Sex and the shifting biodiversity dynamics of marine animals in deep time

Deciphering dynamic interactions between spermatozoa and the ovarian microenvironment through integrated multi-omics approaches in viviparous Sebastes schlegelii

The ovarian microenvironment plays a crucial role in ensuring the reproductive success of viviparous teleosts. However, the molecular mechanism underlying the interaction between spermatozoa and the ovarian microenvironment has remained elusive. This study aimed to contribute to a better understanding of this process in black rockfish (Sebastes schlegelii) using integrated multi-omics approaches. The results demonstrated significant upregulation of ovarian complement-related proteins and pattern recognition receptors, along with remodeling of glycans on the surface of spermatozoa at the early spermatozoa-storage stage (1 month after mating). As spermatozoa were stored over time, ovarian complement proteins were progressively repressed by tryptophan and hippurate, indicating a remarkable adaptation of spermatozoa to the ovarian microenvironment. Before fertilization, a notable upregulation of cellular junction proteins was observed. The study revealed that spermatozoa bind to ZPB2a protein through GSTM3 and that ZPB2a promotes spermatozoa survival and movement in a GSTM3-dependent manner. These findings shed light on a key mechanism that influences the dynamics of spermatozoa in the female reproductive tract, providing valuable insights into the molecular networks regulating spermatozoa adaptation and survival in species with internal fertilization.

How predictable are mass extinction events?

Many modern extinction drivers are shared with past mass extinction events, such as rapid climate warming, habitat loss, pollution and invasive species. This commonality presents a key question: can the extinction risk of species during past mass extinction events inform our predictions for a modern biodiversity crisis? To investigate if it is possible to establish which species were more likely to go extinct during mass extinctions, we applied a functional trait-based model of extinction risk using a machine learning algorithm to datasets of marine fossils for the end-Permian, end-Triassic and end-Cretaceous mass extinctions. Extinction selectivity was inferred across each individual mass extinction event, before testing whether the selectivity patterns obtained could be used to 'predict' the extinction selectivity exhibited during the other mass extinctions. Our analyses show that, despite some similarities in extinction selectivity patterns between ancient crises, the selectivity of mass extinction events is inconsistent, which leads to a poor predictive performance. This lack of predictability is attributed to evolution in marine ecosystems, particularly during the Mesozoic Marine Revolution, associated with shifts in community structure alongside coincident Earth system changes. Our results suggest that past extinctions are unlikely to be informative for predicting extinction risk during a projected mass extinction.

Fossil bacula of five species of Borophaginae (Family: Canidae): Implications for their reproductive biology

The baculum of mammals offers the opportunity to study the reproductive biology of extinct species given that it is a fossilizable part of the male genitalia and that its size and shape correlate with several aspects of the reproductive biology of extant mammals. Fossil bacula, however, are rare. Currently, bacula have been described from only two extinct species of canids, one from the subfamily Caninae and the other from the extinct subfamily Hesperocyoninae. Here, I describe the bacula of five extinct species of Borophaginae, each of which was found with other skeletal elements that have enabled identification to the species level. Two specimens (Aelurodon ferox and Aelurodon stirtoni) are largely complete, while the baculum from Carpocyon compressus is complete but still embedded in matrix that obscures some of its features. The bacula of Paratomarctus euthos and Desmocyon thomsoni are incomplete, but they provide useful information nonetheless. These borophagine bacula are similar to extant canines in being robust, having a urethral groove, and a simple distal end. These features suggest that the Borophaginae had long-lasting copulation and possibly spontaneous ovulation, similar to the extant canines. However, unlike the straight baculum of extant canines, borophagine bacula are ventrally curved (arched), which is also observed in the hesperocyonine baculum. The implication of this curvature for the reproductive biology of these animals remains unknown.

Post-extinction recovery of the Phanerozoic oceans and biodiversity hotspots

The fossil record of marine invertebrates has long fuelled the debate as to whether or not there are limits to global diversity in the sea1-5. Ecological theory states that, as diversity grows and ecological niches are filled, the strengthening of biological interactions imposes limits on diversity6,7. However, the extent to which biological interactions have constrained the growth of diversity over evolutionary time remains an open question1-5,8-11. Here we present a regional diversification model that reproduces the main Phanerozoic eon trends in the global diversity of marine invertebrates after imposing mass extinctions. We find that the dynamics of global diversity are best described by a diversification model that operates widely within the exponential growth regime of a logistic function. A spatially resolved analysis of the ratio of diversity to carrying capacity reveals that less than 2% of the global flooded continental area throughout the Phanerozoic exhibits diversity levels approaching ecological saturation. We attribute the overall increase in global diversity during the Late Mesozoic and Cenozoic eras to the development of diversity hotspots under prolonged conditions of Earth system stability and maximum continental fragmentation. We call this the 'diversity hotspots hypothesis', which we propose as a non-mutually exclusive alternative to the hypothesis that the Mesozoic marine revolution led this macroevolutionary trend12,13.

