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The ocean—the Earth’s largest ecosystem—is increasingly affected by anthropogenic climate change 1 , 2 . Large and globally consistent shifts have been detected in species phenology, range extension and community composition in marine ecosystems 3 – 5 . However, despite evidence for ongoing change, it remains unknown whether marine ecosystems have entered an Anthropocene 6 state beyond the natural decadal to centennial variability. This is because most observational time series lack a long-term baseline, and the few time series that extend back into the pre-industrial era have limited spatial coverage 7 , 8 . Here we use the unique potential of the sedimentary record of planktonic foraminifera—ubiquitous marine zooplankton—to provide a global pre-industrial baseline for the composition of modern species communities. We use a global compilation of 3,774 seafloor-derived planktonic foraminifera communities of pre-industrial age 9 and compare these with communities from sediment-trap time series that have sampled plankton flux since ad 1978 (33 sites, 87 observation years). We find that the Anthropocene assemblages differ from their pre-industrial counterparts in proportion to the historical change in temperature. We observe community changes towards warmer or cooler compositions that are consistent with historical changes in temperature in 85% of the cases. These observations not only confirm the existing evidence for changes in marine zooplankton communities in historical times, but also demonstrate that Anthropocene communities of a globally distributed zooplankton group systematically differ from their unperturbed pre-industrial state. Seafloor-derived planktonic foraminifera communities of pre-industrial age are compared with communities from sediment-trap time series and show that Anthropocene communities of a globally distributed zooplankton group differ from their unperturbed pre-industrial state.

The latitudinal diversity gradient (LDG) is a prevalent feature of modern ecosystems across diverse clades 1 – 4 . Recognized for well over a century, the causal mechanisms for LDGs remain disputed, in part because numerous putative drivers simultaneously covary with latitude 1 , 3 , 5 . The past provides the opportunity to disentangle LDG mechanisms because the relationships among biodiversity, latitude and possible causal factors have varied over time 6 – 9 . Here we quantify the emergence of the LDG in planktonic foraminifera at high spatiotemporal resolution over the past 40 million years, finding that a modern-style gradient arose only 15 million years ago. Spatial and temporal models suggest that LDGs for planktonic foraminifera may be controlled by the physical structure of the water column. Steepening of the latitudinal temperature gradient over 15 million years ago, associated with an increased vertical temperature gradient at low latitudes, may have enhanced niche partitioning and provided more opportunities for speciation at low latitudes. Supporting this hypothesis, we find that higher rates of low-latitude speciation steepened the diversity gradient, consistent with spatiotemporal patterns of depth partitioning by planktonic foraminifera. Extirpation of species from high latitudes also strengthened the LDG, but this effect tended to be weaker than speciation. Our results provide a step change in understanding the evolution of marine LDGs over long timescales. Quantification of planktonic fossils from the past 40 million years shows that the present-day diversity gradient arose only 15 million years ago as the climate started to cool.

The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence (Dendroica, Plethodon and Heliconius). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.

Planktonic foraminifera are one of the most abundant and diverse protists in the oceans. Their utility as paleo proxies requires rigorous taxonomy and comparison with living and genetically related counterparts. We merge genetic and fossil evidence of \"Globigerinoides\", characterized by supplementary apertures on spiral side, in a new approach to trace their \"total evidence phylogeny\" since their first appearance in the latest Paleogene. Combined fossil and molecular genetic data indicate that this genus, as traditionally understood, is polyphyletic. Both datasets indicate the existence of two distinct lineages that evolved independently. One group includes \"Globigerinoides\" trilobus and its descendants, the extant \"Globigerinoides\" sacculifer, Orbulina universa and Sphaeroidinella dehiscens. The second group includes the Globigerinoides ruber clade with the extant G. conglobatus and G. elongatus and ancestors. In molecular phylogenies, the trilobus group is not the sister taxon of the ruber group. The ruber group clusters consistently together with the modern Globoturborotalita rubescens as a sister taxon. The re-analysis of the fossil record indicates that the first \"Globigerinoides\" in the late Oligocene are ancestral to the trilobus group, whereas the ruber group first appeared at the base of the Miocene with representatives distinct from the trilobus group. Therefore, polyphyly of the genus \"Globigerinoides\" as currently defined can only be avoided either by broadening the genus concept to include G. rubescens and a large number of fossil species without supplementary apertures, or if the trilobus group is assigned to a separate genus. Since the former is not feasible due to the lack of a clear diagnosis for such a broad genus, we erect a new genus Trilobatus for the trilobus group (type species Globigerina triloba Reuss) and amend Globoturborotalita and Globigerinoides to clarify morphology and wall textures of these genera. In the new concept, Trilobatus n. gen. is paraphyletic and gave rise to the Praeorbulina/Orbulina and Sphaeroidinellopsis/Sphaeroidinella lineages.

