundance. Denticle morphology was influenced more by life-history traits than by species, where demersal species were largely characterized by generalized function and defense denticles, whereas pelagic and benthopelagic species were characterized by drag-reduction denticles. Almost all species possessed abrasion strength or defense denticles on the snout, precluding their utility for separating species. In a separate manipulative experiment, samples of denticles were collected from sediments in two aquaria with known elasmobranchs to determine their utility for reliably separating species. Visual examination of denticles, morphometric measurements, scaled photographs, and reference collections allowed for some precise identification, but not always to the species level. Ongoing work to develop denticle reference collections could help to identify past and present families and, in some cases, species.

Biogeographic response of marine plankton to Cenozoic environmental changes

In palaeontological studies, groups with consistent ecological and morphological traits across a clade's history (functional groups)1 afford different perspectives on biodiversity dynamics than do species and genera2,3, which are evolutionarily ephemeral. Here we analyse Triton, a global dataset of Cenozoic macroperforate planktonic foraminiferal occurrences4, to contextualize changes in latitudinal equitability gradients1, functional diversity, palaeolatitudinal specialization and community equitability. We identify: global morphological communities becoming less specialized preceding the richness increase after the Cretaceous-Palaeogene extinction; ecological specialization during the Early Eocene Climatic Optimum, suggesting inhibitive equatorial temperatures during the peak of the Cenozoic hothouse; increased specialization due to circulation changes across the Eocene-Oligocene transition, preceding the loss of morphological diversity; changes in morphological specialization and richness about 19 million years ago, coeval with pelagic shark extinctions5; delayed onset of changing functional group richness and specialization between hemispheres during the mid-Miocene plankton diversification. The detailed nature of the Triton dataset permits a unique spatiotemporal view of Cenozoic pelagic macroevolution, in which global biogeographic responses of functional communities and richness are decoupled during Cenozoic climate events. The global response of functional groups to similar abiotic selection pressures may depend on the background climatic state (greenhouse or icehouse) to which a group is adapted.

An 800-year record of benthic foraminifer images and 2D morphometrics from the Santa Barbara Basin

The Santa Barbara Basin is an extraordinary archive of environmental and ecological change, where varved sediments preserve microfossils that provide an annual to decadal record of the dynamics of surrounding ecosystems. Of the microfossils preserved in these sediments, benthic foraminifera are the most abundant seafloor-dwelling organisms. While they have been extensively utilized for geochemical and paleoceanographic work, studies of their morphology are lacking. Here we use a high-throughput imaging method (AutoMorph) designed to extract 2D data from photographic images of fossils to produce a large image and 2D shape dataset of recent benthic foraminifera from two core records sampled from the center of the Santa Barbara Basin that span an ~800-year-long interval during the Common Era (1249-2008 CE). Information on more than 36,000 objects is included, of which more than 22,000 are complete or partially-damaged benthic foraminifera. The dataset also includes other biogenic microfossils including ostracods, pteropods, diatoms, radiolarians, fish teeth, and shark dermal denticles. We describe our sample preparation, imaging, and identification techniques, and outline potential data uses.

In search of the origin of crown Mysticeti

Recent research on mysticete fossils from the Late Eocene and Oligocene has revolutionised our understanding of the diversity and evolutionary scenarios for early baleen whales. For example, aetiocetids are a possible, though controversial, lineage that bridges the gap between the toothed and baleen-bearing mysticetes, and eomysticetids show a further transitional step towards the baleen-bearing status, with the presence of non-functional dentition in adults. However, information about the origin of crown mysticetes, including the most recent common ancestor of all extant lineages and its descendants, is critical to further understanding the evolution of baleen whales. The phylogenetic positions of the Oligocene Toipahautea, Whakakai, Horopeta, and Mauicetus from New Zealand remain unresolved and problematic, but all four genera show a close relationship with crown mysticetes. The original and subsequent cladistic analyses have consistently revealed a sister relationship between the Toipahautea-to-Mauicetus grade and crown mysticetes, and Horopeta has been placed close to the cetotheriids within the crown group. This review aims to stimulate more research on this topic by elucidating the origin of crown mysticetes, which likely experienced a poorly known radiation event during the Oligocene that established the modern lineages.