Drivers of diversification in freshwater gastropods vary over deep time

Unravelling the drivers of species diversification through geological time is of crucial importance for our understanding of long-term evolutionary processes. Numerous studies have proposed different sets of biotic and abiotic controls of speciation and extinction rates, but typically they were inferred for a single, long geological time frame. However, whether the impact of biotic and abiotic controls on diversification changes over time is poorly understood. Here, we use a large fossil dataset, a multivariate birth-death model and a comprehensive set of biotic and abiotic predictors, including a new index to quantify tectonic complexity, to estimate the drivers of diversification for European freshwater gastropods over the past 100 Myr. The effects of these factors on origination and extinction are estimated across the entire time frame as well as within sequential time windows of 20 Myr each. Our results find support for temporal heterogeneity in the factors associated with changes in diversification rates. While the factors impacting speciation and extinction rates vary considerably over time, diversity-dependence and topography are consistently important. Our study highlights that a high level of heterogeneity in diversification rates is best captured by incorporating time-varying effects of biotic and abiotic factors.

Biotic and Abiotic Controls on the Phanerozoic History of Marine Animal Biodiversity

During the past 541 million years, marine animals underwent three intervals of diversification (early Cambrian, Ordovician, Cretaceous–Cenozoic) separated by nondirectional fluctuation, suggesting diversity-dependent dynamics with the equilibrium diversity shifting through time. Changes in factors such as shallow-marine habitat area and climate appear to have modulated the nondirectional fluctuations. Directional increases in diversity are best explained by evolutionary innovations in marine animals and primary producers coupled with stepwise increases in the availability of food and oxygen. Increasing intensity of biotic interactions such as predation and disturbance may have led to positive feedbacks on diversification as ecosystems became more complex. Important areas for further research include improving the geographic coverage and temporal resolution of paleontological data sets, as well as deepening our understanding of Earth system evolution and the physiological and ecological traits that modulated organismal responses to environmental change.

Bottom-up controls, ecological revolutions and diversification in the oceans through time

Animals originated in the oceans and evolved there for hundreds of millions of years before adapting to terrestrial environments. Today, oceans cover more than two-thirds of Earth and generate as much primary production as land. The path from the first macrobiota to modern marine biodiversity involved parallel increases in terrestrial nutrient input, marine primary production, species' abundance, metabolic rates, ecotypic diversity and taxonomic diversity. Bottom-up theories of ecosystem cascades arrange these changes in a causal sequence. At the base of marine food webs, nutrient fluxes and atmosphere-ocean chemistry interact with phytoplankton to regulate production. First-order consumers (e.g., zooplankton) might propagate changes in quantity and quality of phytoplankton to changes in abundance and diversity of larger predators (e.g., nekton). However, many uncertainties remain about the mechanisms and effect size of bottom-up control, particularly in oceans across the entire history of animal life. Here, we review modern and fossil evidence for hypothesized bottom-up pathways, and we assess the ramifications of these processes for four key intervals in marine ecosystems: the Ediacaran-Cambrian (635-485 million years ago), the Ordovician (485-444 million years ago), the Devonian (419-359 million years ago) and the Mesozoic (252-66 million years ago). We advocate for a clear articulation of bottom-up hypotheses to better understand causal relationships and proposed effects, combined with additional ecological experiments, paleontological documentation, isotope geochemistry and geophysical reconstructions. How small-scale ecological change transitions into large-scale evolutionary change remains an outstanding question for empirical and theoretical research.

Evolution and extinction can occur rapidly: a modeling approach

Fossil record of Earth describing the last 500 million years is characterized by evolution discontinuity as well as recurring global extinctions of some species and their replacement by new types, the causes of which are still debate. We developed a model of evolutionary self-development of a large ecosystem. This model of biota evolution based on the universal laws of living systems functioning: reproduction, dependence of reproduction efficiency and mortality on biota density, mutational variability in the process of reproduction and selection of the most adapted individuals. We have shown that global extinctions and phases of rapid growth and biodiversity stasis can be a reflection of the emergence of bistability in a self-organizing system, which is the Earth’s biota. Bistability was found to be characteristic only for ecosystems with predominant sexual reproduction. The reason for the transition from one state to another is the selection of the most adapted individuals. That is, we explain the characteristics of the Earth’s fossil record during the last 500 million years by the internal laws of Earth’s ecosystem functioning, which appeared at a certain stage of evolution as a result of the emergence of life forms with an increased adaptive diversification associated with sexual dimorphism.

Speciation across the Tree of Life

Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.

