The enigma of Oligocene climate and global surface temperature evolution

Water wisteria genome reveals environmental adaptation and heterophylly regulation in amphibious plants

Heterophylly is a phenomenon whereby an individual plant dramatically changes leaf shape in response to the surroundings. Hygrophila difformis (Acanthaceae; water wisteria), has recently emerged as a model plant to study heterophylly because of its striking leaf shape variation in response to various environmental factors. When submerged, H. difformis often develops complex leaves, but on land it develops simple leaves. Leaf complexity is also influenced by other factors, such as light density, humidity, and temperature. Here, we sequenced and assembled the H. difformis chromosome-level genome (scaffold N50: 60.43 Mb, genome size: 871.92 Mb), which revealed 36 099 predicted protein-coding genes distributed over 15 pseudochromosomes. H. difformis diverged from its relatives during the Oligocene climate-change period and expanded gene families related to its amphibious habit. Genes related to environmental stimuli, leaf development, and other pathways were differentially expressed in submerged and terrestrial conditions, possibly modulating morphological and physiological acclimation to changing environments. We also found that auxin plays a role in H. difformis heterophylly. Finally, we discovered candidate genes that respond to different environmental conditions and elucidated the role of LATE MERISTEM IDENTITY 1 (LMI1) in heterophylly. We established H. difformis as a model for studying interconnections between environmental adaptation and morphogenesis.

Evolutionary palaeoecology of European rhinocerotids across the Oligocene-Miocene transition

The Oligocene-Miocene transition witnessed great environmental and faunal changes, spanning from late Oligocene to early Miocene (MP28-MN3). Its drivers and consequences on mammals are, however, poorly understood. Rhinocerotoids are among the most affected taxa, reflected by great taxonomical and morphological changes. However, potential associated changes in ecology have not been explored. Here, we investigated the palaeoecology of 10 rhinocerotid species coming from 15 localities across Western Europe and ranging from MP28 to MN3. We explored evolutionary trends for diet, physiology and habitat via dental wear, hypoplasia, body mass and stable isotopy. All rhinocerotids studied were C3 feeders, whether browsing or mixed-feeding, but clear dietary differences were observed at some localities and between Oligocene and Miocene rhinocerotids. The prevalence of hypoplasia was low (less than 10%) to moderate (less than 20%), but there were great differences by loci, species and localities. Body mass covaried with hypoplasia prevalence, suggesting that larger species might be more susceptible to stresses and environmental changes. We reconstructed similar warm conditions at all localities except Gaimersheim, but found greater variations in precipitation. Indeed, a clear shift in δ13C values was noticed at the end of the Oligocene, consistent with climatic and vegetation changes reported at that time.

A 485-million-year history of Earth's surface temperature

A long-term record of global mean surface temperature (GMST) provides critical insight into the dynamical limits of Earth's climate and the complex feedbacks between temperature and the broader Earth system. Here, we present PhanDA, a reconstruction of GMST over the past 485 million years, generated by statistically integrating proxy data with climate model simulations. PhanDA exhibits a large range of GMST, spanning 11° to 36°C. Partitioning the reconstruction into climate states indicates that more time was spent in warmer rather than colder climates and reveals consistent latitudinal temperature gradients within each state. There is a strong correlation between atmospheric carbon dioxide (CO2) concentrations and GMST, identifying CO2 as the dominant control on variations in Phanerozoic global climate and suggesting an apparent Earth system sensitivity of ~8°C.

Decoding the Chloroplast Genome of Tetrastigma (Vitaceae): Variations and Phylogenetic Selection Insights

