Cenozoic sea-level and cryospheric evolution from deep-sea geochemical and continental margin records

The fate of South America's endemic mammalian fauna in response to the most dramatic Cenozoic climate disruption

Around 34 Mya, the Eocene-Oligocene transition (EOT) marked the most dramatic global climatic cooling of the Cenozoic. On a planetary scale, paleontological evidence suggests that this transition was associated with major faunal turnovers, sometimes even regarded as a mass extinction crisis. In South America, there is no consensus on the response of the endemic mammals to this transition. Here, using a vetted fossil dataset and cutting-edge Bayesian methods, we analyzed the dynamics of South American mammal (SAM) diversification and their possible drivers across latitude (tropical vs. extratropical), taxonomic groups, and trophic guilds throughout the Eocene-Oligocene (ca. 56 to 23 Ma). Our results did not evidence any mass extinction among SAM at the EOT. Instead, they experienced a gradual and long-term diversity decline from the middle Eocene to the early Oligocene, followed by a sudden waxing-and-waning diversity associated with a large taxonomic-but not ecological-turnover. Tropical and extratropical lineages have had very distinct macroevolutionary histories. No effective change in the pace at which tropical lineages diversify was found, thus favoring the tropical stability hypothesis proposed by Wallace. Diversity-dependent effects, temperature, and Andean uplift were recovered as probable drivers of SAM diversification across the period. Contrasting evidence casts doubt on the common hypothesis primarily linking Oligocene faunal changes to grassland expansion. Our findings illustrate the uniqueness of the deep-time interplay between endemic SAM and their physical environment in a context of climatic shift, highlighting the need to consider regional idiosyncrasies for understanding the coevolution of life and climate.

Dynamic interplay between niche variation and flight adaptability drove a hundred million years' dispersion in iconic lacewings

The form and change of animal biogeography reflects the long-term interplay between organisms and their environment, involving physiological limitation, dispersal capability, and adaptive evolution versus plate tectonics, global climatic shifts, and changing landscapes. This is especially manifest for lineages with extended geological histories, which, therefore, evokes questions as to the associated processes producing such patterns. Insects, as the earliest flying animals, have exceptional abilities for expanding their range and habitats and to avoid detrimental conditions. They are ideal for exploring historical biogeography augmented via adaptation. Here, we employ beaded lacewings as a model to explore such patterns and likely processes, particularly given that they differ notably from the commonly observed pattern of a latitudinal diversity gradient. Furthermore, owing to their good fossil record it can be observed that their distributions varied remarkably through time. Ecological niche modeling and evaluation demonstrate their niche variation and niche breadth expansion intermittently accompanying global climate change. However, different niche relevant variables changed under patterns of either phylogenetic conservatism or evolutionary lability. By assessing wing morphological disparity and modeling flight aerodynamics, we uncovered a continuous improvement of flight efficiency through beaded-lacewing history as well as a Paleogene divergence in strategy, which reveals a long-term associated path with the niche variation. Our results unveil the adaptive evolution and dispersal history of beaded lacewings through 170 My, achieved by dynamic strategies in niche shift and flight adaptation as responses to a changing planet.

The many origins of extremophile fishes

Extremophiles survive in environments that are considered uninhabitable for most living things. The evolution of extremophiles is of great interest because of how they may have contributed to the assembly of ecosystems, yet the evolutionary dynamics that drive extremophile evolution remain obscure. Here, we investigate the evolution of extremophiles in Zoarcoidea, a lineage of over 300 species of fishes that have colonized both poles, the deep sea, and hydrothermal vents. We show that a pulse of habitat invasion occurred across over 20 different zoarcoid lineages within the last 8 million years, far after the origin of their prototypical innovation for surviving in cold water: type III antifreeze protein. Instead, a secondary burst of anatomical, physiological and life history traits and a handful of founder events in extreme ecosystems appear to have propelled zoarcoid diversification. These results decentralize the role of prototypical changes to organismal biology in shaping extremophile radiations and provide a clear example of how a combination of ancient adaptations and recent contingency shapes the origination of lineages in challenging habitats.

Obliquity disruption and Antarctic ice sheet dynamics over a 2.4-Myr astronomical grand cycle

Marine δ18O data reveal astronomical forcing of the climate and cryosphere during the Miocene, when atmospheric Pco2 was on par with emissions scenarios over the next century. This inspired hypotheses for how Milankovitch cycles, ice-ocean interactions, and greenhouse gases influence ice volume. Mass balance controls for marine and terrestrial ice sheets differ, and proxy data collected far from Antarctica provide valuable but limited insight into regional processes. We evaluate clast abundance data from Antarctic marine sedimentary records, observing a strong signal of eccentricity and precession coincident with a terrestrial ice sheet and a clear obliquity signal at the margins of a marine ice sheet. These analyses are integrated with a synthesis of proxy data, and we argue that high variance in obliquity forcing (mediated and enhanced by the ocean and atmosphere) can inhibit ice sheet growth, even when insolation forcing is conducive to glaciation. This "obliquity disruption" explains cryosphere variability before the existence of large northern hemisphere ice sheets.

First insights into the life history of the early Miocene deer Procervulus ginsburgi from Spain

The small-sized cervid Procervulus is considered as the most basal member of the Cervidae and one of the earliest ruminants bearing antler-like appendages. The Iberian Miocene record of this stem-cervid is extensively documented and largely overlaps with the Miocene Climatic Optimum (MCO), a transient period of global warming of particular interest when comparing present and near future conditions. Despite receiving a substantial amount of attention, histological studies on Procervulus are very scarce and only limited to postcranial remains of Procervulus praelucidus from Germany (MN3). Here we focus for the first time on the dental histology of Procervulus ginsburgi from the Early Miocene Iberian site of Artesilla (MN4, 16.49 Ma), and examine its daily enamel secretion rate (DSR), enamel extension rate (EER) and crown formation time (CFT). Results reveal a brief CTF and high DSR and EER for P. ginsburgi and suggest a fast development at least early in its ontogeny. In addition, the pronounced growth rate of P. ginsburgi emerges as higher than that of the roe deer C. capreolus-documented as an r-strategist and here examined as a possible extant analog. Overall, our findings point toward a fast life history strategy for P. ginsburgi, which unexpectedly contrasts with that of the 2 million-year-older P. praelucidus from Wintershof-West, with a marked slower growth and maturation. When these results are analyzed together with other evidence, the somewhat drier and more open conditions of Artesilla as a result of the effects of the MCO seem to be the explanation for the different life history and ecology between these Procervulus species. More generally, this study illustrates that life histories within a single genus evolve in response not only to internal constraints but also to the environments, as predicted by the Life History Theory.

Enhancing in search of Milankovitch cycles from stratigraphic record using convex optimization algorithm

Accurately identifying Milankovitch cycles has been a significant challenge in cyclostratigraphic studies, as it is essential for improving geochronology. This manuscript focuses on developing a method that distinguishes Milankovitch cycles from sedimentary noise to enhance stratigraphic precision. Despite their often-conspicuous magnitude, these periodicities frequently intertwine with noise, posing a challenge for conventional spectral analysis. Therefore, to address this issue, we have developed an algorithm that enhances the resolution of the Milankovitch signal by employing convex optimization in spectral analysis. To evaluate the effectiveness of this new algorithm, we applied it to four distinct types of local stratigraphy where the Milankovitch signal has been confirmed. These include the stratigraphic sections in the middle Miocene molluscan beds of Java and the Mahakam Delta, Pleistocene sediments of Hominin Flores, and the Towuti Lake in Sulawesi Island, Indonesia. Our findings demonstrate the preservation of all targeted signals, with a confidence level surpassing 99%. By setting the significance level to 1%, we can reject the null hypothesis, which assumes noise or the absence of a Milankovitch signal in the stratigraphic data being tested. The absence of deviations from the identified periodicities further strengthens the Milankovitch signal, underscoring the robustness of our algorithm. However, we acknowledge that achieving optimal results still hinges on the accurate selection of the initial parameters z and λ.