Causes of global extinctions in the history of life: facts and hypotheses

Paleontologists define global extinctions on Earth as a loss of about three-quarters of plant and animal species over a relatively short period of time. At least five global extinctions are documented in the Phanerozoic fossil record (~500-million-year period): ~65, 200, 260, 380, and 440 million years ago. In addition, there is evidence of global extinctions in earlier periods of life on Earth - during the Late Cambrian (~500 million years ago) and Ediacaran periods (more than 540 million years ago). There is still no common opinion on the causes of their occurrence. The current study is a systematized review of the data on recorded extinctions of complex life forms on Earth from the moment of their occurrence during the Ediacaran period to the modern period. The review discusses possible causes for mass extinctions in the light of the influence of abiogenic factors, planetary or astronomical, and the consequences of their actions. We evaluate the pros and cons of the hypothesis on the presence of periodicity in the extinction of Phanerozoic marine biota. Strong evidence that allows us to hypothesize that additional mechanisms associated with various internal biotic factors are responsible for the emergence of extinctions in the evolution of complex life forms is discussed. Developing the idea of the internal causes of periodicity and discontinuity in evolution, we propose our own original hypothesis, according to which the bistability phenomenon underlies the complex dynamics of the biota development, which is manifested in the form of global extinctions. The bistability phenomenon arises only in ecosystems with predominant sexual reproduction. Our hypothesis suggests that even in the absence of global abiotic catastrophes, extinctions of biota would occur anyway. However, our hypothesis does not exclude the possibility that in different periods of the Earth's history the biota was subjected to powerful external influences that had a significant impact on its further development, which is reflected in the Earth's fossil record.

The spatial structure of Phanerozoic marine animal diversity

The global fossil record of marine animals has fueled long-standing debates about diversity change through time and the drivers of this change. However, the fossil record is not truly global. It varies considerably in geographic scope and in the sampling of environments among intervals of geological time. We account for this variability using a spatially explicit approach to quantify regional-scale diversity through the Phanerozoic. Among-region variation in diversity is comparable to variation through time, and much of this is explained by environmental factors, particularly the extent of reefs. By contrast, influential hypotheses of diversity change through time, including sustained long-term increases, have little explanatory power. Modeling the spatial structure of the fossil record transforms interpretations of Phanerozoic diversity patterns and their macroevolutionary explanations. This necessitates a refocus of deep-time diversification studies.

Crinoid respiration and the distribution of energetic strategies among marine invertebrates

During the Mesozoic, the radiation of durophagous marine predators caused the ecological and evolutionary diminution of once-successful groups, including stalked, suspension-feeding echinoderms known as crinoids. Featherstars, crinoids that shed the stalk during development and exhibit anti-predatory adaptations such as high motility, defied this trend, and today they are widespread and diverse across ocean depths. As a ‘success story’ of the Mesozoic Marine Revolution, featherstars could be used to reveal how some marine lineages succeeded in the face of increased predation over geological time. However, current limited understanding of crinoid functional anatomy has inhibited such study. Using microphotography, scanning electron microscopy and computed tomography, I characterize the structure and variation of crinoid circulatory anatomy and explore differences between featherstars and stalked forms. Contrary to previous accounts, I find support for the role of coelomic circulation in crinoid respiration. This includes a previously undocumented case of positive allometry: larger crinoids have more complex circulatory anatomy. Moreover, quantitative analysis of coelomic anatomy shows that the circulatory system is generally more complex in featherstars than in stalked crinoids. The adaptations that allowed featherstars to persist in shallow water apparently entailed an increase in the functional capacity of the circulatory system, possibly due to consistently greater metabolic rates.

Ecological Expansion and Extinction in the Late Ediacaran: Weighing the Evidence for Environmental and Biotic Drivers

The Ediacara Biota, Earth's earliest communities of complex, macroscopic, multicellular organisms, appeared during the late Ediacaran Period, just prior to the Cambrian Explosion. Ediacara fossil assemblages consist of exceptionally preserved soft-bodied forms of enigmatic morphology and affinity which nonetheless represent a critical stepping-stone in the evolution of complex animal ecosystems. The Ediacara Biota has historically been divided into three successive Assemblages-the Avalon, the White Sea, and the Nama. Although the oldest (Avalon) Assemblage documents the initial appearance of several groups of Ediacara taxa, the two younger (White Sea and Nama) Assemblages record a particularly striking suite of ecological innovations, including the appearance of diverse Ediacara body plans-in tandem with the rise of bilaterian animals-as well as the emergence of novel ecological strategies such as movement, sexual reproduction, biomineralization, and the development of dense, heterogeneous benthic communities. Many of these ecological innovations appear to be linked to adaptations to heterogeneous substrates and shallow and energetic marine settings. In spite of these innovations, the majority of Ediacara taxa disappear by the end of the Ediacaran, with interpretations for this disappearance historically ranging from the closing of preservational windows to environmentally or biotically mediated extinction. However, in spite of the unresolved affinity and eventual extinction of individual Ediacara taxa, these distinctive ecological strategies persist across the Ediacaran-Cambrian boundary and are characteristic of younger animal-dominated communities of the Phanerozoic. The late Ediacaran emergence of these strategies may, therefore, have facilitated subsequent radiations of the Cambrian. In this light, the Ediacaran and Cambrian Periods, although traditionally envisioned as separate worlds, are likely to have been part of an ecological and evolutionary continuum.