Rising carbon dioxide emissions are provoking ocean warming and acidification 1,2 , altering plankton habitats and threatening calcifying organisms 3 , such as the planktonic foraminifera (PF). Whether the PF can cope with these unprecedented rates of environmental change, through lateral migrations and vertical displacements, is unresolved. Here we show, using data collected over the course of a century as FORCIS 4 global census counts, that the PF are displaying evident poleward migratory behaviours, increasing their diversity at mid- to high latitudes and, for some species, descending in the water column. Overall foraminiferal abundances have decreased by 24.2 ± 0.1% over the past eight decades. Beyond lateral migrations 5 , our study has uncovered intricate vertical migration patterns among foraminiferal species, presenting a nuanced understanding of their adaptive strategies. In the temperature and calcite saturation states projected for 2050 and 2100, low-latitude foraminiferal species will face physicochemical environments that surpass their current ecological tolerances. These species may replace higher-latitude species through poleward shifts, which would reduce low-latitude foraminiferal diversity. Our insights into the adaptation of foraminifera during the Anthropocene suggest that migration will not be enough to ensure survival. This underscores the urgent need for us to understand how the interplay of climate change, ocean acidification and other stressors will impact the survivability of large parts of the marine realm.

The geographic ranges of marine organisms, including planktonic foraminifera 1 , diatoms, dinoflagellates 2 , copepods 3 and fish 4 , are shifting polewards owing to anthropogenic climate change 5 . However, the extent to which species will move and whether these poleward range shifts represent precursor signals that lead to extinction is unclear 6 . Understanding the development of marine biodiversity patterns over geological time and the factors that influence them are key to contextualizing these current trends. The fossil record of the macroperforate planktonic foraminifera provides a rich and phylogenetically resolved dataset that provides unique opportunities for understanding marine biogeography dynamics and how species distributions have responded to ancient climate changes. Here we apply a bipartite network approach to quantify group diversity, latitudinal specialization and latitudinal equitability for planktonic foraminifera over the past eight million years using Triton, a recently developed high-resolution global dataset of planktonic foraminiferal occurrences 7 . The results depict a global, clade-wide shift towards the Equator in ecological and morphological community equitability over the past eight million years in response to temperature changes during the late Cenozoic bipolar ice sheet formation. Collectively, the Triton data indicate the presence of a latitudinal equitability gradient among planktonic foraminiferal functional groups which is coupled to the latitudinal biodiversity gradient only through the geologically recent past (the past two million years). Before this time, latitudinal equitability gradients indicate that higher latitudes promoted community equitability across ecological and morphological groups. Observed range shifts among marine planktonic microorganisms 1 , 2 , 8 in the recent and geological past suggest substantial poleward expansion of marine communities even under the most conservative future global warming scenarios. Analysis of Triton, a high-resolution dataset documenting the macroperforate planktonic foraminifera fossil record, reveals a global climate-linked equatorward shift of ecological and morphological community equitability over the past 8 million years.

