Late Miocene climate cooling and intensification of southeast Asian winter monsoon

East Asian winter monsoon intensification over the Northwest Pacific Ocean driven by late Miocene atmospheric CO2 decline

East Asian winter monsoon (EAWM) activity has had profound effects on environmental change throughout East Asia and the western Pacific. Much attention has been paid to Quaternary EAWM evolution, while long-term EAWM fluctuation characteristics and drivers remain unclear, particularly during the late Miocene when marked global climate and Asian paleogeographic changes occurred. To clarify understanding of late Miocene EAWM evolution, we developed a high-precision 9-million-year-long stacked EAWM record from Northwest Pacific Ocean abyssal sediments based on environmental magnetism, sedimentology, and geochemistry, which reveals a strengthened late Miocene EAWM. Our paleoclimate simulations also indicate that atmospheric CO2 decline played a vital role in this EAWM intensification over the Northwest Pacific Ocean compared to other factors, including central Asian orogenic belt and northeastern Tibetan Plateau uplift and Antarctic ice-sheet expansion. Our results expand understanding of EAWM evolution from inland areas to the open ocean and indicate the importance of atmospheric CO2 fluctuations on past EAWM variability over large spatial scales.

Genome sequences and population genomics reveal climatic adaptation and genomic divergence between two closely related sweetgum species

Understanding the genetic basis of population divergence and adaptation is an important goal in population genetics and evolutionary biology. However, the relative roles of demographic history, gene flow, and/or selective regime in driving genomic divergence, climatic adaptation, and speciation in non-model tree species are not yet fully understood. To address this issue, we generated whole-genome resequencing data of Liquidambar formosana and L. acalycina, which are broadly sympatric but altitudinally segregated in the Tertiary relict forests of subtropical China. We integrated genomic and environmental data to investigate the demographic history, genomic divergence, and climatic adaptation of these two sister species. We inferred a scenario of allopatric species divergence during the late Miocene, followed by secondary contact during the Holocene. We identified multiple genomic islands of elevated divergence that mainly evolved through divergence hitchhiking and recombination rate variation, likely fostered by long-term refugial isolation and recent differential introgression in low-recombination genomic regions. We also found some candidate genes with divergent selection signatures potentially involved in climatic adaptation and reproductive isolation. Our results contribute to a better understanding of how late Tertiary/Quaternary climatic change influenced speciation, genomic divergence, climatic adaptation, and introgressive hybridization in East Asia's Tertiary relict flora. In addition, they should facilitate future evolutionary, conservation genomics, and molecular breeding studies in Liquidambar, a genus of important medicinal and ornamental values.

Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

Chloroplast genome analysis and evolutionary insights in the versatile medicinal plant Calendula officinalis L

Calendula officinalis L.is a versatile medicinal plant with numerous applications in various fields. However, its chloroplast genome structure, features, phylogeny, and patterns of evolution and mutation remain largely unexplored. This study examines the chloroplast genome, phylogeny, codon usage bias, and divergence time of C. officinalis, enhancing our understanding of its evolution and adaptation. The chloroplast genome of C. officinalis is a 150,465 bp circular molecule with a G + C content of 37.75% and comprises 131 genes. Phylogenetic analysis revealed a close relationship between C. officinalis, C. arvensis, and Osteospermum ecklonis. A key finding is the similarity in codon usage bias among these species, which, coupled with the divergence time analysis, supports their close phylogenetic proximity. This similarity in codon preference and divergence times underscores a parallel evolutionary adaptation journey for these species, highlighting the intricate interplay between genetic evolution and environmental adaptation in the Asteraceae family. Moreover unique evolutionary features in C. officinalis, possibly associated with certain genes were identified, laying a foundation for future research into the genetic diversity and medicinal value of C. officinalis.

Accelerated marine carbon cycling forced by tectonic degassing over the Miocene Climate Optimum

Global warming during the Miocene Climate Optimum (MCO, ∼17-14 million years ago) is associated with massive carbon emissions sourced from the flood basalt volcanism and ocean crustal production. However, the perturbation of tectonic carbon degassing on the interaction between climate change and carbon cycle remains unclear. Here, through time-evolutive phase analysis of new and published high-resolution benthic foraminiferal oxygen (δ18O) and carbon (δ13C) isotope records from the global ocean, we find that variations in the marine carbon cycle lead the climate-cryosphere system (δ13C-lead-δ18O) on 405,000-year eccentricity timescales during the MCO. This is in contrast to the previously reported climate-lead-carbon (δ18O-lead-δ13C) scenario during most of the Oligo-Miocene (∼34-6 million years ago). Further sensitivity analysis and model simulations suggest that the elevated atmospheric CO2 concentrations and the resulting greenhouse effect strengthened the low-latitude hydrological cycle during the MCO, accelerating the response of marine carbon cycle to eccentricity forcing. Tropical climate processes played a more important role in regulating carbon-cycle variations when Earth's climate was in a warm regime, as opposed to the dominant influence of polar ice-sheet dynamics during the Plio-Pleistocene (after ∼6 million years ago).

Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics

Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium (14 plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a time-calibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic activities jointly shaped the distribution range and drove evolutionary radiation of Lilium, including the Middle Miocene Climate Optimum (MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau (QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere.

Impact of the climatic changes in the Pliocene-Pleistocene transition on Irano-Turanian species. The radiation of genus Jurinea (Compositae)

The Irano-Turanian region is one of the world's richest floristic regions and the centre of diversity for numerous xerophytic plant lineages. However, we still have limited knowledge on the timing of evolution and biogeographic history of its flora, and potential drivers of diversification remain underexplored. To fill this knowledge gap, we focus on the Eurasian genus Jurinea (ca. 200 species), one of the largest plant radiations that diversified in the region. We applied a macroevolutionary integrative approach to explicitly test diversification hypotheses and investigate the relative roles of geography vs. ecology and niche conservatism vs. niche lability in speciation processes. To do so, we gathered a sample comprising 77% of total genus richness and obtained data about (1) its phylogenetic history, recovering 502 nuclear loci sequences; (2) growth forms; (3) ecological niche, compiling data of 21 variables for more than 2500 occurrences; and (4) paleoclimatic conditions, to estimate climatic stability. Our results revealed that climate was a key factor in the evolutionary dynamics of Jurinea. The main diversification and biogeographic events that occurred during past climate changes, which led to colder and drier conditions, are the following: (1) the origin of the genus (10.7 Ma); (2) long-distance dispersals from the Iranian Plateau to adjacent regions (∼7-4 Ma); and (3) the diversification shift during Pliocene-Pleistocene Transition (ca. 3 Ma), when net diversification rate almost doubled. Our results supported the pre-adaptation hypothesis, i.e., the evolutionary success of Jurinea was linked to the retention of the ancestral niche adapted to aridity. Interestingly, the paleoclimatic analyses revealed that in the Iranian Plateau long-term climatic stability favoured old-lineage persistence, resulting in current high species richness of semi-arid and cold adapted clades; whereas moderate climate oscillations stimulated allopatric diversification in the lineages distributed in the Circumboreal region. In contrast, growth form lability and high niche disparity among closely related species in the Central Asian clade suggest adaptive radiation to mountain habitats. In sum, the radiation of Jurinea is the result of both adaptive and non-adaptive processes influenced by climatic, orogenic and ecological factors.

Deconstructing age estimates for angiosperms

Estimates of the age of angiosperms from molecular phylogenies vary considerably. As in all estimates of evolutionary timescales from phylogenies, generating these estimates requires assumptions about the rate that molecular sequences are evolving (using clock models) and the time duration of the branches in a phylogeny (using fossil calibrations and branching processes). Often, it is difficult to demonstrate that these assumptions reflect current knowledge of molecular evolution or the fossil record. In this study we re-estimate the age of angiosperms using a minimal set of assumptions, therefore avoiding many of the assumptions inherent to other methods. The age estimates we generate are similar for each of the four datasets analysed, ranging from 130 to 400 Ma, but are far less precise than in previous studies. We demonstrate that this reduction in precision results from making less stringent assumptions about both rate and time, and that the analysed molecular dataset has very little effect on age estimates.

What the geological past can tell us about the future of the ocean's twilight zone

Paleontological reconstructions of plankton community structure during warm periods of the Cenozoic (last 66 million years) reveal that deep-dwelling 'twilight zone' (200-1000 m) plankton were less abundant and diverse, and lived much closer to the surface, than in colder, more recent climates. We suggest that this is a consequence of temperature's role in controlling the rate that sinking organic matter is broken down and metabolized by bacteria, a process that occurs faster at warmer temperatures. In a warmer ocean, a smaller fraction of organic matter reaches the ocean interior, affecting food supply and dissolved oxygen availability at depth. Using an Earth system model that has been evaluated against paleo observations, we illustrate how anthropogenic warming may impact future carbon cycling and twilight zone ecology. Our findings suggest that significant changes are already underway, and without strong emissions mitigation, widespread ecological disruption in the twilight zone is likely by 2100, with effects spanning millennia thereafter.