Shifting Antarctic Circumpolar Current south of Africa over the past 1.9 million years

The Antarctic Circumpolar Current (ACC) dominates the transfer of heat, salt, and tracers around the Southern Ocean (SO), driving the upwelling of carbon-rich deep waters around Antarctica. Paleoclimate reconstructions reveal marked variability in SO circulation; however, few records exist coupling quantitative reconstructions of ACC flow with tracers of SO upwelling spanning multiple Pleistocene glacial cycles. Here, we reconstruct near-bottom flow speed variability in the SO south of Africa, revealing systematic glacial-interglacial variations in the strength and/or proximity of ACC jets. These are superimposed by warmer-than-present "super-interglacials," whereby extreme slowdown in the midlatitude ACC (41°S) is opposed by faster flow at higher latitudes (>54°S), implying poleward strengthening of the ACC. Coupled with reconstructions of the subsurface-deep stable carbon isotope gradient, we show that the reorganization of ACC coincides with the upwelling of isotopically light deep waters around Antarctica, likely contributing to the interglacial rise in atmospheric carbon dioxide (CO2) levels.

Out of and in East Asia: phylogeny, biogeography and diversification of Thalictroideae (Ranunculaceae) in the Northern Hemisphere

BACKGROUND AND AIMS

Understanding the biogeographical patterns and processes underlying the distribution of diversity within the Northern Hemisphere has fascinated botanists and biogeographers for over a century. However, as a well-known centre of species diversity in the Northern Hemisphere, whether East Asia acted as a source and/or a sink of plant diversity of the Northern Hemisphere remains unclear. Here, we used Thalictroideae, a subfamily widely distributed in the Northern Hemisphere with the majority of species in East Asia, to investigate the role of East Asia in shaping the biogeographical patterns of the Northern Hemisphere and to test whether East Asia acted as a museum or a cradle for herbaceous taxa.

METHODS

Based on six plastid and one nuclear DNA regions, we generated the most comprehensive phylogeny for Thalictroideae, including 217 taxa (~66 % species) from all ten of the currently recognized genera. Within this phylogenetic framework, we then estimated divergence times, ancestral ranges and diversification rates.

KEY RESULTS

The monophyletic Thalictroideae contains three major clades. All genera with more than one species are strongly supported as monophyletic except for Isopyrum, which is nested in Enemion. The most recent common ancestor of Thalictroideae occurred in East Asia in the late Eocene (~36 Mya). From the Miocene onwards, ≥46 dispersal events were inferred to be responsible for the current distribution of this subfamily. East Asian Thalictroideae lineages experienced a rapid accumulation at ~10 Mya.

CONCLUSIONS

The biogeographical patterns of Thalictroideae support the 'out of and in East Asia' hypothesis, i.e. East Asia is both a source and a sink of biodiversity of the Northern Hemisphere. The global cooling after the middle Miocene Climatic Optimum, combined with the exposed land bridges owing to sea-level decline, might jointly have caused the bidirectional plant exchanges between East Asia and other Northern Hemisphere regions. East Asia serves as evolutionary museums and cradles for the diversity of Thalictroideae and probably for other herbaceous lineages.

Eccentricity pacing and rapid termination of the early Antarctic ice ages

Earth's obliquity and eccentricity cycles are strongly imprinted on Earth's climate and widely used to measure geological time. However, the record of these imprints on the oxygen isotope record in deep-sea benthic foraminifera (δ18Ob) shows contradictory signals that violate isotopic principles and cause controversy over climate-ice sheet interactions. Here, we present a δ18Ob record of high fidelity from International Ocean Drilling Program (IODP) Site U1406 in the northwest Atlantic Ocean. We compare our record to other records for the time interval between 28 and 20 million years ago, when Earth was warmer than today, and only Antarctic ice sheets existed. The imprint of eccentricity on δ18Ob is remarkably consistent globally whereas the obliquity signal is inconsistent between sites, indicating that eccentricity was the primary pacemaker of land ice volume. The larger eccentricity-paced early Antarctic ice ages were vulnerable to rapid termination. These findings imply that the self-stabilizing hysteresis effects of large land-based early Antarctic ice sheets were strong enough to maintain ice growth despite consecutive insolation-induced polar warming episodes. However, rapid ice age terminations indicate that resistance to melting was weaker than simulated by numerical models and regularly overpowered, sometimes abruptly.

Cryptic Hybridization Dynamics in a Three-Way Hybrid Zone of Dinopium Flamebacks on a Tropical Island

Island ecosystems have emerged as vital model systems for evolutionary and speciation studies due to their unique environmental conditions and biodiversity. This study investigates the population divergence, hybridization dynamics, and evolutionary history of hybridizing golden-backed and red-backed Dinopium flameback woodpeckers on the island of Sri Lanka, providing insights into speciation processes within an island biogeographic context. Utilizing genomic analysis based on next-generation sequencing, we revealed that the Dinopium hybrid zone on this island is a complex three-way hybrid zone involving three genetically distinct populations: two cryptic populations of golden-backed D. benghalense in the north and one island-endemic red-backed population of D. psarodes in the south of Sri Lanka. Our findings indicate asymmetric introgressive hybridization, where alleles from the southern D. psarodes introgress into the northern D. benghalense genome while phenotype remains adapted to their respective northern arid and southern wet habitats. The discovery of two genetically distinct but phenotypically similar D. benghalense populations in northern Sri Lanka highlights the process of cryptic population differentiation within island ecosystems. These populations trace their ancestry back to a common ancestor, similar to the Indian form D. b. tehminae, which colonized Sri Lanka from mainland India during the late Pleistocene. Subsequent divergence within the island, driven by selection, isolation by distance, and genetic drift, led to the current three populations. Our findings provide evidence of cryptic diversification and within-island population divergence, highlighting the complexity of hybridization and speciation processes. These findings further emphasize the intricate nature of evolutionary dynamics in island ecosystems.

Bayesian tip-dated timeline for diversification and major biogeographic events in Muroidea (Rodentia), the largest mammalian radiation

BACKGROUND

Extinct organisms provide vital information about the time of origination and biogeography of extant groups. The development of phylogenetic methods to study evolutionary processes through time has revolutionized the field of evolutionary biology and led to an unprecedented expansion of our knowledge of the tree of life. Recent developments applying Bayesian approaches, using fossil taxa as tips to be included alongside their living relatives, have revitalized the use of morphological data in evolutionary tree inferences. Eumuroida rodents represent the largest group of mammals including more than a quarter of all extant mammals and have a rich fossil record spanning the last ~ 45 million years. Despite this wealth of data, our current understanding of the classification, major biogeographic patterns, and divergence times for this group comes from molecular phylogenies that use fossils only as a source of node calibrations. However, node calibrations impose several constraints on tree topology and must necessarily make a priori assumptions about the placement of fossil taxa without testing their placement in the tree.

RESULTS

We present the first morphological dataset with extensive fossil sampling for Muroidea. By applying Bayesian morphological clocks with tip dating and process-based biogeographic models, we provide a novel hypothesis for muroid relationships and revised divergence times for the clade that incorporates uncertainty in the placement of all fossil species. Even under strong violation of the clock model, we found strong congruence between results for divergence times, providing a robust timeline for muroid diversification. This new timeline was used for biogeographic analyses, which revealed a dynamic scenario mostly explained by dispersal events between and within the Palearctic and North African regions.

CONCLUSIONS

Our results provide important insights into the evolution of Muroidea rodents and clarify the evolutionary pathways of their main lineages. We exploited the advantage of tip dating Bayesian approaches in morphology-based datasets and provided a classification of the largest superfamily of mammals resulting from robust phylogenetic inference, inferring the biogeographical history, diversification, and divergence times of its major lineages.