Foraminifera are a group of mostly marine protists with high taxonomic diversity. Species identification is often complex, as both morphological and molecular approaches can be challenging due to a lack of unique characters and reference sequences. An integrative approach combining state of the art morphological and molecular tools is therefore promising. In this study, we analysed large benthic Foraminifera of the genus Amphisorus from Western Australia and Indonesia. Based on previous findings on high morphological variability observed in the Soritidae and the discontinuous distribution of Amphisorus along the coast of western Australia, we expected to find multiple morphologically and genetically unique Amphisorus types. In order to gain detailed insights into the diversity of Amphisorus , we applied micro CT scanning and shotgun metagenomic sequencing. We identified four distinct morphotypes of Amphisorus , two each in Australia and Indonesia, and showed that each morphotype is a distinct genotype. Furthermore, metagenomics revealed the presence of three dinoflagellate symbiont clades. The most common symbiont was Fugacium Fr5, and we could show that its genotypes were mostly specific to Amphisorus morphotypes. Finally, we assembled the microbial taxa associated with the two Western Australian morphotypes, and analysed their microbial community composition. Even though each Amphisorus morphotype harboured distinct bacterial communities, sampling location had a stronger influence on bacterial community composition, and we infer that the prokaryotic community is primarily shaped by the microhabitat rather than host identity. The integrated approach combining analyses of host morphology and genetics, dinoflagellate symbionts, and associated microbes leads to the conclusion that we identified distinct, yet undescribed taxa of Amphisorus . We argue that the combination of morphological and molecular methods provides unprecedented insights into the diversity of foraminifera, which paves the way for a deeper understanding of their biodiversity, and facilitates future taxonomic and ecological work.

Photosymbiosis, a mode of mixotrophy by algal endosymbiosis, provides key advantages to pelagic life in oligotrophic oceans. Despite its ecological importance, mechanisms underlying its emergence and association with the evolutionary success of photosymbiotic lineages remain unclear. We used planktonic foraminifera, a group of pelagic test-forming protists with an excellent fossil record, to reveal the history of symbiont acquisition among their three main extant clades. We used single-cell 18S rRNA gene amplicon sequencing to reveal symbiont identity and mapped the symbiosis on a phylogeny time-calibrated by fossil data. We show that the highly specific symbiotic interaction with dinoflagellates emerged in the wake of a major extinction of symbiont-bearing taxa at the end of the Eocene. In contrast, less specific and low-light-adapted symbioses with pelagophytes emerged 20 million years later, in multiple independent lineages in the Late Neogene, at a time when the vertical structure of pelagic ecosystems was transformed by global cooling. We infer that in foraminifera, photosymbiosis can evolve easily and that its establishment leads to diversification and ecological dominance to such an extent, that the proliferation of new symbioses is prevented by the incumbent lineages.

The planktonic foraminifera genus Globigerinoides provides a prime example of a species-rich genus in which genetic and morphological divergence are uncorrelated. To shed light on the evolutionary processes that lead to the present-day diversity of Globigerinoides, we investigated the genetic, ecological and morphological divergence of its constituent species. We assembled a global collection of single-cell barcode sequences and show that the genus consists of eight distinct genetic types organized in five extant morphospecies. Based on morphological evidence, we reassign the species Globoturborotalita tenella to Globigerinoides and amend Globigerinoides ruber by formally proposing two new subspecies, G. ruber albus n.subsp. and G. ruber ruber in order to express their subspecies level distinction and to replace the informal G. ruber \"white\" and G. ruber \"pink\", respectively. The genetic types within G. ruber and Globigerinoides elongatus show a combination of endemism and coexistence, with little evidence for ecological differentiation. CT-scanning and ontogeny analysis reveal that the diagnostic differences in adult morphologies could be explained by alterations of the ontogenetic trajectories towards final (reproductive) size. This indicates that heterochrony may have caused the observed decoupling between genetic and morphological diversification within the genus. We find little evidence for environmental forcing of either the genetic or the morphological diversification, which allude to biotic interactions such as symbiosis, as the driver of speciation in Globigerinoides.

Metabarcoding is a cornerstone of modern ecology, but its accuracy is dependent on the chosen gene marker. While the small subunit ribosomal DNA (SSU) is a powerful tool to describe protist diversity, its reliability in retrieving the composition of communities is less obvious. It is particularly challenging to obtain quantitative estimates of abundance in planktonic foraminifera, where the variability of the SSU gene copy number can span three orders of magnitude. As an alternative, we explored the potential of the mitochondrial cytochrome c oxidase subunit I (COI) marker. We developed a reference barcode library of 130 sequences of a 1200 bp long COI fragment belonging to 26 morphospecies of foraminifera and performed 201 single-cell qPCR quantifications to evaluate the relationship between the number of COI copies, and the size of individual foraminifera. We found that the COI evolves between 25 and 1000 times slower than the SSU and therefore has a poor taxonomic resolution. However, we observed a significant relationship between COI copy number and foraminifera size. These results suggest that SSU and COI can play complementary roles: the SSU is well-suited for capturing taxonomic diversity, while the COI is useful to retrieve crude information on the community composition.