Tetrastigma (Vitaceae) is known for its ornamental, medicinal, and ecological significance. However, the structural and variational characteristics of the Tetrastigma chloroplast genome and their impact on phylogenetic relationships remain underexplored. This study utilized bioinformatics methods to assemble and annotate the chloroplast genomes of 10 Tetrastigma species and compare them with five previously sequenced species. This study analyzed gene composition, simple sequence repeats, and codon usage patterns, revealing a high A/T content, uniquely identified pentanucleotide repeats in five species and several preferred codons. In addition, comparative analyses were conducted of the chloroplast genomes of 15 Tetrastigma species, examining their structural differences and identifying polymorphic hotspots (rps16, rps16-trnQ, trnS, trnD, psbC-trnS-psbZ, accD-psaI, psbE-petL-petG, etc.) suitable for DNA marker development. Furthermore, phylogenetic and selective pressure analyses were performed based on the chloroplast genomes of these 15 Tetrastigma species, validating and elucidating intra-genus relationships within Tetrastigma. Futhermore, several genes under positive selection, such as atpF and accD, were identified, shedding light on the adaptive evolution of Tetrastigma. Utilizing 40 Vitaceae species, the divergence time of Tetrastigma was estimated, clarifying the evolutionary relationships within Tetrastigma relative to other genera. The analysis revealed diverse divergences of Tetrastigma in the Miocene and Pliocene, with possible ancient divergence events before the Eocene. Furthermore, family-level selective pressure analysis identified key features distinguishing Tetrastigma from other genera, showing a higher degree of purifying selection. This research enriches the chloroplast genome data for Tetrastigma and offers new insights into species identification, phylogenetic analysis, and adaptive evolution, enhancing our understanding of the genetic diversity and evolutionary history of these species.

Oxygen isotope ensemble reveals Earth's seawater, temperature, and carbon cycle history

Earth's persistent habitability since the Archean remains poorly understood. Using an oxygen isotope ensemble approach-comprising shale, iron oxide, carbonate, silica, and phosphate records-we reconcile a multibillion-year history of seawater δ18O, temperature, and marine and terrestrial clay abundance. Our results reveal a rise in seawater δ18O and a temperate Proterozoic climate distinct to interpretations of a hot early Earth, indicating a strongly buffered climate system. Precambrian sediments are enriched in marine authigenic clay, with prominent reductions occurring in concert with Paleozoic and Cenozoic cooling, the expansion of siliceous life, and the radiation of land plants. These findings support the notion that shifts in the locus and extent of clay formation contributed to seawater 18O enrichment, clement early Earth conditions, major climate transitions, and climate stability through the reverse weathering feedback.

Shallow Whole-Genome Sequencing of Aedes japonicus and Aedes koreicus from Italy and an Updated Picture of Their Evolution Based on Mitogenomics and Barcoding

Aedes japonicus and Aedes koreicus are two invasive mosquitoes native to East Asia that are quickly establishing in temperate regions of Europe. Both species are vectors of arboviruses, but we currently lack a clear understanding of their evolution. Here, we present new short-read, shallow genome sequencing of A. japonicus and A. koreicus individuals from northern Italy, which we used for downstream phylogenetic and barcode analyses. We explored associated microbial DNA and found high occurrences of Delftia bacteria in both samples, but neither Asaia nor Wolbachia. We then assembled complete mitogenomes and used these data to infer divergence times estimating the split of A. japonicus from A. koreicus in the Oligocene, which was more recent than that previously reported using mitochondrial markers. We recover a younger age for most other nodes within Aedini and other Culicidae. COI barcoding and phylogenetic analyses indicate that A. japonicus yaeyamensis, A. japonicus amamiensis, and the two A. koreicus sampled from Europe should be considered as separate species within a monophyletic species complex. Our studies further clarify the evolution of A. japonicus and A. koreicus, and indicate the need to obtain whole-genome data from putative species in order to disentangle their complex patterns of evolution.

Rearranging and completing the puzzle: Phylogenomic analysis of bark beetles Dendroctonus reveals new hypotheses about genus diversification