Sea level rise and the evolution of aggression on islands

Why aggressive traits evolve in some species but not in others is poorly understood. We modeled the population dynamics of the extinct Mauritius dodo and Rodrigues solitaire to examine divergent pathways in the evolution of aggression. Whereas the dodo conformed to island syndrome predictions of tameness, its sister-taxon the solitaire evolved strong sexual dimorphism and aggressive traits. We computed rates of change in island size from sea level modeling and connected island size change to population dynamics by integrating a Hawk-Dove game theory model for territory competition with a population model. We find that the rapid rate of decrease in island size likely was an important trigger for the onset of aggressive behavior and that aggressive behavior becomes fixed if a tipping point is reached where island size falls below a critical threshold.

Re-organization of Pacific overturning circulation across the Miocene Climate Optimum

The response of the ocean overturning circulation to global warming remains controversial. Here, we integrate a multiproxy record from International Ocean Discovery Program Site U1490 in the western equatorial Pacific with published data from the Pacific, Southern and Indian Oceans to investigate the evolution of deep water circulation during the Miocene Climate Optimum (MCO) and Middle Miocene Climate Transition (MMCT). We find that the northward export of southern-sourced deep waters was closely tied to high-latitude climate and Antarctic ice cover variations. Global warming during the MCO drove a progressive decrease in carbonate ion concentration and density stratification, shifting the overturning from intermediate to deeper waters. In the western equatorial Pacific, carbonate dissolution was compensated by increased pelagic productivity, resulting in overall elevated carbonate accumulation rates after ~16 Ma. Stepwise global cooling and Antarctic glacial expansion during the MMCT promoted a gradual improvement in carbonate preservation and the initiation of a near-modern Pacific overturning circulation. We infer that changes in the latitudinal thermal gradient and in Southern Ocean zonal wind stress and upper ocean stratification drove radically different modes of deep water formation and overturning across the MCO and MMCT.

The Sequential Direct and Indirect Effects of Mountain Uplift, Climatic Niche, and Floral Trait Evolution on Diversification Dynamics in an Andean Plant Clade

Why and how organismal lineages radiate is commonly studied through either assessing abiotic factors (biogeography, geomorphological processes, and climate) or biotic factors (traits and interactions). Despite increasing awareness that both abiotic and biotic processes may have important joint effects on diversification dynamics, few attempts have been made to quantify the relative importance and timing of these factors, and their potentially interlinked direct and indirect effects, on lineage diversification. We here combine assessments of historical biogeography, geomorphology, climatic niche, vegetative, and floral trait evolution to test whether these factors jointly, or in isolation, explain diversification dynamics of a Neotropical plant clade (Merianieae, Melastomataceae). After estimating ancestral areas and the changes in niche and trait disparity over time, we employ Phylogenetic Path Analyses as a synthesis tool to test eleven hypotheses on the individual direct and indirect effects of these factors on diversification rates. We find strongest support for interlinked effects of colonization of the uplifting Andes during the mid-Miocene and rapid abiotic climatic niche evolution in explaining a burst in diversification rate in Merianieae. Within Andean habitats, later increases in floral disparity allowed for the exploitation of wider pollination niches (i.e., shifts from bee to vertebrate pollinators), but did not affect diversification rates. Our approach of including both vegetative and floral trait evolution, rare in assessments of plant diversification in general, highlights that the evolution of woody habit and larger flowers preceded the colonization of the Andes, but was likely critical in enabling the rapid radiation in montane environments. Overall, and in concert with the idea that ecological opportunity is a key element of evolutionary radiations, our results suggest that a combination of rapid niche evolution and trait shifts was critical for the exploitation of newly available niche space in the Andes in the mid-Miocene. Further, our results emphasize the importance of incorporating both abiotic and biotic factors into the same analytical framework if we aim to quantify the relative and interlinked effects of these processes on diversification.

Identification of the mode of evolution in incomplete carbonate successions

BACKGROUND

The fossil record provides the unique opportunity to observe evolution over millions of years, but is known to be incomplete. While incompleteness varies spatially and is hard to estimate for empirical sections, computer simulations of geological processes can be used to examine the effects of the incompleteness in silico. We combine simulations of different modes of evolution (stasis, (un)biased random walks) with deposition of carbonate platforms strata to examine how well the mode of evolution can be recovered from fossil time series, and how test results vary between different positions in the carbonate platform and multiple stratigraphic architectures generated by different sea level curves.

RESULTS

Stratigraphic architecture and position along an onshore-offshore gradient has only a small influence on the mode of evolution recovered by statistical tests. For simulations of random walks, support for the correct mode decreases with time series length. Visual examination of trait evolution in lineages shows that rather than stratigraphic incompleteness, maximum hiatus duration determines how much fossil time series differ from the original evolutionary process. Gradual directional evolution is more susceptible to stratigraphic effects, turning it into punctuated evolution. In contrast, stasis remains unaffected.

CONCLUSIONS

• Fossil time series favor the recognition of both stasis and complex, punctuated modes of evolution. • Not stratigraphic incompleteness, but the presence of rare, prolonged gaps has the largest effect on trait evolution. This suggests that incomplete sections with regular hiatus frequency and durations can potentially preserve evolutionary history without major biases. Understanding external controls on stratigraphic architectures such as sea level fluctuations is crucial for distinguishing between stratigraphic effects and genuine evolutionary process.

Geologically constrained 2-million-year-long simulations of Antarctic Ice Sheet retreat and expansion through the Pliocene

Pliocene global temperatures periodically exceeded modern levels, offering insights into ice sheet sensitivity to warm climates. Ice-proximal geologic records from this period provide crucial but limited glimpses of Antarctic Ice Sheet behavior. We use an ice sheet model driven by climate model snapshots to simulate transient glacial cyclicity from 4.5 to 2.6 Ma, providing spatial and temporal context for geologic records. By evaluating model simulations against a comprehensive synthesis of geologic data, we translate the intermittent geologic record into a continuous reconstruction of Antarctic sea level contributions, revealing a dynamic ice sheet that contributed up to 25 m of glacial-interglacial sea level change. Model grounding line behavior across all major Antarctic catchments exhibits an extended period of receded ice during the mid-Pliocene, coincident with proximal geologic data around Antarctica but earlier than peak warmth in the Northern Hemisphere. Marine ice sheet collapse is triggered with 1.5 °C model subsurface ocean warming.

Cenozoic history of the tropical marine biodiversity hotspot

The region with the highest marine biodiversity on our planet is known as the Coral Triangle or Indo-Australian Archipelago (IAA)1,2. Its enormous biodiversity has long attracted the interest of biologists; however, the detailed evolutionary history of the IAA biodiversity hotspot remains poorly understood3. Here we present a high-resolution reconstruction of the Cenozoic diversity history of the IAA by inferring speciation-extinction dynamics using a comprehensive fossil dataset. We found that the IAA has exhibited a unidirectional diversification trend since about 25 million years ago, following a roughly logistic increase until a diversity plateau beginning about 2.6 million years ago. The growth of diversity was primarily controlled by diversity dependency and habitat size, and also facilitated by the alleviation of thermal stress after 13.9 million years ago. Distinct net diversification peaks were recorded at about 25, 20, 16, 12 and 5 million years ago, which were probably related to major tectonic events in addition to climate transitions. Key biogeographic processes had far-reaching effects on the IAA diversity as shown by the long-term waning of the Tethyan descendants versus the waxing of cosmopolitan and IAA taxa. Finally, it seems that the absence of major extinctions and the Cenozoic cooling have been essential in making the IAA the richest marine biodiversity hotspot on Earth.