Editorial: Sharks and Skates-Ecology, Distribution and Conservation

The class Chondrichthyes (sharks, rays and chimeras) is one of the three lineages of fishes and the most evolutionary distinct radiation of vertebrates [...].

Teeth outside the mouth: The evolution and development of shark denticles

Vertebrate skin appendages are incredibly diverse. This diversity, which includes structures such as scales, feathers, and hair, likely evolved from a shared anatomical placode, suggesting broad conservation of the early development of these organs. Some of the earliest known skin appendages are dentine and enamel-rich tooth-like structures, collectively known as odontodes. These appendages evolved over 450 million years ago. Elasmobranchs (sharks, skates, and rays) have retained these ancient skin appendages in the form of both dermal denticles (scales) and oral teeth. Despite our knowledge of denticle function in adult sharks, our understanding of their development and morphogenesis is less advanced. Even though denticles in sharks appear structurally similar to oral teeth, there has been limited data directly comparing the molecular development of these distinct elements. Here, we chart the development of denticles in the embryonic small-spotted catshark (Scyliorhinus canicula) and characterize the expression of conserved genes known to mediate dental development. We find that shark denticle development shares a vast gene expression signature with developing teeth. However, denticles have restricted regenerative potential, as they lack a sox2+ stem cell niche associated with the maintenance of a dental lamina, an essential requirement for continuous tooth replacement. We compare developing denticles to other skin appendages, including both sensory skin appendages and avian feathers. This reveals that denticles are not only tooth-like in structure, but that they also share an ancient developmental gene set that is likely common to all epidermal appendages.

Integrating deep-time palaeontology in conservation prioritisation

Halting biodiversity loss under growing anthropogenic pressure is arguably the greatest environmental challenge we face. Given that not all species are equally threatened and that resources are always limited, establishing robust prioritisation schemes is critical for implementing effective conservation actions. To this end, the International Union for Conservation of Nature (IUCN) Red List of Threatened Species has become a widely used source of information on species’ extinction risk. Various metrics have been proposed that combine IUCN status with different aspects of biodiversity to identify conservation priorities. However, current strategies do not take full advantage of palaeontological data, with conservation palaeobiology often focussing on the near-time fossil record (the last 2 million years). Here, we make a case for the value of the deep-time (over 2 million years ago), as it can offer tangible parallels with today’s biodiversity crisis and inform on the intrinsic traits that make species prone to extinction. As such, palaeontological data holds great predictive power, which could be harnessed to flag species likely to be threatened but that are currently too poorly known to be identified as such. Finally, we identify key IUCN-based prioritisation metrics and outline opportunities for integrating palaeontological data to validate their implementation. Although the human signal of the current extinction crisis makes direct comparisons with the geological past challenging, the deep-time fossil record has more to offer to conservation than is currently recognised.

An epithelial signalling centre in sharks supports homology of tooth morphogenesis in vertebrates

Development of tooth shape is regulated by the enamel knot signalling centre, at least in mammals. Fgf signalling regulates differential proliferation between the enamel knot and adjacent dental epithelia during tooth development, leading to formation of the dental cusp. The presence of an enamel knot in non-mammalian vertebrates is debated given differences in signalling. Here, we show the conservation and restriction of fgf3, fgf10, and shh to the sites of future dental cusps in the shark (Scyliorhinus canicula), whilst also highlighting striking differences between the shark and mouse. We reveal shifts in tooth size, shape, and cusp number following small molecule perturbations of canonical Wnt signalling. Resulting tooth phenotypes mirror observed effects in mammals, where canonical Wnt has been implicated as an upstream regulator of enamel knot signalling. In silico modelling of shark dental morphogenesis demonstrates how subtle changes in activatory and inhibitory signals can alter tooth shape, resembling developmental phenotypes and cusp shapes observed following experimental Wnt perturbation. Our results support the functional conservation of an enamel knot-like signalling centre throughout vertebrates and suggest that varied tooth types from sharks to mammals follow a similar developmental bauplan. Lineage-specific differences in signalling are not sufficient in refuting homology of this signalling centre, which is likely older than teeth themselves.