Weakening of the South Asian summer monsoon linked to interhemispheric ice-sheet growth since 12 Ma

The evolution and driving mechanism of the South Asian summer monsoon (SASM) are still poorly understood. We here present a 12-Myr long SASM record by analyzing the strontium and neodymium isotopic composition of detrital components at IODP Exp. 359 Site U1467 from the northern Indian Ocean. The provenance investigation demonstrates that more dust enriched in εNd from northeastern Africa and the Arabian Peninsula was transported to the study site by monsoonal and Shamal winds during the summer monsoon season. A two-step weakening of the SASM wind since ~12 Ma is proposed based on the εNd record. This observational phenomenon is supported by climate modeling results, demonstrating that the SASM evolution was mainly controlled by variations in the gradient between the Mascarene High and the Indian Low, associated with meridional shifts of the Hadley Cell and the Intertropical Convergence Zone, which were caused by interhemispheric ice-sheet growth since the Middle Miocene.

Late Cenozoic cooling restructured global marine plankton communities

The geographic ranges of marine organisms, including planktonic foraminifera¹, diatoms, dinoflagellates², copepods³ and fish⁴, are shifting polewards owing to anthropogenic climate change⁵. However, the extent to which species will move and whether these poleward range shifts represent precursor signals that lead to extinction is unclear⁶. Understanding the development of marine biodiversity patterns over geological time and the factors that influence them are key to contextualizing these current trends. The fossil record of the macroperforate planktonic foraminifera provides a rich and phylogenetically resolved dataset that provides unique opportunities for understanding marine biogeography dynamics and how species distributions have responded to ancient climate changes. Here we apply a bipartite network approach to quantify group diversity, latitudinal specialization and latitudinal equitability for planktonic foraminifera over the past eight million years using Triton, a recently developed high-resolution global dataset of planktonic foraminiferal occurrences⁷. The results depict a global, clade-wide shift towards the Equator in ecological and morphological community equitability over the past eight million years in response to temperature changes during the late Cenozoic bipolar ice sheet formation. Collectively, the Triton data indicate the presence of a latitudinal equitability gradient among planktonic foraminiferal functional groups which is coupled to the latitudinal biodiversity gradient only through the geologically recent past (the past two million years). Before this time, latitudinal equitability gradients indicate that higher latitudes promoted community equitability across ecological and morphological groups. Observed range shifts among marine planktonic microorganisms^1,2,8 in the recent and geological past suggest substantial poleward expansion of marine communities even under the most conservative future global warming scenarios.

CO2-forced Late Miocene cooling and ecosystem reorganizations in East Asia

In parallel with pronounced cooling in the oceans, vast areas of the continents experienced enhanced aridification and restructuring of vegetation and animal communities during the Late Miocene. Debate continues over whether pCO2-induced global cooling was the primary driver of this climate and ecosystem upheaval on land. Here we present an 8 to 5 Ma land surface temperatures (LST) record from East Asia derived from paleosol carbonate clumped isotopes and integrated with climate model simulations. The LST cooled by ~7 °C between 7.5 and 5.7 Ma, followed by rapid warming across the Miocene-Pliocene transition (5.5 to 5 Ma). These changes occurred synchronously with variations in alkenone and Mg/Ca-based sea surface temperatures and with hydroclimate and ecosystem shifts in East Asia, highlighting a global climate forcing mechanism. Our modeling experiments additionally demonstrate that pCO2-forced cooling would have altered moisture transfer and pathways and driven extensive aridification in East Asia. We, thus, conclude that the East Asian hydroclimate and ecosystem shift was primarily controlled by pCO2-forced global cooling between 8 and 5 Ma.

The fungal ecology of the Brassington Formation (Middle Miocene) of Derbyshire, United Kingdom, and a new method for palaeoclimate reconstruction

Fossil fungi from periods warmer than modern climates provide unique insights into the future impacts of anthropogenic climate change. Here we report the fossil fungal assemblage from the late Middle Miocene Kenslow Member of central England, associated with climatic conditions warmer than the present-day. The identification of 110 morphotypes, which primarily relate to moist environments and the presence of wood, have been used to develop a new nearest living relative palaeoclimate reconstruction. The fungal assemblage indicates a Köppen–Geiger climate class, represented by temperate conditions, no dry season, and warm summers. This new fungal-based palaeoclimate reconstruction technique holds exciting potential to explore critically important but poorly understood palaeoenvironments, and the resulting qualitative inferences align well with previously published palaeobotanical quantitative estimates of palaeoclimate. These findings show that diverse fungal assemblages can successfully be used to reconstruct past climates for the first time.