Earliest evidence of human occupations and technological complexity above the 45th North parallel in Western Europe. The site of Lunery-Rosieres la-Terre-des-Sablons (France, 1.1 Ma)

The site of LuneryRosieres la-Terre-des-Sablons (Lunery, Cher, France) comprises early evidence of human occupation in mid-latitudes in Western Europe. It demonstrates hominin presence in the Loire River Basin during the Early Pleistocene at the transition between an interglacial stage and the beginning of the following glacial stage. Three archaeological levels sandwiched and associated with two diamicton levels deposited on the downcutting river floor indicate repeated temporary occupations. Lithic material yields evidence of simple and more complex core technologies on local Jurassic siliceous rocks and Oligocene millstone. Hominins availed of natural stone morphologies to produce flakes with limited preparation. Some cores show centripetal management and a partially prepared striking platform. The mean ESR age of 1175 ka ± 98 ka obtained on fluvial sediments overlying the archaeological levels could correspond to the transition between marine isotopic stages (MIS) 37 and 36, during the normal Cobb Mountain subchron, and in particular at the beginning of MIS 36. The Lunery site shows that hominins were capable of adapting to early glacial environmental conditions and adopting appropriate strategies for settling in mid-latitude zones. These areas cannot be considered as inhospitable at that time as Lunery lies at some distance from the forming ice cap.

The Central Paratethys Sea-rise and demise of a Miocene European marine biodiversity hotspot

The Miocene Climate Optimum (MCO, ~ 17-14 Ma) was a time of extraordinary marine biodiversity in the Circum-Mediterranean Region. This boom is best recorded in the deposits of the vanished Central Paratethys Sea, which covered large parts of central to southeastern Europe. This sea harbored an extraordinary tropical to subtropical biotic diversity. Here, we present a georeferenced dataset of 859 gastropod species and discuss geodynamics and climate as the main drivers to explain the changes in diversity. The tectonic reorganization around the Early/Middle Miocene boundary resulted in the formation of an archipelago-like landscape and favorable conditions of the MCO allowed the establishment of coral reefs. Both factors increased habitat heterogeneity, which boosted species richness. The subsequent cooling during the Middle Miocene Climate Transition (~ 14-13 Ma) caused a drastic decline in biodiversity of about 67%. Among the most severely hit groups were corallivorous gastropods, reflecting the loss of coral reefs. Deep-water faunas experienced a loss by 57% of the species due to changing patterns in circulation. The low sea level led to a biogeographic fragmentation reflected in higher turnover rates. The largest turnover occurred with the onset of the Sarmatian when bottom water dysoxia eradicated the deep-water fauna whilst surface waters-dwelling planktotrophic species underwent a crisis.

Mitochondrial Genome Characteristics Reveal Evolution of Acanthopsetta nadeshnyi (Jordan and Starks, 1904) and Phylogenetic Relationships

In the present study, the mitochondrial genomic characteristics of Acanthopsetta nadeshnyi have been reported and have depicted the phylogenetic relationship among Pleuronectidae. Combined with a comparative analysis of 13 PCGs, the TN93 model was used to review the neutral evolution and habitat evolution catalysis of the mitogenome to verify the distancing and purification selectivity of the mitogenome in Pleuronectidae. At the same time, a species differentiation and classification model based on mitogenome analysis data was established. This study is expected to provide a new perspective on the phylogenetic relationship and taxonomic status of A. nadeshnyi and lay a foundation for further exploration of environmental and biological evolutionary mechanisms.

Biogeography of Greater Antillean freshwater fishes, with a review of competing hypotheses

In biogeography, vicariance and long-distance dispersal are often characterised as competing scenarios. However, they are related concepts, both relying on collective geological, ecological, and phylogenetic evidence. This is illustrated by freshwater fishes, which may immigrate to islands either when freshwater connections are temporarily present and later severed (vicariance), or by unusual means when ocean gaps are crossed (long-distance dispersal). Marine barriers have a strong filtering effect on freshwater fishes, limiting immigrants to those most capable of oceanic dispersal. The roles of vicariance and dispersal are debated for freshwater fishes of the Greater Antilles. We review three active hypotheses [Cretaceous vicariance, Greater Antilles-Aves Ridge (GAARlandia), long-distance dispersal] and propose long-distance dispersal to be an appropriate model due to limited support for freshwater fish use of landspans. Greater Antillean freshwater fishes have six potential source bioregions (defined from faunal similarity): Northern Gulf of México, Western Gulf of México, Maya Terrane, Chortís Block, Eastern Panamá, and Northern South America. Faunas of the Greater Antilles are composed of taxa immigrating from many of these bioregions, but there is strong compositional disharmony between island and mainland fish faunas (>90% of Antillean species are cyprinodontiforms, compared to <10% in Northern Gulf of México and Northern South America, and ≤50% elsewhere), consistent with a hypothesis of long-distance dispersal. Ancestral-area reconstruction analysis indicates there were 16 or 17 immigration events over the last 51 million years, 14 or 15 of these by cyprinodontiforms. Published divergence estimates and evidence available for each immigration event suggests they occurred at different times and by different pathways, possibly with rafts of vegetation discharged from rivers or washed to sea during storms. If so, ocean currents likely provide critical pathways for immigration when flowing from one landmass to another. On the other hand, currents create dispersal barriers when flowing perpendicularly between landmasses. In addition to high salinity tolerance, cyprinodontiforms collectively display a variety of adaptations that could enhance their ability to live with rafts (small body size, viviparity, low metabolism, amphibiousness, diapause, self-fertilisation). These adaptations likely also helped immigrants establish island populations after arrival and to persist long term thereafter. Cichlids may have used a pseudo bridge (Nicaragua Rise) to reach the Greater Antilles. Gars (Lepisosteidae) may have crossed the Straits of Florida to Cuba, a relatively short crossing that is not a barrier to gene flow for several cyprinodontiform immigrants. Indeed, widespread distributions of Quaternary migrants (Cyprinodon, Gambusia, Kryptolebias), within the Greater Antilles and among neighbouring bioregions, imply that long-distance dispersal is not necessarily inhibitory for well-adapted species, even though it appears to be virtually impossible for all other freshwater fishes.

Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses

Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth Bradypus is consistently recovered as a megatherioid, and Choloepus as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae," whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an a posteriori removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.

The rise of baobab trees in Madagascar

The baobab trees (genus Adansonia) have attracted tremendous attention because of their striking shape and distinctive relationships with fauna1. These spectacular trees have also influenced human culture, inspiring innumerable arts, folklore and traditions. Here we sequenced genomes of all eight extant baobab species and argue that Madagascar should be considered the centre of origin for the extant lineages, a key issue in their evolutionary history2,3. Integrated genomic and ecological analyses revealed the reticulate evolution of baobabs, which eventually led to the species diversity seen today. Past population dynamics of Malagasy baobabs may have been influenced by both interspecific competition and the geological history of the island, especially changes in local sea levels. We propose that further attention should be paid to the conservation status of Malagasy baobabs, especially of Adansonia suarezensis and Adansonia grandidieri, and that intensive monitoring of populations of Adansonia za is required, given its propensity for negatively impacting the critically endangered Adansonia perrieri.

Orbital- and millennial-scale Asian winter monsoon variability across the Pliocene-Pleistocene glacial intensification

Intensification of northern hemisphere glaciation (iNHG), ~2.7 million years ago (Ma), led to establishment of the Pleistocene to present-day bipolar icehouse state. Here we document evolution of orbital- and millennial-scale Asian winter monsoon (AWM) variability across the iNHG using a palaeomagnetically dated centennial-resolution grain size record between 3.6 and 1.9 Ma from a previously undescribed loess-palaeosol/red clay section on the central Chinese Loess Plateau. We find that the late Pliocene-early Pleistocene AWM was characterized by combined 41-kyr and ~100-kyr cycles, in response to ice volume and atmospheric CO2 forcing. Northern hemisphere ice sheet expansion, which was accompanied by an atmospheric CO2 concentration decline, substantially increased glacial AWM intensity  and its orbitally oscillating amplitudes across the iNHG. Superposed on orbital variability, we find that millennial AWM intensity fluctuations persisted during both the warmer (higher-CO2) late Pliocene and colder (lower-CO2) early Pleistocene, in response to both external astronomical forcing and internal climate dynamics.