Studies carried out on bark beetles within Dendroctonus have been extensive and revealed diverse information in different areas of their natural history, taxonomy, evolution, and interactions, among others. Despite these efforts, phylogenetic hypotheses have remained obscured mainly due to limited information analyzed (taxonomic, gene sampling, or both) in studies focused on obtaining evolutionary hypotheses for this genus. With the aim of filling these gaps in the evolutionary history for Dendroctonus, we analyzed ∼1800 loci mapped to a reference genome obtained for 20 of the 21 species recognized to date, minimizing the impact of missing information and improving the assumption of orthology in a phylogenomic framework. We obtained congruent phylogenetic topologies from two phylogenomic inference strategies: loci concatenation (ML framework) and a multispecies coalescent model (MSC) through the analysis of site pattern frequencies (SNPs). Dendroctonus is composed of two major clades (A and B), each containing five and four subclades, respectively. According to our divergence dating analysis, the MRCA for Dendroctonus dates back to the early Eocene, while the MRCA for each major clade diverged in the mid-Eocene. Interestingly, most of the speciation events of extant species occurred during the Miocene, which could be correlated with the diversification of pine trees (Pinus). The MRCA for Dendroctonus inhabited large regions of North America, with all ancestors and descendants of clade A having diversified within this region. The Mexican Transition Zone is important in the diversification processes for the majority of clade A species. For clade B, we identified two important colonization events to the Old World from America: the first in the early Oligocene from the Arctic to Asia (via Beringia), and the second during the Miocene from the Arctic-Western-Alleghany region to Europe and Siberia (also via Beringia). Our genomic analyses also supported the existence of hidden structured lineages within the frontalis complex, and also that D. beckeri represent a lineage independent from D. valens, as previously suggested. The information presented here updates the knowledge concerning the diversification of a genus with remarkable ecological and economic importance.

Genome assembly and resequencing analyses provide new insights into the evolution, domestication and ornamental traits of crape myrtle

Crape myrtle (Lagerstroemia indica) is a globally used ornamental woody plant and is the representative species of Lagerstroemia. However, studies on the evolution and genomic breeding of L. indica have been hindered by the lack of a reference genome. Here we assembled the first high-quality genome of L. indica using PacBio combined with Hi-C scaffolding to anchor the 329.14-Mb genome assembly into 24 pseudochromosomes. We detected a previously undescribed independent whole-genome triplication event occurring 35.5 million years ago in L. indica following its divergence from Punica granatum. After resequencing 73 accessions of Lagerstroemia, the main parents of modern crape myrtle cultivars were found to be L. indica and L. fauriei. During the process of domestication, genetic diversity tended to decrease in many plants, but this was not observed in L. indica. We constructed a high-density genetic linkage map with an average map distance of 0.33 cM. Furthermore, we integrated the results of quantitative trait locus (QTL) using genetic mapping and bulk segregant analysis (BSA), revealing that the major-effect interval controlling internode length (IL) is located on chr1, which contains CDL15, CRG98, and GID1b1 associated with the phytohormone pathways. Analysis of gene expression of the red, purple, and white flower-colour flavonoid pathways revealed that differential expression of multiple genes determined the flower colour of L. indica, with white flowers having the lowest gene expression. In addition, BSA of purple- and green-leaved individuals of populations of L. indica was performed, and the leaf colour loci were mapped to chr12 and chr17. Within these intervals, we identified MYB35, NCED, and KAS1. Our genome assembly provided a foundation for investigating the evolution, population structure, and differentiation of Myrtaceae species and accelerating the molecular breeding of L. indica.

Why we should be looking for longitudinal patterns in biodiversity

Our understanding of global diversity patterns relies overwhelmingly on ecological and evolutionary correlates of latitude, and largely ignores longitude. However, the two major explanations of biodiversity patterns – energy and stability – are confounded across latitudes, and longitude offers potential solutions. Recent literature shows that the global biogeography of the Cenozoic world is structured by longitudinal barriers. In a few well-studied regions, such as South Africa’s Cape, the Himalayas and the Amazon-Andes continuum, there are strong longitudinal gradients in biodiversity. Often, such gradients occur where high and low past climatic velocities are juxtaposed, and there is clear evidence of higher biodiversity at the climatically-stable end. Understanding longitudinal biodiversity variations more widely can offer new insights towards biodiversity conservation in the face of anthropogenic climatic change.

Comparison and Phylogenetic Analysis of Mitochondrial Genomes of Talpidae Animals