Weakened pacific overturning circulation, winter monsoon dominance and tectonism re-organized Japan Sea paleoceanography during the Late Miocene global cooling

The Late Miocene global cooling (LMGC; approximately 7.9–5.8 Ma) was associated with remarkable changes in monsoon dynamics, biogenic bloom in the global oceans, and the rise of modern ecosystems at the expense of old biota. However, the possible linkage between the environmental changes and ecosystem shifts during the LMGC is still debated. In this paper, we show the high-resolution changes in the fluxes of selected radiolarian species, suggesting a drastic reorganization in the paleoceanography and ecosystem in the Japan Sea during the LMGC. The endemic radiolarian Cycladophora nakasekoi dominated the Japan Sea until 7.4 Ma when the Japan Sea sediment changed from dark radiolarian-rich sediment to organic-poor diatom ooze. Changes in the fluxes of C. nakasekoi and Tricolocapsa papillosa, the latter related to changes in the Pacific central water (PCW), show 100, 200, and ~ 500 ka cycles with their high flux mostly within the darker sediment intervals during the low-eccentricity period until 7.4 Ma, suggesting that orbitally paced PCW inflow might have been the major nutrient source into the Japan Sea. At about 7.4 Ma, these species decreased at the expense of increased Larcopyle weddellium, a radiolarian related to the North Pacific intermediate water (NPIW), and Cycladophora sphaeris, a subarctic radiolarian species, implying a decrease in PCW inflow and an increase in the inflow of NPIW and subarctic shallow water. Such a change would have been related to the LMGC-induced weakening in the Pacific Meridional overturning circulation and the southward shift of the subarctic front due to intensified East Asian winter monsoon. Such a drastic reorganization in the hydrography in the Japan Sea probably caused changes in nutrient provenance from the PCW to the NPIW and resulted in faunal turnover, marked by the disappearance of the old regional and endemic faunal components, such as C. nakasekoi.

Need for split: integrative taxonomy reveals unnoticed diversity in the subaquatic species of Pseudohygrohypnum (Pylaisiaceae, Bryophyta)

We present an integrative molecular and morphological study of subaquatic representatives of the genus Pseudohygrohypnum (Pylaisiaceae, Bryophyta), supplemented by distribution modelling of the revealed phylogenetic lineages. Phylogenetic analyses of nuclear and plastid datasets combined with the assemble species by automatic partitioning (ASAP) algorithm revealed eight distinct species within the traditionally circumscribed P. eugyrium and P. subeugyrium. These species are therefore yet another example of seemingly widely distributed taxa that harbour molecularly well-differentiated lineages with narrower distribution ranges. Studied accessions that were previously assigned to P. eugyrium form three clearly allopatric lineages, associated with temperate regions of Europe, eastern North America and eastern Asia. Remarkably, accessions falling under the current morphological concept of P. subeugyrium were shown to be even more diverse, containing five phylogenetic lineages. Three of these lineages occur under harsh Asian continental climates from cool-temperate to Arctic regions, while the remaining two, referred to P. subeugyrium s.str. and P. purpurascens, have more oceanic North Atlantic and East Asian distributions. Niche identity and similarity tests suggested no similarity in the distributions of the phylogenetically related lineages but revealed the identity of two East Asian species and the similarity of two pairs of unrelated species. A morphological survey confirmed the distinctness of all eight phylogenetic lineages, requiring the description of five new species. Pseudohygrohypnum appalachianum and P. orientale are described for North American and East Asian plants of P. eugyrium s.l., while P. sibiricum, P. subarcticum and P. neglectum are described for the three continental, predominantly Asian lineages of P. subeugyrium s.l. Our results highlight the importance of nontropical Asia as a center of bryophyte diversity. Phylogenic dating suggests that the diversification of subaquatic Pseudohygrohypnum lineages appeared in late Miocene, while mesophilous species of the genus split before Miocene cooling, in climatic conditions close to those where the ancestor of Pseudohygrohypnum appeared. We speculate that radiation of the P. subeugyrium complex in temperate Asia might have been driven by progressive cooling, aridification, and increases in seasonality, temperature and humidity gradients. Our results parallel those of several integrative taxonomic studies of North Asian mosses, which have resulted in a number of newly revealed species. These include various endemics from continental areas of Asia suggesting that the so-called Rapoport's rule of low diversity and wide distribution range in subpolar regions might not be applicable to bryophytes. Rather, the strong climatic oscillations in these regions may have served as a driving force of speciation and niche divergence.