Comparative plastome analysis of the sister genera Ceratocephala and Myosurus (Ranunculaceae) reveals signals of adaptive evolution to arid and aquatic environments

BACKGROUND

Expansion and contraction of inverted repeats can cause considerable variation of plastid genomes (plastomes) in angiosperms. However, little is known about whether structural variations of plastomes are associated with adaptation to or occupancy of new environments. Moreover, adaptive evolution of angiosperm plastid genes remains poorly understood. Here, we sequenced the complete plastomes for four species of xerophytic Ceratocephala and hydrophytic Myosurus, as well as Ficaria verna. By an integration of phylogenomic, comparative genomic, and selection pressure analyses, we investigated evolutionary patterns of plastomes in Ranunculeae and their relationships with adaptation to dry and aquatic habitats.

RESULTS

Owing to the significant contraction of the boundary of IRA/LSC towards the IRA, plastome sizes and IR lengths of Myosurus and Ceratocephala are smaller within Ranunculeae. Compared to other Ranunculeae, the Myosurus plastome lost clpP and rps16, one copy of rpl2 and rpl23, and one intron of rpoC1 and rpl16, and the Ceratocephala plastome added an infA gene and lost one copy of rpl2 and two introns of clpP. A total of 11 plastid genes (14%) showed positive selection, two genes common to Myosurus and Ceratocephala, seven in Ceratocephala only, and two in Myosurus only. Four genes showed strong signals of episodic positive selection. The rps7 gene of Ceratocephala and the rpl32 and ycf4 genes of Myosurus showed an increase in the rate of variation close to 3.3 Ma.

CONCLUSIONS

The plastomic structure variations as well as the positive selection of two plastid genes might be related to the colonization of new environments by the common ancestor of Ceratocephala and Myosurus. The seven and two genes under positive selection might be related to the adaptation to dry and aquatic habitats in Ceratocephala and Myosurus, respectively. Moreover, intensified aridity and frequent sea-level fluctuations, as well as global cooling, might have favored an increased rate of change in some genes at about 3.3 Ma, associated with adaptation to dry and aquatic environments, respectively. These findings suggest that changing environments might have influenced structural variations of plastomes and fixed new mutations arising on some plastid genes owing to adaptation to specific habitats.

Drivers of the artiodactyl turnover in insular western Europe at the Eocene-Oligocene Transition

Simultaneously investigating the effects of abiotic and biotic factors on diversity dynamics is essential to understand the evolutionary history of clades. The Grande Coupure corresponds to a major faunal turnover at the Eocene-Oligocene transition (EOT) (~34.1 to 33.55 Mya) and is defined in western Europe as an extinction of insular European mammals coupled with the arrival of crown clades from Asia. Here, we focused on the species-rich group of endemic European artiodactyls to determine the drivers of the Grande Coupure during the major environmental disruptions at the EOT. Using Bayesian birth-death models, we analyzed an original high-resolution fossil dataset (90 species, >2,100 occurrences) from southwestern France (Quercy area) and estimated the regional diversification and diversity dynamics of endemic and immigrant artiodactyls. We show that the endemic artiodactyl radiation was mainly related to the Eocene tropical conditions, combined with biotic controls on speciation and clade-related diversity dependence. We further highlight that the major environmental changes at the transition (77% of species became extinct) and the concurrent increase in seasonality in Europe during the Oligocene were likely the main drivers of their decline. Surprisingly, our results do not support the widely-held hypothesis of active competition between endemic and immigrant artiodactyls but rather suggest a passive or opportunistic replacement by immigrants, which is further supported by morphological clustering of specific ecological traits across the Eocene-Oligocene transition. Our analyses provide insights into the evolutionary and ecological processes driving the diversification and decline of mammalian clades during a major biological and climatic crisis.

Geodynamically corrected Pliocene shoreline elevations in Australia consistent with midrange projections of Antarctic ice loss

The Mid-Pliocene represents the most recent interval in Earth history with climatic conditions similar to those expected in the coming decades. Mid-Pliocene sea level estimates therefore provide important constraints on projections of future ice sheet behavior and sea level change but differ by tens of meters due to local distortion of paleoshorelines caused by mantle dynamics. We combine an Australian sea level marker compilation with geodynamic simulations and probabilistic inversions to quantify and remove these post-Pliocene vertical motions at continental scale. Dynamic topography accounts for most of the observed sea level marker deflection, and correcting for this effect and glacial isostatic adjustment yields a Mid-Pliocene global mean sea level of +16.0 (+10.4 to +21.5) m (50th/16th to 84th percentiles). Recalibration of recent high-end sea level projections using this revised estimate implies a more stable Antarctic Ice Sheet under future warming scenarios, consistent with midrange forecasts of sea level rise that do not incorporate a marine ice cliff instability.

An Updated Review of Fossil Pollen Evidence for the Study of the Origin, Evolution and Diversification of Caribbean Mangroves

Recently, the evolutionary history of the Caribbean mangroves has been reconsidered using partial palynological databases organized by the time intervals of interest, namely Late Cretaceous to Eocene for the origin, the Eocene-Oligocene transition for major turnover and Neogene to Quaternary for diversification. These discussions have been published in a set of sequential papers, but the raw information remains unknown. This paper reviews all the information available and provides the first comprehensive and updated compilation of the abovementioned partial databases. This compilation is called CARMA-F (CARibbean MAngroves-Fossil) and includes nearly 90 localities from the present and past Caribbean coasts, ranging from the Late Cretaceous to the Pliocene. Details on the Quaternary localities (CARMA-Q) will be published later. CARMA-F lists and illustrates the fossil pollen from past mangrove taxa and their extant representatives, and includes a map of the studied localities and a conventional spreadsheet with the raw data. The compilation is the most complete available for the study of the origin, evolution and diversification of Caribbean mangroves, and is open to modifications for adapting it to the particular interests of each researcher.

A 50-million-year-old, three-dimensionally preserved bat skull supports an early origin for modern echolocation

Bats are among the most recognizable, numerous, and widespread of all mammals. But much of their fossil record is missing, and bat origins remain poorly understood, as do the relationships of early to modern bats. Here, we describe a new early Eocene bat that helps bridge the gap between archaic stem bats and the hyperdiverse modern bat radiation of more than 1,460 living species. Recovered from ∼50 million-year-old cave sediments in the Quercy Phosphorites of southwestern France, Vielasia sigei's remains include a near-complete, three-dimensionally preserved skull-the oldest uncrushed bat cranium yet found. Phylogenetic analyses of a 2,665 craniodental character matrix, with and without 36.8 kb of DNA sequence data, place Vielasia outside modern bats, with total evidence tip-dating placing it sister to the crown clade. Vielasia retains the archaic dentition and skeletal features typical of early Eocene bats, but its inner ear shows specializations found in modern echolocating bats. These features, which include a petrosal only loosely attached to the basicranium, an expanded cochlea representing ∼25% basicranial width, and a long basilar membrane, collectively suggest that the kind of laryngeal echolocation used by most modern bats predates the crown radiation. At least 23 individuals of V. sigei are preserved together in a limestone cave deposit, indicating that cave roosting behavior had evolved in bats by the end of the early Eocene; this period saw the beginning of significant global climate cooling that may have been an evolutionary driver for bats to first congregate in caves.