Rarity and persistence

Rarity is a population characteristic that is usually associated with a high risk of extinction. We argue here, however, that chronically rare species (those with low population densities over many generations across their entire ranges) may have individual-level traits that make populations more resistant to extinction. The major obstacle to persistence at low density is successful fertilisation (union between egg and sperm), and chronically rare species are more likely to survive when (1) fertilisation occurs inside or close to an adult, (2) mate choice involves long-distance signals, (3) adults or their surrogate gamete dispersers are highly mobile, or (4) the two sexes are combined in a single individual. In contrast, external fertilisation and wind- or water-driven passive dispersal of gametes, or sluggish or sedentary adult life habits in the absence of gamete vectors, appear to be incompatible with sustained rarity. We suggest that the documented increase in frequency of these traits among marine genera over geological time could explain observed secular decreases in rates of background extinction. Unanswered questions remain about how common chronic rarity actually is, which traits are consistently associated with chronic rarity, and how chronically rare species are distributed among taxa, and among the world's ecosystems and regions.

Emergence of modern marine ecosystems

The structure and function of marine ecosystems are not fixed. Instead, major innovations - from the origin of oxygenic photosynthesis, to the evolution of reefs or of deep bioturbation, to the rise of pelagic calcifiers - have changed biogeochemical cycles and ecosystem dynamics. As a result, modern marine ecosystems are fundamentally different from those in the distant past.

Plate tectonic regulation of global marine animal diversity

Valentine and Moores [Valentine JW, Moores EM (1970) Nature 228:657-659] hypothesized that plate tectonics regulates global biodiversity by changing the geographic arrangement of continental crust, but the data required to fully test the hypothesis were not available. Here, we use a global database of marine animal fossil occurrences and a paleogeographic reconstruction model to test the hypothesis that temporal patterns of continental fragmentation have impacted global Phanerozoic biodiversity. We find a positive correlation between global marine invertebrate genus richness and an independently derived quantitative index describing the fragmentation of continental crust during supercontinental coalescence-breakup cycles. The observed positive correlation between global biodiversity and continental fragmentation is not readily attributable to commonly cited vagaries of the fossil record, including changing quantities of marine rock or time-variable sampling effort. Because many different environmental and biotic factors may covary with changes in the geographic arrangement of continental crust, it is difficult to identify a specific causal mechanism. However, cross-correlation indicates that the state of continental fragmentation at a given time is positively correlated with the state of global biodiversity for tens of millions of years afterward. There is also evidence to suggest that continental fragmentation promotes increasing marine richness, but that coalescence alone has only a small negative or stabilizing effect. Together, these results suggest that continental fragmentation, particularly during the Mesozoic breakup of the supercontinent Pangaea, has exerted a first-order control on the long-term trajectory of Phanerozoic marine animal diversity.

The timetable of evolution

The integration of fossils, phylogeny, and geochronology has resulted in an increasingly well-resolved timetable of evolution. Life appears to have taken root before the earliest known minimally metamorphosed sedimentary rocks were deposited, but for a billion years or more, evolution played out beneath an essentially anoxic atmosphere. Oxygen concentrations in the atmosphere and surface oceans first rose in the Great Oxygenation Event (GOE) 2.4 billion years ago, and a second increase beginning in the later Neoproterozoic Era [Neoproterozoic Oxygenation Event (NOE)] established the redox profile of modern oceans. The GOE facilitated the emergence of eukaryotes, whereas the NOE is associated with large and complex multicellular organisms. Thus, the GOE and NOE are fundamental pacemakers for evolution. On the time scale of Earth's entire 4 billion-year history, the evolutionary dynamics of the planet's biosphere appears to be fast, and the pace of evolution is largely determined by physical changes of the planet. However, in Phanerozoic ecosystems, interactions between new functions enabled by the accumulation of characters in a complex regulatory environment and changing biological components of effective environments appear to have an important influence on the timing of evolutionary innovations. On the much shorter time scale of transient environmental perturbations, such as those associated with mass extinctions, rates of genetic accommodation may have been limiting for life.