Global warming-induced Asian hydrological climate transition across the Miocene-Pliocene boundary

Across the Miocene-Pliocene boundary (MPB; 5.3 million years ago, Ma), late Miocene cooling gave way to the early-to-middle Pliocene Warm Period. This transition, across which atmospheric CO2 concentrations increased to levels similar to present, holds potential for deciphering regional climate responses in Asia-currently home to more than half of the world's population- to global climate change. Here we find that CO2-induced MPB warming both increased summer monsoon moisture transport over East Asia, and enhanced aridification over large parts of Central Asia by increasing evaporation, based on integration of our ~1-2-thousand-year (kyr) resolution summer monsoon records from the Chinese Loess Plateau aeolian red clay with existing terrestrial records, land-sea correlations, and climate model simulations. Our results offer palaeoclimate-based support for 'wet-gets-wetter and dry-gets-drier' projections of future regional hydroclimate responses to sustained anthropogenic forcing. Moreover, our high-resolution monsoon records reveal a dynamic response to eccentricity modulation of solar insolation, with predominant 405-kyr and ~100-kyr periodicities between 8.1 and 3.4 Ma.

Tectonic and climatic drivers of Asian monsoon evolution

Asian Monsoon rainfall supports the livelihood of billions of people, yet the relative importance of different drivers remains an issue of great debate. Here, we present 30 million-year model-based reconstructions of Indian summer monsoon and South East Asian monsoon rainfall at millennial resolution. We show that precession is the dominant direct driver of orbital variability, although variability on obliquity timescales is driven through the ice sheets. Orographic development dominated the evolution of the South East Asian monsoon, but Indian summer monsoon evolution involved a complex mix of contributions from orography (39%), precession (25%), atmospheric CO2 (21%), ice-sheet state (5%) and ocean gateways (5%). Prior to 15 Ma, the Indian summer monsoon was broadly stable, albeit with substantial orbital variability. From 15 Ma to 5 Ma, strengthening was driven by a combination of orography and glaciation, while closure of the Panama gateway provided the prerequisite for the modern Indian summer monsoon state through a strengthened Atlantic meridional overturning circulation.

Genome-wide analysis reveals signatures of complex introgressive gene flow in macaques (genus Macaca)

The genus Macaca serves as an ideal research model for speciation and introgressive gene flow due to its short period of diversification (about five million years ago) and rapid radiation of constituent species. To understand evolutionary gene flow in macaques, we sequenced four whole genomes (two M. arctoides and two M. thibetana) and combined them with publicly available macaque genome data for genome-wide analyses. We analyzed 14 individuals from nine Macaca species covering all Asian macaque species groups and detected extensive gene flow signals, with the strongest signals between the fascicularis and silenus species groups. Notably, we detected bidirectional gene flow between M. fascicularis and M. nemestrina. The estimated proportion of the genome inherited via gene flow between the two species was 6.19%. However, the introgression signals found among studied island species, such as Sulawesi macaques and M. fuscata, and other species were largely attributed to the genomic similarity of closely related species or ancestral introgression. Furthermore, gene flow signals varied in individuals of the same species (M. arctoides, M. fascicularis, M. mulatta, M. nemestrina and M. thibetana), suggesting very recent gene flow after the populations split. Pairwise sequentially Markovian coalescence (PSMC) analysis showed all macaques experienced a bottleneck five million years ago, after which different species exhibited different fluctuations in demographic history trajectories, implying they have experienced complicated environmental variation and climate change. These results should help improve our understanding of the complicated evolutionary history of macaques, particularly introgressive gene flow.