An ancient river landscape preserved beneath the East Antarctic Ice Sheet

The East Antarctic Ice Sheet (EAIS) has its origins ca. 34 million years ago. Since then, the impact of climate change and past fluctuations in the EAIS margin has been reflected in periods of extensive vs. restricted ice cover and the modification of much of the Antarctic landscape. Resolving processes of landscape evolution is therefore critical for establishing ice sheet history, but it is rare to find unmodified landscapes that record past ice conditions. Here, we discover an extensive relic pre-glacial landscape preserved beneath the central EAIS despite millions of years of ice cover. The landscape was formed by rivers prior to ice sheet build-up but later modified by local glaciation before being dissected by outlet glaciers at the margin of a restricted ice sheet. Preservation of the relic surfaces indicates an absence of significant warm-based ice throughout their history, suggesting any transitions between restricted and expanded ice were rapid.

Multi-proxy evidence for sea level fall at the onset of the Eocene-Oligocene transition

Continental-scale expansion of the East Antarctic Ice Sheet during the Eocene-Oligocene Transition (EOT) is one of the largest non-linear events in Earth's climate history. Declining atmospheric carbon dioxide concentrations and orbital variability triggered glacial expansion and strong feedbacks in the climate system. Prominent among these feedbacks was the repartitioning of biogeochemical cycles between the continental shelves and the deep ocean with falling sea level. Here we present multiple proxies from a shallow shelf location that identify a marked regression and an elevated flux of continental-derived organic matter at the earliest stage of the EOT, a time of deep ocean carbonate dissolution and the extinction of oligotrophic phytoplankton groups. We link these observations using an Earth System model, whereby this first regression delivers a pulse of organic carbon to the oceans that could drive the observed patterns of deep ocean dissolution and acts as a transient negative feedback to climate cooling.

Enhanced clay formation key in sustaining the Middle Eocene Climatic Optimum

The Middle Eocene Climatic Optimum (around 40 million years ago) was a roughly 400,000-year-long global warming phase associated with an increase in atmospheric CO2 concentrations and deep-ocean acidification that interrupted the Eocene's long-term cooling trend. The unusually long duration, compared with early Eocene global warming phases, is puzzling as temperature-dependent silicate weathering should have provided a negative feedback, drawing down CO2 over this timescale. Here we investigate silicate weathering during this climate warming event by measuring lithium isotope ratios (reported as δ7Li), which are a tracer for silicate weathering processes, from a suite of open-ocean carbonate-rich sediments. We find a positive δ7Li excursion-the only one identified for a warming event so far -of ~3‰. Box model simulations support this signal to reflect a global shift from congruent weathering, with secondary mineral dissolution, to incongruent weathering, with secondary mineral formation. We surmise that, before the climatic optimum, there was considerable soil shielding of the continents. An increase in continental volcanism initiated the warming event, but it was sustained by an increase in clay formation, which sequestered carbonate-forming cations, short-circuiting the carbonate-silicate cycle. Clay mineral dynamics may play an important role in the carbon cycle for climatic events occurring over intermediate (i.e., 100,000 year) timeframes.

Evolutionary history of the Arctic flora

The Arctic tundra is a relatively young and new type of biome and is especially sensitive to the impacts of global warming. However, little is known about how the Arctic flora was shaped over time. Here we investigate the origin and evolutionary dynamics of the Arctic flora by sampling 32 angiosperm clades that together encompass 3626 species. We show that dispersal into the Arctic and in situ diversification within the Arctic have similar trends through time, initiating at approximately 10-9 Ma, increasing sharply around 2.6 Ma, and peaking around 1.0-0.7 Ma. Additionally, we discover the existence of a long-term dispersal corridor between the Arctic and western North America. Our results suggest that the initiation and diversification of the Arctic flora might have been jointly driven by progressive landscape and climate changes and sea-level fluctuations since the early Late Miocene. These findings have important conservation implications given rapidly changing climate conditions in the Arctic.

Speciation across the Earth driven by global cooling in terrestrial orchids

Although climate change has been implicated as a major catalyst of diversification, its effects are thought to be inconsistent and much less pervasive than localized climate or the accumulation of species with time. Focused analyses of highly speciose clades are needed in order to disentangle the consequences of climate change, geography, and time. Here, we show that global cooling shapes the biodiversity of terrestrial orchids. Using a phylogeny of 1,475 species of Orchidoideae, the largest terrestrial orchid subfamily, we find that speciation rate is dependent on historic global cooling, not time, tropical distributions, elevation, variation in chromosome number, or other types of historic climate change. Relative to the gradual accumulation of species with time, models specifying speciation driven by historic global cooling are over 700 times more likely. Evidence ratios estimated for 212 other plant and animal groups reveal that terrestrial orchids represent one of the best-supported cases of temperature-spurred speciation yet reported. Employing >2.5 million georeferenced records, we find that global cooling drove contemporaneous diversification in each of the seven major orchid bioregions of the Earth. With current emphasis on understanding and predicting the immediate impacts of global warming, our study provides a clear case study of the long-term impacts of global climate change on biodiversity.

A punctuated equilibrium analysis of the climate evolution of cenozoic exhibits a hierarchy of abrupt transitions

The Earth's climate has experienced numerous critical transitions during its history, which have often been accompanied by massive and rapid changes in the biosphere. Such transitions are evidenced in various proxy records covering different timescales. The goal is then to identify, date, characterize, and rank past critical transitions in terms of importance, thus possibly yielding a more thorough perspective on climatic history. To illustrate such an approach, which is inspired by the punctuated equilibrium perspective on the theory of evolution, we have analyzed 2 key high-resolution datasets: the CENOGRID marine compilation (past 66 Myr), and North Atlantic U1308 record (past 3.3 Myr). By combining recurrence analysis of the individual time series with a multivariate representation of the system based on the theory of the quasi-potential, we identify the key abrupt transitions associated with major regime changes that separate various clusters of climate variability. This allows interpreting the time-evolution of the system as a trajectory taking place in a dynamical landscape, whose multiscale features describe a hierarchy of metastable states and associated tipping points.

Constraining the contribution of the Antarctic Ice Sheet to Last Interglacial sea level

Polar temperatures during the Last Interglacial [LIG; ~129 to 116 thousand years (ka)] were warmer than today, making this time period an important testing ground to better understand how ice sheets respond to warming. However, it remains debated how much and when the Antarctic and Greenland ice sheets changed during this period. Here, we present a combination of new and existing absolutely dated LIG sea-level observations from Britain, France, and Denmark. Because of glacial isostatic adjustment (GIA), the LIG Greenland ice melt contribution to sea-level change in this region is small, which allows us to constrain Antarctic ice change. We find that the Antarctic contribution to LIG global mean sea level peaked early in the interglacial (before 126 ka), with a maximum contribution of 5.7 m (50th percentile, 3.6 to 8.7 m central 68% probability) before declining. Our results support an asynchronous melt history over the LIG, with an early Antarctic contribution followed by later Greenland Ice Sheet mass loss.