Novel duplication remnant in the first complete mitogenome of Hemitriakis japanica and the unique phylogenetic position of family Triakidae

In this study, we firstly determined the complete mitogenome of the Japanese topeshark (Hemitriakis japonica), which belong to the family Triakidae and was assessed as Endangered A2d on the IUCN Red List in 2021. The mitogenome is 17,301 bp long, has a high AT content (60.0%), and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a control region and specially a 594 bp-long non-coding region between Cytb gene and tRNA-Thr gene. The novel non-coding region share high sequence similarity with segments of the former and latter genes, so it was recognized as a duplication remnant. In addition, the Cytb gene and tRNA-Thr gene tandemly duplicated twice while accompanied by being deleted once at least. This is the first report of mitogenomic gene-arrangement in Triakidae. The phylogenetic trees were constructed using Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 51 shark species and two outgroups. In summary, basing on a novel type of gene rearrangements in houndshark mitogenome, the possibly rearranged process was analyzed and contributed further insight of shark mitogenomes evolution and phylogeny.

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Overfishing drives over one-third of all sharks and rays toward a global extinction crisis

The scale and drivers of marine biodiversity loss are being revealed by the International Union for Conservation of Nature (IUCN) Red List assessment process. We present the first global reassessment of 1,199 species in Class Chondrichthyes-sharks, rays, and chimeras. The first global assessment (in 2014) concluded that one-quarter (24%) of species were threatened. Now, 391 (32.6%) species are threatened with extinction. When this percentage of threat is applied to Data Deficient species, more than one-third (37.5%) of chondrichthyans are estimated to be threatened, with much of this change resulting from new information. Three species are Critically Endangered (Possibly Extinct), representing possibly the first global marine fish extinctions due to overfishing. Consequently, the chondrichthyan extinction rate is potentially 25 extinctions per million species years, comparable to that of terrestrial vertebrates. Overfishing is the universal threat affecting all 391 threatened species and is the sole threat for 67.3% of species and interacts with three other threats for the remaining third: loss and degradation of habitat (31.2% of threatened species), climate change (10.2%), and pollution (6.9%). Species are disproportionately threatened in tropical and subtropical coastal waters. Science-based limits on fishing, effective marine protected areas, and approaches that reduce or eliminate fishing mortality are urgently needed to minimize mortality of threatened species and ensure sustainable catch and trade of others. Immediate action is essential to prevent further extinctions and protect the potential for food security and ecosystem functions provided by this iconic lineage of predators.

Feeding ecology has shaped the evolution of modern sharks

Sharks are iconic predators in today's oceans, yet their modern diversity has ancient origins. In particular, present hypotheses suggest that a combination of mass extinction, global climate change, and competition has regulated the community structure of dominant mackerel (Lamniformes) and ground (Carcharhiniformes) sharks over the last 66 million years. However, while these scenarios advocate an interplay of major abiotic and biotic events, the precise drivers remain obscure. Here, we focus on the role of feeding ecology using a geometric morphometric analysis of 3,837 fossil and extant shark teeth. Our results reveal that morphological segregation rather than competition has characterized lamniform and carcharhiniform evolution. Moreover, although lamniforms suffered a long-term disparity decline potentially linked to dietary "specialization," their recent disparity rivals that of "generalist" carcharhiniforms. We further confirm that low eustatic sea levels impacted lamniform disparity across the end-Cretaceous mass extinction. Adaptations to changing prey availability and the proliferation of coral reef habitats during the Paleogene also likely facilitated carcharhiniform dispersals and cladogenesis, underpinning their current taxonomic dominance. Ultimately, we posit that trophic partitioning and resource utilization shaped past shark ecology and represent critical determinants for their future species survivorship.

An early Miocene extinction in pelagic sharks

Shark populations have been decimated in recent decades because of overfishing and other anthropogenic stressors; however, the long-term impacts of such changes in marine predator abundance and diversity are poorly constrained. We present evidence for a previously unknown major extinction event in sharks that occurred in the early Miocene, ~19 million years ago. During this interval, sharks virtually disappeared from open-ocean sediments, declining in abundance by >90% and morphological diversity by >70%, an event from which they never recovered. This abrupt extinction occurred independently from any known global climate event and ~2 million to 5 million years before diversifications in the highly migratory, large-bodied predators that dominate pelagic ecosystems today, indicating that the early Miocene was a period of rapid, transformative change for open-ocean ecosystems.