Inferring historical survivals of climate relicts: the effects of climate changes, geography, and population-specific factors on herbaceous hydrangeas

Climate relicts hold considerable importance because they have resulted from numerous historical changes. However, there are major interspecific variations among the ways by which they survived climate changes. Therefore, investigating the factors and timing that affected population demographics can expand our understanding of how climate relicts responded to historical environmental changes. Here, we examined herbaceous hydrangeas of genus Deinanthe in East Asia, which show limited distributions and a remarkable disjunction between Japan and central China. Chloroplast genome and restriction site-associated DNA sequencing revealed that speciation event occurred in the late Miocene (ca. 7-9 Mya) in response to global climate change. Two lineages apparently remained not branched until the middle Quaternary, and afterwards started to diverge to regional population groups. The narrow endemic species in central China showed lower genetic diversity (He = 0.082), as its population size rapidly decreased during the Holocene due to isolation in montane refugia. Insular populations in the three Japanese islands (He = 0.137-0.160) showed a genetic structure that was inconsistent with sea barriers, indicating that it was shaped in the glacial period when its range retreated to coastal refugia on the exposed sea floor. Demographic modelling by stairway-plot analysis reconstructed variable responses of Japanese populations: some experienced glacial bottlenecks in refugial isolation, while post-glacial range expansion seemingly exerted founder effects on other populations. Overall, this study demonstrated the involvement of not just one, but multiple factors, such as the interplay between climate changes, geography, and other population-specific factors, that determine the demographics of climate relicts.

Paleoceanographic Perturbations and the Marine Carbonate System during the Middle to Late Miocene Carbonate Crash—A Critical Review

This study intends to review and assess the middle to late Miocene Carbonate Crash (CC) events in the low to mid latitudes of the Pacific, Indian, Caribbean and Atlantic Oceans as part of the global paleoceanographic reorganisations between 12 and 9 Ma with an emphasis on record preservation and their relation to mass accumulation rates (MAR). In the Eastern Pacific the accumulation changes in carbonate and opal probably reflect an El-Niño-like state of low productivity, which marks the beginning of the CC-event (11.5 Ma), followed by decreased preservation and influx of corrosive bottom waters (10.3 to 10.1 Ma). At the same time in the Atlantic, carbonate preservation considerably increases, suggesting basin-to-basin fractionation. The low-latitude Indian Ocean, the Pacific and the Caribbean are all characterised by a similar timing of preservation increase starting at ~9.6–9.4 Ma, while their MARs show drastic changes with different timing of events. The Atlantic preservation pattern shows an increase as early as 11.5 Ma and becomes even better after 10.1 Ma. The shallow Indian Ocean (Mascarene plateau) is characterised by low carbonate accumulation throughout and increasing preservation after 9.4 Ma. At the same time, the preservation in the Atlantic, including the Caribbean, is increasing due to enhanced North Atlantic deep-water formation, leading to the increase in carbonate accumulation at 10 Ma. Moreover, the shoaling of the Central American Isthmus might have helped to enhance Caribbean preservation after 9.4 Ma. Lower nannoplankton productivity in the Atlantic should have additionally contributed to low mass accumulation rates during the late CC-interval. Overall, it can be inferred that these carbonate minima events during the Miocene may be the result of decreased surface ocean productivity and oceanographically driven increased seafloor dissolution.

Angiosperms at the edge: Extremity, diversity, and phylogeny

A hallmark of flowering plants is their ability to invade some of the most extreme and dynamic habitats, including cold and dry biomes, to a far greater extent than other land plants. Recent work has provided insight to the phylogenetic distribution and evolutionary mechanisms which have enabled this success, yet needed is a synthesis of evolutionary perspectives with plant physiological traits, morphology, and genomic diversity. Linking these disparate components will not only lead to better understand the evolutionary parallelism and diversification of plants with these two strategies, but also to provide the framework needed for directing future research. We summarize the primary physiological and structural traits involved in response to cold- and drought stress, outline the phylogenetic distribution of these adaptations, and describe the recurring association of these changes with rapid diversification events that occurred in multiple lineages over the past 15 million years. Across these threefold facets of dry-cold correlation (traits, phylogeny, and time) we stress the contrast between (a) the amazing diversity of solutions flowering plants have developed in the face of extreme environments and (b) a broad correlation between cold and dry adaptations that in some cases may hint at deep common origins.