Biogeographic diversification of Actaea (Ranunculaceae): Insights into the historical assembly of deciduous broad-leaved forests in the Northern Hemisphere

The deciduous broad-leaved forests (DBLFs) cover large temperate and subtropical high-altitude regions in the Northern Hemisphere. They are home to rich biodiversity, especially to numerous endemic and relict species. However, we know little about how this vegetation in the Northern Hemisphere has developed through time. Here, we used Actaea (Ranunculaceae), an herbaceous genus almost exclusively growing in the understory of the Northern Hemisphere DBLFs, to shed light on the historical assembly of this biome in the Northern Hemisphere. We present a complete species-level phylogenetic analysis of Actaea based on five plastid and nuclear loci. Using the phylogenetic framework, we estimated divergence times, ancestral ranges, and diversification rates. Phylogenetic analyses strongly support Actaea as monophyletic. Sections Podocarpae and Oligocarpae compose a clade, sister to all other Actaea. The sister relationship between sections Chloranthae and Souliea is strongly supported. Section Dichanthera is not monophyletic unless section Cimicifuga is included. Actaea originated in East Asia, likely the Qinghai-Tibet Plateau, in the late Paleocene (c. 57 Ma), and subsequently dispersed into North America in the middle Eocene (c. 43 Ma) via the Thulean bridge. Actaea reached Europe twice, Japan twice, and Taiwan once, and all these five colonization events occurred in the late Miocene-early Pliocene, a period when sea level dropped. Actaea began to diversify at c. 43 Ma. The section-level diversification took place at c. 27-37 Ma and the species-level diversification experienced accelerations twice, which occurred at c. 15 Ma and c. 5 Ma, respectively. Our findings suggest that the Northern Hemisphere DBLFs might have risen in the middle Eocene and further diversified in the late Eocene-Oligocene, middle Miocene and early Pliocene, in association with climatic deterioration during these four periods.

Genomics of cold adaptations in the Antarctic notothenioid fish radiation

Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes.

Climate-controlled submarine landslides on the Antarctic continental margin

Antarctica's continental margins pose an unknown submarine landslide-generated tsunami risk to Southern Hemisphere populations and infrastructure. Understanding the factors driving slope failure is essential to assessing future geohazards. Here, we present a multidisciplinary study of a major submarine landslide complex along the eastern Ross Sea continental slope (Antarctica) that identifies preconditioning factors and failure mechanisms. Weak layers, identified beneath three submarine landslides, consist of distinct packages of interbedded Miocene- to Pliocene-age diatom oozes and glaciomarine diamicts. The observed lithological differences, which arise from glacial to interglacial variations in biological productivity, ice proximity, and ocean circulation, caused changes in sediment deposition that inherently preconditioned slope failure. These recurrent Antarctic submarine landslides were likely triggered by seismicity associated with glacioisostatic readjustment, leading to failure within the preconditioned weak layers. Ongoing climate warming and ice retreat may increase regional glacioisostatic seismicity, triggering Antarctic submarine landslides.

Phylogeny and biogeography of Tiliacoreae (Menispermaceae), a tribe restricted to tropical rainforests

BACKGROUND AND AIMS

Modern tropical rainforests house the highest biodiversity of Earth's terrestrial biomes and are distributed in three low-latitude areas. However, the biogeographical patterns and processes underlying the distribution of biodiversity among these three areas are still poorly known. Here, we used Tiliacoreae, a tribe of pantropical lianas with a high level of regional endemism, to provide new insights into the biogeographical relationships of tropical rainforests among different continents.

METHODS

Based on seven plastid and two nuclear DNA regions, we reconstructed a phylogeny for Tiliacoreae with the most comprehensive sampling ever. Within the phylogenetic framework, we then estimated divergence times and investigated the spatiotemporal evolution of the tribe.

KEY RESULTS

The monophyletic Tiliacoreae contain three major clades, which correspond to Neotropical, Afrotropical and Indo-Malesian/Australasian areas, respectively. Both Albertisia and Anisocycla are not monophyletic. The most recent common ancestor of Tiliacoreae occurred in Indo-Malesia, the Afrotropics and Neotropics in the early Eocene, then rapidly diverged into three major clades between 48 and 46 Ma. Three dispersals from Indo-Malesia to Australasia were inferred, one in the middle Eocene and two in the late Oligocene-late Miocene, and two dispersals from the Afrotropics to Indo-Malesia occurred in the late Eocene-Oligocene.

CONCLUSIONS

The three main clades of Anisocycla correspond to three distinct genera [i.e. Anisocycla sensu stricto and two new genera (Georgesia and Macrophragma)]. Epinetrum is a member of Albertisia. Our findings highlight that sea-level fluctuations and climate changes in the Cenozoic have played important roles in shaping the current distribution and endemism of Tiliacoreae, hence contributing to the knowledge on the historical biogeography of tropical rainforests on a global scale.

The PaleoJump database for abrupt transitions in past climates

Tipping points (TPs) in Earth's climate system have been the subject of increasing interest and concern in recent years, given the risk that anthropogenic forcing could cause abrupt, potentially irreversible, climate transitions. Paleoclimate records are essential for identifying past TPs and for gaining a thorough understanding of the underlying nonlinearities and bifurcation mechanisms. However, the quality, resolution, and reliability of these records can vary, making it important to carefully select the ones that provide the most accurate representation of past climates. Moreover, as paleoclimate time series vary in their origin, time spans, and periodicities, an objective, automated methodology is crucial for identifying and comparing TPs. To address these challenges, we introduce the open-source PaleoJump database, which contains a collection of carefully selected, high-resolution records originating in ice cores, marine sediments, speleothems, terrestrial records, and lake sediments. These records describe climate variability on centennial, millennial and longer time scales and cover all the continents and ocean basins. We provide an overview of their spatial distribution and discuss the gaps in coverage. Our statistical methodology includes an augmented Kolmogorov-Smirnov test and Recurrence Quantification Analysis; it is applied here, for illustration purposes, to selected records in which abrupt transitions are automatically detected and the presence of potential tipping elements is investigated. These transitions are shown in the PaleoJump database along with other essential information about the records, including location, temporal scale and resolution, as well as temporal plots. This open-source database represents, therefore, a valuable resource for researchers investigating TPs in past climates.

Effects of environment and metacommunity delineation on multiple dimensions of stream fish beta diversity

Introduction

Beta diversity represents changes in community composition among locations across a landscape. While the effects of human activities on beta diversity are becoming clearer, few studies have considered human effects on the three dimensions of beta diversity: taxonomic, functional, and phylogenetic. Including anthropogenic factors and multiple dimensions of biodiversity may explain additional variation in stream fish beta diversity, providing new insight into how metacommunities are structured within different spatial delineations.

Methods

In this study, we used a 350 site stream fish abundance dataset from South Carolina, United States to quantify beta diversity explainable by spatial, natural environmental, and anthropogenic variables. We investigated three spatial delineations: (1) a single whole-state metacommunity delineated by political boundaries, (2) two metacommunities delineated by a natural geomorphic break separating uplands from lowlands, and (3) four metacommunities delineated by natural watershed boundaries. Within each metacommunity we calculated taxonomic, functional, and phylogenetic beta diversity and used variation partitioning to quantify spatial, natural environmental, and anthropogenic contributions to variations in beta diversity.

Results

We explained 25–81% of the variation in stream fish beta diversity. The importance of these three factors in structuring metacommunities differed among the diversity dimensions, providing complementary perspectives on the processes shaping beta diversity in fish communities. The effect of spatial, natural environmental, and anthropogenic factors varied among the spatial delineations, which indicate conclusions drawn from variation partitioning may depend on the spatial delineation chosen by researchers.

Discussion

Our study highlights the importance of considering human effects on metacommunity structure, quantifying multiple dimensions of beta diversity, and careful consideration of user-defined metacommunity boundaries in beta diversity analyses.

The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights

Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.

Global impact and selectivity of the Cretaceous-Paleogene mass extinction among sharks, skates, and rays

The Cretaceous-Paleogene event was the last mass extinction event, yet its impact and long-term effects on species-level marine vertebrate diversity remain largely uncharacterized. We quantified elasmobranch (sharks, skates, and rays) speciation, extinction, and ecological change resulting from the end-Cretaceous event using >3200 fossil occurrences and 675 species spanning the Late Cretaceous-Paleocene interval at global scale. Elasmobranchs declined by >62% at the Cretaceous-Paleogene boundary and did not fully recover in the Paleocene. The end-Cretaceous event triggered a heterogeneous pattern of extinction, with rays and durophagous species reaching the highest levels of extinction (>72%) and sharks and nondurophagous species being less affected. Taxa with large geographic ranges and/or those restricted to high-latitude settings show higher survival. The Cretaceous-Paleogene event drastically altered the evolutionary history of marine ecosystems.