Talpidae is a model group for evolutionary studies due to their highly specialized morphologies and diverse lifestyles. Mitochondrial genomes are molecular markers commonly used in species evolution and phylogenetic studies. In this study, the complete mitochondrial genome sequence of Scaptochirus moschatus was obtained by Illumina NovaSeq sequencing. The complete mitochondrial genomes of 14 Talpidae species (including Scaptochirus moschatus obtained in the present study) and the cytochrome b (Cyt b) gene sequences of 48 Talpidae species were downloaded from the NCBI database for comparison and phylogenetic studies to analyze the phylogenetic relationships and to find the possible reasons of the niche differentiation and ecotype specialization of Talpidae animals. The results showed that the mitochondrial genome sequences of 14 species belonging to the family Talpidae were 16,528 to 16,962 bp, all containing 13 protein-coding genes, 22 tRNA, two rRNA, and a non-coding region (control region). The difference in the number of repetitive repeats in the control region is responsible for the difference in the length of Talpidae mitochondrial genome sequences. Combining the divergence time of Talpidae animals with the geological history, it is found that the niche differentiation and ecotype divergence of Talpidae is closely related to historically global climate changes. Semi-aquatic groups diverged in the early Oligocene (about 31.22 MYA), probably in response to the global climate transition from warm to cool. During the early Miocene (about 19.54 MYA), some species of Talpidae moved to underground habitats and formed fossorial groups that were adept at digging due to the effects of the glaciation. In the middle Miocene (about 16.23 MYA), some Talpidae animals returned to the ground and formed semi-fossorial shrew moles as global climate warming again.

The PhanSST global database of Phanerozoic sea surface temperature proxy data

Paleotemperature proxy data form the cornerstone of paleoclimate research and are integral to understanding the evolution of the Earth system across the Phanerozoic Eon. Here, we present PhanSST, a database containing over 150,000 data points from five proxy systems that can be used to estimate past sea surface temperature. The geochemical data have a near-global spatial distribution and temporally span most of the Phanerozoic. Each proxy value is associated with consistent and queryable metadata fields, including information about the location, age, and taxonomy of the organism from which the data derive. To promote transparency and reproducibility, we include all available published data, regardless of interpreted preservation state or vital effects. However, we also provide expert-assigned diagenetic assessments, ecological and environmental flags, and other proxy-specific fields, which facilitate informed and responsible reuse of the database. The data are quality control checked and the foraminiferal taxonomy has been updated. PhanSST will serve as a valuable resource to the paleoclimate community and has myriad applications, including evolutionary, geochemical, diagenetic, and proxy calibration studies.

Enhanced ocean oxygenation during Cenozoic warm periods

Dissolved oxygen (O₂) is essential for most ocean ecosystems, fuelling organisms’ respiration and facilitating the cycling of carbon and nutrients. Oxygen measurements have been interpreted to indicate that the ocean’s oxygen-deficient zones (ODZs) are expanding under global warming^1,2. However, models provide an unclear picture of future ODZ change in both the near term and the long term^3–6. The paleoclimate record can help explore the possible range of ODZ changes in warmer-than-modern periods. Here we use foraminifera-bound nitrogen (N) isotopes to show that water-column denitrification in the eastern tropical North Pacific was greatly reduced during the Middle Miocene Climatic Optimum (MMCO) and the Early Eocene Climatic Optimum (EECO). Because denitrification is restricted to oxygen-poor waters, our results indicate that, in these two Cenozoic periods of sustained warmth, ODZs were contracted, not expanded. ODZ contraction may have arisen from a decrease in upwelling-fuelled biological productivity in the tropical Pacific, which would have reduced oxygen demand in the subsurface. Alternatively, invigoration of deep-water ventilation by the Southern Ocean may have weakened the ocean’s ‘biological carbon pump’, which would have increased deep-ocean oxygen. The mechanism at play would have determined whether the ODZ contractions occurred in step with the warming or took centuries or millennia to develop. Thus, although our results from the Cenozoic do not necessarily apply to the near-term future, they might imply that global warming may eventually cause ODZ contraction.

By using foraminifera-bound nitrogen isotopes, it is shown that, during two warm periods of the Cenozoic, oxygen-deficient zones contracted rather than expanded, suggesting that global warming may not necessarily lead to increased oceanic anoxia.