High-latitude biomes and rock weathering mediate climate-carbon cycle feedbacks on eccentricity timescales

The International Ocean Discovery Programme (IODP) and its predecessors generated a treasure trove of Cenozoic climate and carbon cycle dynamics. Yet, it remains unclear how climate and carbon cycle interacted under changing geologic boundary conditions. Here, we present the carbon isotope (δ¹³C) megasplice, documenting deep-ocean δ¹³C evolution since 35 million years ago (Ma). We juxtapose the δ¹³C megasplice with its δ¹⁸O counterpart and determine their phase-difference on ~100-kyr eccentricity timescales. This analysis reveals that 2.4-Myr eccentricity cycles modulate the δ¹³C-δ¹⁸O phase relationship throughout the Oligo-Miocene (34-6 Ma), potentially through changes in continental weathering. At 6 Ma, a striking switch from in-phase to anti-phase behaviour occurs, signalling a reorganization of the climate-carbon cycle system. We hypothesize that this transition is consistent with Arctic cooling: Prior to 6 Ma, low-latitude continental carbon reservoirs expanded during astronomically-forced cool spells. After 6 Ma, however, continental carbon reservoirs contract rather than expand during cold periods due to competing effects between Arctic biomes (ice, tundra, taiga). We conclude that, on geologic timescales, System Earth experienced state-dependent modes of climate–carbon cycle interaction.

Climate and carbon cycle interactions during major Earth system changes through the Cenozoic remain unclear. Here, the authors present a combined δ¹³C-δ¹⁸O megasplice for the last 35 Ma which allows them to identify three marked intervals of distinct climate–carbon cycle interactions.

A Narrow Endemic or a Species Showing Disjunct Distribution? Studies on Meehania montis-koyae Ohwi (Lamiaceae)

Meehania montis-koyae Ohwi (Lamiaceae), which has been considered a narrow endemic and endangered species in Japan, was found in eastern China in 2011. China and Japan belong to the same floristic region and share many plant species, but it is very rare that Japanese narrow endemic species are newly found outside of the country. We examined herbarium specimens of both countries, and conducted analyses of molecular phylogenetics, population genetics, and divergence time estimation using two nuclear (ITS and ETS) gene regions and MIG-seq data. Chinese plants tend to become larger than Japanese, and they are different in leaf shape and floral features. Molecular phylogenetic analysis shows Chinese and Japanese M. montis-koyae are the closest relatives to each other. Population genetic analysis indicates no current gene flow between the Chinese and Japanese populations, and divergence time analysis shows they were separated during the late Miocene. We reach the conclusion that Chinese and Japanese M. montis-koyae have already become distinct biological entities, and a new taxon name Meehania zheminensis A. Takano, Pan Li, G.-H.Xia is proposed for the Chinese plants. A key to Asian Meehania species is provided.

"Into and Out of" the Qinghai-Tibet Plateau and the Himalayas: Centers of origin and diversification across five clades of Eurasian montane and alpine passerine birds

Encompassing some of the major hotspots of biodiversity on Earth, large mountain systems have long held the attention of evolutionary biologists. The region of the Qinghai-Tibet Plateau (QTP) is considered a biogeographic source for multiple colonization events into adjacent areas including the northern Palearctic. The faunal exchange between the QTP and adjacent regions could thus represent a one-way street ("out of" the QTP). However, immigration into the QTP region has so far received only little attention, despite its potential to shape faunal and floral communities of the QTP. In this study, we investigated centers of origin and dispersal routes between the QTP, its forested margins and adjacent regions for five clades of alpine and montane birds of the passerine superfamily Passeroidea. We performed an ancestral area reconstruction using BioGeoBEARS and inferred a time-calibrated backbone phylogeny for 279 taxa of Passeroidea. The oldest endemic species of the QTP was dated to the early Miocene (ca. 20 Ma). Several additional QTP endemics evolved in the mid to late Miocene (12-7 Ma). The inferred centers of origin and diversification for some of our target clades matched the "out of Tibet hypothesis' or the "out of Himalayas hypothesis" for others they matched the "into Tibet hypothesis." Three radiations included multiple independent Pleistocene colonization events to regions as distant as the Western Palearctic and the Nearctic. We conclude that faunal exchange between the QTP and adjacent regions was bidirectional through time, and the QTP region has thus harbored both centers of diversification and centers of immigration.