Peak Cenozoic warmth enabled deep-sea sand deposition

The early Eocene (~ 56-48 million years ago) was marked by peak Cenozoic warmth and sea levels, high CO₂, and largely ice-free conditions. This time has been described as a period of increased continental erosion and silicate weathering. However, these conclusions are based largely on geochemical investigation of marine mudstones and carbonates or study of intermontane Laramide basin settings. Here, we evaluate the marine coarse siliciclastic response to early Paleogene hothouse climatic and oceanographic conditions. We compile an inventory of documented sand-rich (turbidite) deep-marine depositional systems, recording 59 instances of early Eocene turbidite systems along nearly all continental margins despite globally-elevated sea levels. Sand-rich systems were widespread on active margins (42 instances), but also on passive margins (17 instances). Along passive margins, 13 of 17 early Eocene systems are associated with known Eocene-age fluvial systems, consistent with a fluvial clastic response to Paleogene warming. We suggest that deep-marine sedimentary basins preserve clastic records of early Eocene climatic extremes. We also suggest that in addition to control by eustasy and tectonism, climate-driven increases in sediment supply (e.g., drainage integration, global rainfall, denudation) may significantly contribute to the global distribution and volume of coarse-grained deep-marine deposition despite high sea level.

Evolution in the dark: Unexpected genetic diversity and morphological stasis in the blind, aquifer-dwelling catfish Horaglanis

The lateritic aquifers of the southern Indian state of Kerala harbour a unique assemblage of enigmatic stygobitic fishes which are encountered very rarely, only when they surface during the digging and cleaning of homestead wells. Here, we focus on one of the most unusual members of this group, the catfish Horaglanis, a genus of rarely-collected, tiny, blind, pigment less, and strictly aquifer-residing species. A six-year exploratory and citizen-science backed survey supported by molecular phylogenetic analysis reveals novel insights into the diversity, distribution and population structure of Horaglanis. The genus is characterized by high levels of intraspecific and interspecific genetic divergence, with phylogenetically distinct species recovered above a 7.0% genetic-distance threshold in the mitochondrial cytochrome oxidase subunit 1 gene. Contrasting with this deep genetic divergence, however, is a remarkable stasis in external morphology. We identify and describe a new cryptic species, Horaglanis populi, a lineage that is the sister group of all currently known species. All four species are represented by multiple haplotypes. Mismatch distribution reveals that populations have not experienced recent expansions.

Asymmetric migration dynamics of the tropical Asian and Australasian floras

The tropical Asian and Australasian floras have a close relationship, and is a vital distribution pattern of seed plants worldwide. As estimated, more than 81 families and 225 genera of seed plants distributed between tropical Asia and Australasia. However, the evolutionary dynamics of two floras were still vague. Here, a total of 29 plant lineages, represented the main clades of seed plants and different habits, were selected to investigate the biotic interchange between tropical Asia and Australasia by integrated dated phylogenies, biogeography, and ancestral state reconstructions. Our statistics indicated that 68 migrations have occurred between tropical Asia and Australasia since the middle Eocene except terminal migrations, and the migration events from tropical Asia to Australasia is more than 2 times of the reverse. Only 12 migrations occurred before 15 Ma, whereas the remaining 56 migrations occurred after 15 Ma. Maximal number of potential dispersal events (MDE) analysis also shows obvious asymmetry, with southward migration as the main feature, and indicates the climax of bi-directional migrations occurred after 15 Ma. We speculate that the formation of island chains after the Australian-Sundaland collision and climate changes have driven seed plant migrations since the middle Miocene. Furthermore, biotic dispersal and stable habitat may be crucial for floristic interchange between tropical Asia and Australasia.

Marine facies differentiation along complex paleotopography: an example from the Middle Miocene (Serravallian) of Lower Austria

In the area of Bad Deutsch-Altenburg (Hainburg Mountains, Lower Austria) a Middle Miocene transgression over Mesozoic basement was explored in the course of the Danube power plant project "Hainburg". The Mesozoic basement forms a narrow ridge dipping to the northeast towards the Vienna Basin, covered by various Miocene sediments. The ridge represents a specific paleotopography that required a detailed study with 78 shallow, fully cored drill holes in an area of c. 0.5 km². Ten drillings were selected for this study based on sedimentary composition and position relative to the Mesozoic ridge. These 10 cores, ranging in drilling depth from 26.5 to 96.4 m, were studied in respect to sedimentology, corallinacean algae, calcareous nannoplankton, foraminifers and ostracodes to reconstruct sediment distribution and paleoenvironment. Sediment distribution clearly shows that the Mesozoic ridge formed a physical barrier with siliciclastics dominating in the SW of the ridge and carbonate sediments prevailing in the NE. Based on biostratigraphy (calcareous nannoplankton, foraminifera, ostracodes, dinoflagellates) the majority of the sediments can be dated to the late Badenian (early Serravallian) only in some drillholes lower Sarmatian (upper Serravallian) sediments were detected. In terms of sequence stratigraphy, the Badenian sediments represent the transgressive and highstand systems tract of 3^rd order sequence TB 2.5 (bound by the lowstands Ser 2 and Ser 3), the lower Sarmatian sediments can be correlated to sequence TB 2.6. Carbonate sediments show a wide spectrum of 13 facies which are mostly dominated by coralline algae. According to the relative positions of the drill holes a water depth between 0 and about 50 m can be reconstructed what is supported by the occurrence of the benthic biota. This biota indicates that the sedimentary succession started from the very beginning under full marine conditions. Except of basal conglomerates/breccias water energy conditions were low and turbidity high. Close to the Sarmatian boundary a reduction in salinity and depth may have occurred which is also observed in the Sarmatian sediments. Carbonate sediments and, in particular, larger benthic foraminifers indicate tropical to warm-temperate conditions for the late Badenian of the studied sections. The siliciclastic sediments NW of the Mesozoic ridge reflect riverine input indicated by the occurrence of freshwater ostracodes and characean oogonias. Calcareous nannoplankton and dinoflagellates show a high share of reworking from Upper Cretaceaous and Paleogene sediments.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s00015-022-00425-w.

Innovations and stepwise evolution of CBFs/DREB1s and their regulatory networks in angiosperms

The C-repeat binding factors/dehydration-responsive element binding protein 1s (CBFs/DREB1s) have been identified as major regulators of cold acclimation in many angiosperm plants. However, their origin and evolutionary process associated to cold responsiveness are still lacking. By integrating multi-omics data of genomes, transcriptomes, and CBFs/DREB1s genome-wide binding profiles, we unveil the origin and evolution of CBFs/DREB1s and their regulatory network. Gene collinearity and phylogeny analyses show that CBF/DREB1 is an innovation evolved from tandem duplication-derived DREB III gene. A subsequent event of ε-whole genome duplication led to two CBF/DREB1 archetypes (Clades I and II) in ancient angiosperms. In contrast to cold-insensitivity of Clade I and their parent DREB III genes, Clade II evolved a further innovation in cold-sensitive response and was stepwise expanded in eudicots and monocots by independent duplications. In geological time, the duplication events were mainly enriched around the Cretaceous-Paleogene (K-Pg) boundary and/or in the Late Cenozoic Ice Age, when the global average temperature significantly decreased. Consequently, the duplicated CBF/DREB1 genes contributed to the rewiring of CBFs/DREB1s-regulatory network for cold tolerance. Altogether, our results highlight an origin and convergent evolution of CBFs/DREB1s and their regulatory network probably for angiosperms adaptation to global cooling.