Total evidence time-scaled phylogenetic and biogeographic models for the evolution of sea cows (Sirenia, Afrotheria)

Molecular phylogenetic studies that have included sirenians from the genera Trichechus, Dugong, and Hydrodamalis have resolved their interrelationships but have yielded divergence age estimates that are problematically discordant. The ages of these lineage splits have profound implications for how to interpret the sirenian fossil record-including clade membership, biogeographic patterns, and correlations with Earth history events. In an effort to address these issues, here we present a total evidence phylogenetic analysis of Sirenia that includes living and fossil species and applies Bayesian tip-dating methods to estimate their interrelationships and divergence times. In addition to extant sirenians, our dataset includes 56 fossil species from 106 dated localities and numerous afrotherian outgroup taxa. Genetic, morphological, temporal, and biogeographic data are assessed simultaneously to bring all available evidence to bear on sirenian phylogeny. The resulting time-tree is then used for Bayesian geocoordinates reconstruction analysis, which models ancestral geographic areas at splits throughout the phylogeny, thereby allowing us to infer the direction and timing of dispersals. Our results suggest that Pan-Sirenia arose in North Africa during the latest Paleocene and that the Eocene evolution of stem sirenians was primarily situated in the Tethyan realm. In the late Eocene, some lineages moved into more northern European latitudes, an area that became the source region for a key trans-Atlantic dispersal towards the Caribbean and northern-adjacent west Atlantic. This event led to the phylogenetic and biogeographic founding of crown Sirenia with the Dugongidae-Trichechidae split occurring at the Eocene-Oligocene boundary (~33.9 Ma), temporally coincident with the onset of dropping global sea levels and temperatures. This region became the nexus of sirenian diversification and supported taxonomically-rich dugongid communities until the earliest Pliocene. The Dugonginae-Hydrodamalinae split occurred near Florida during the early Miocene (~21.2 Ma) and was followed by a west-bound dispersal that gave rise to the Pacific hydrodamalines. The late middle Miocene (~12.2 Ma) split of Dugong from all other dugongines also occurred near Florida and our analyses suggest that the Indo-Pacific distribution of modern dugongs is the result of a trans-Pacific dispersal. From at least the early Miocene, trichechid evolution was based entirely in South America, presumably within the Pebas Wetlands System. We infer that the eventual establishment of Amazon drainage into the South Atlantic allowed the dispersal of Trichechus out of South America no earlier than the mid-Pliocene. Our analyses provide a new temporal and biogeographic framework for understanding major events in sirenian evolution and their possible relationships to oceanographic and climatic changes. These hypotheses can be further tested with the recovery and integration of new fossil evidence.

Archaeal lipids trace ecology and evolution of marine ammonia-oxidizing archaea

Archaeal membrane lipids are widely used for paleotemperature reconstructions, yet these molecular fossils also bear rich information about ecology and evolution of marine ammonia-oxidizing archaea (AOA). Here we identified thermal and nonthermal behaviors of archaeal glycerol dialkyl glycerol tetraethers (GDGTs) by comparing the GDGT-based temperature index (TEX₈₆) to the ratio of GDGTs with two and three cyclopentane rings (GDGT-2/GDGT-3). Thermal-dependent biosynthesis should increase TEX₈₆ and decrease GDGT-2/GDGT-3 when the ambient temperature increases. This presumed temperature-dependent (PTD) trend is observed in GDGTs derived from cultures of thermophilic and mesophilic AOA. The distribution of GDGTs in suspended particulate matter (SPM) and sediments collected from above the pycnocline-shallow water samples-also follows the PTD trend. These similar GDGT distributions between AOA cultures and shallow water environmental samples reflect shallow ecotypes of marine AOA. While there are currently no cultures of deep AOA clades, GDGTs derived from deep water SPM and marine sediment samples exhibit nonthermal behavior deviating from the PTD trend. The presence of deep AOA increases the GDGT-2/GDGT-3 ratio and distorts the temperature-controlled correlation between GDGT-2/GDGT-3 and TEX₈₆. We then used Gaussian mixture models to statistically characterize these diagnostic patterns of modern AOA ecology from paleo-GDGT records to infer the evolution of marine AOA from the Mid-Mesozoic to the present. Long-term GDGT-2/GDGT-3 trends suggest a suppression of today's deep water marine AOA during the Mesozoic-early Cenozoic greenhouse climates. Our analysis provides invaluable insights into the evolutionary timeline and the expansion of AOA niches associated with major oceanographic and climate changes.