The emergence of Miocene reefs in South China Sea and its resilient adaptability under varying eustatic, climatic and oceanographic conditions

During the Miocene, extensive carbonate deposition thrived over wide latitudinal ranges in Southeast Asia despite perturbations of the global climate and thermohaline circulation that affected the Asian continent. Nevertheless, the mechanisms of its emergence, adaptability in siliciclastic-dominated margins and demise, especially in southern South China Sea (SCS), are largely speculative and remains enigmatic along with a scarcity of constraints on paleoclimatic and palaeoceanographic conditions. Here we show, through newly acquired high-resolution geophysical data and accurate stratigraphic records based on strontium isotopic dating, the evolution of these platforms from ~15.5–9.5 Ma is initially tied to tectonics and eustasy, and ultimately, after ~9.5 Ma, to changes in the global climate patterns and consequent palaeoceanographic conditions. Our results demonstrate at least two paleodeltas that provided favourable substratum of elevated sand bars, which conditioning the emergence of the buildups that inadvertently mirrored the underlying strata. We show unprecedented evidences for ocean current fluctuations linked to the intensification of the Asian summer monsoon winds resulting in the formation of drifts and moats, which extirpated the platforms through sediment removal and starvation. This work highlights the imperative role of palaeoceanography in creating favourable niches for reefal development that can be applicable to carbonate platforms elsewhere.

Reprogramming of Retrotransposon Activity during Speciation of the Genus Citrus

Speciation of the genus Citrus from a common ancestor has recently been established to begin ∼8 Ma during the late Miocene, a period of major climatic alterations. Here, we report the changes in activity of Citrus LTR retrotransposons during the process of diversification that gave rise to the current Citrus species. To reach this goal, we analyzed four pure species that diverged early during Citrus speciation, three recent admixtures derived from those species and an outgroup of the Citrus clade. More than 30,000 retrotransposons were grouped in ten linages. Estimations of LTR insertion times revealed that retrotransposon activity followed a species-specific pattern of change that could be ascribed to one of three different models. In some genomes, the expected pattern of gradual transposon accumulation was suddenly arrested during the radiation of the ancestor that gave birth to the current Citrus species. The individualized analyses of retrotransposon lineages showed that in each and every species studied, not all lineages follow the general pattern of the species itself. For instance, in most of the genomes, the retrotransposon activity of elements from the SIRE lineage reached its highest level just before Citrus speciation, while for Retrofit elements, it has been steadily growing. Based on these observations, we propose that Citrus retrotransposons may respond to stressful conditions driving speciation as a part of the genetic response involved in adaptation. This proposal implies that the evolving conditions of each species interact with the internal regulatory mechanisms of the genome controlling the proliferation of mobile elements.

Evolutionary history of field mice (Murinae: Apodemus), with emphasis on morphological variation among species in China and description of a new species

Mice of the genus Apodemus are widely distributed across Eurasia. Several species of this genus are hosts of important zoonotic diseases and parasites. The evolutionary history and dispersal routes of these mice remain unclear and the distribution of these species in China was poorly explored in previous studies. We here investigate the divergence times and historical geographical evolution of Apodemus and study the taxonomy of species in China by integrating molecular and morphological data. The crown age of this genus is dated to the Late Miocene, approximately 9.84 Mya. Western and Central Asia were inferred as the most likely ancestral area of this genus. Moreover, we recognize nine living species of Apodemus in China: Apodemus uralensis, A. agrarius, A. chevrieri, A. latronum, A. peninsulae, A. draco, A. ilex, A. semotus and A. nigrus sp. nov., the last from the highlands (elevation > 1984 m) of Fanjing Mountain in Guizhou Province and Jinfo Mountain in Chongqing Province. This new species diverged from A. draco, A. semotus and A. ilex approximately 4.53 Mya. The discovery of A. nigrus highlights the importance of high mountains as refugia and ‘isolated ecological islands’ for temperate species in south-eastern China.

Mediterranean isolation preconditioning the Earth System for late Miocene climate cooling

A global Neogene cooling trend culminated ~7 million years ago with the onset of Greenland glaciation. Increased ocean-atmosphere interaction and low- to high-latitude circulation are thought to be key factors in reorganizing late Miocene global temperature and precipitation patterns, but the drivers of this reorganization have yet to be identified. Here, we present new information about the evolution of the Atlantic-Mediterranean gateway that generated Mediterranean overflow. We use sedimentary and palaeogeographic evidence to constrain the timing and dimensions of this gateway and document the initiation of a saline plume of water within the North Atlantic. Today, this saline jet entrains and transports Eastern North Atlantic water and its dissolved inorganic carbon into the interior of the ocean, contributing to the drawdown of CO₂ and the sensitivity of the ocean to atmospheric changes. We show that during the Miocene this transport emerged simultaneously with gateway restriction and propose that the resulting interaction of ocean-surface and ocean-interior carbon inventories would have greatly enhanced ocean-atmosphere exchange, preconditioning the Earth System for late Miocene cooling.