Eccentricity-paced monsoon variability on the northeastern Tibetan Plateau in the Late Oligocene high CO2 world

Constraining monsoon variability and dynamics in the warm unipolar icehouse world of the Late Oligocene can provide important clues to future climate responses to global warming. Here, we present a ~4-thousand year (ka) resolution rubidium-to-strontium ratio and magnetic susceptibility records between 28.1 and 24.1 million years ago from a distal alluvial sedimentary sequence in the Lanzhou Basin (China) on the northeastern Tibetan Plateau margin. These Asian monsoon precipitation records exhibit prominent short (~110-ka) and long (405-ka) eccentricity cycles throughout the Late Oligocene, with a weak expression of obliquity (41-ka) and precession (19-ka and 23-ka) cycles. We conclude that a combination of eccentricity-modulated low-latitude summer insolation and glacial-interglacial Antarctic Ice Sheet fluctuations drove the eccentricity-paced precipitation variability on the northeastern Tibetan Plateau in the Late Oligocene high CO₂ world by governing regional temperatures, water vapor loading in the western Pacific and Indian Oceans, and the Asian monsoon intensity and displacement.

Adaptive ecological niche migration does not negate extinction susceptibility

Extinction rates in the modern world are currently at their highest in 66 million years and are likely to increase with projections of future climate change. Our knowledge of modern-day extinction risk is largely limited to decadal-centennial terrestrial records, while data from the marine realm is typically applied to high-order (> 1 million year) timescales. At present, it is unclear whether fossil organisms with common ancestry and ecological niche exhibit consistent indicators of ecological stress prior to extinction. The marine microfossil record, specifically that of the planktonic foraminifera, allows for high-resolution analyses of large numbers of fossil individuals with incredibly well-established ecological and phylogenetic history. Here, analysis of the isochronous extinction of two members of the planktonic foraminiferal genus Dentoglobigerina shows disruptive selection differentially compounded by permanent ecological niche migration, "pre-extinction gigantism", and photosymbiont bleaching prior to extinction. Despite shared ecological and phylogenetic affinity, and timing of extinction, the marked discrepancies observed within the pre-extinction phenotypic responses are species-specific. These behaviours may provide insights into the nature of evolution and extinction in the open ocean and can potentially assist in the recognition and understanding of marine extinction risk in response to global climate change.

Evolutionary drivers, morphological evolution and diversity dynamics of a surviving mammal clade: cainotherioids at the Eocene-Oligocene transition

The Eocene-Oligocene transition (EOT) represents a period of global environmental changes particularly marked in Europe and coincides with a dramatic biotic turnover. Here, using an exceptional fossil preservation, we document and analyse the diversity dynamics of a mammal clade, Cainotherioidea (Artiodactyla), that survived the EOT and radiated rapidly immediately after. We infer their diversification history from Quercy Konzentrat-Lagerstätte (south-west France) at the species level using Bayesian birth-death models. We show that cainotherioid diversity fluctuated through time, with extinction events at the EOT and in the late Oligocene, and a major speciation burst in the early Oligocene. The latter is in line with our finding that cainotherioids had a high morphological adaptability following environmental changes throughout the EOT, which probably played a key role in the survival and evolutionary success of this clade in the aftermath. Speciation is positively associated with temperature and continental fragmentation in a time-continuous way, while extinction seems to synchronize with environmental change in a punctuated way. Within-clade interactions negatively affected the cainotherioid diversification, while inter-clade competition might explain their final decline during the late Oligocene. Our results provide a detailed dynamic picture of the evolutionary history of a mammal clade in a context of global change.

Sea level and deep-sea temperature reconstructions suggest quasi-stable states and critical transitions over the past 40 million years

Sea level and deep-sea temperature variations are key indicators of global climate changes. For continuous records over millions of years, deep-sea carbonate microfossil-based δ¹⁸O (δ_c) records are indispensable because they reflect changes in both deep-sea temperature and seawater δ¹⁸O (δ_w); the latter are related to ice volume and, thus, to sea level changes. Deep-sea temperature is usually resolved using elemental ratios in the same benthic microfossil shells used for δ_c, with linear scaling of residual δ_w to sea level changes. Uncertainties are large and the linear-scaling assumption remains untested. Here, we present a new process-based approach to assess relationships between changes in sea level, mean ice sheet δ¹⁸O, and both deep-sea δ_w and temperature and find distinct nonlinearity between sea level and δ_w changes. Application to δ_c records over the past 40 million years suggests that Earth's climate system has complex dynamical behavior, with threshold-like adjustments (critical transitions) that separate quasi-stable deep-sea temperature and ice-volume states.