Late Oligocene-early Miocene birth of the Taklimakan Desert

Diversification of flowering plants in space and time

The rapid diversification and high species richness of flowering plants is regarded as 'Darwin's second abominable mystery'. Today the global spatiotemporal pattern of plant diversification remains elusive. Using a newly generated genus-level phylogeny and global distribution data for 14,244 flowering plant genera, we describe the diversification dynamics of angiosperms through space and time. Our analyses show that diversification rates increased throughout the early Cretaceous and then slightly decreased or remained mostly stable until the end of the Cretaceous-Paleogene mass extinction event 66 million years ago. After that, diversification rates increased again towards the present. Younger genera with high diversification rates dominate temperate and dryland regions, whereas old genera with low diversification dominate the tropics. This leads to a negative correlation between spatial patterns of diversification and genus diversity. Our findings suggest that global changes since the Cenozoic shaped the patterns of flowering plant diversity and support an emerging consensus that diversification rates are higher outside the tropics.

Neglected no longer: Phylogenomic resolution of higher-level relationships in Solifugae

Advanced sequencing technologies have expedited resolution of higher-level arthropod relationships. Yet, dark branches persist, principally among groups occurring in cryptic habitats. Among chelicerates, Solifugae ("camel spiders") is the last order lacking a higher-level phylogeny and have thus been historically characterized as "neglected [arachnid] cousins". Though renowned for aggression, remarkable running speed, and xeric adaptation, inferring solifuge relationships has been hindered by inaccessibility of diagnostic morphological characters, whereas molecular investigations have been limited to one of 12 recognized families. Our phylogenomic dataset via capture of ultraconserved elements sampling all extant families recovered a well-resolved phylogeny, with two distinct groups of New World taxa nested within a broader Paleotropical radiation. Divergence times using fossil calibrations inferred that Solifugae radiated by the Permian, and most families diverged prior to the Paleogene-Cretaceous extinction, likely driven by continental breakup. We establish Boreosolifugae new suborder uniting five Laurasian families, and Australosolifugae new suborder uniting seven Gondwanan families using morphological and biogeographic signal.

Rapid strengthening of westerlies accompanied intensification of Northern Hemisphere glaciation

The trigger, pace, and nature of the intensification of Northern Hemisphere Glaciation (iNHG) are uncertain, but can be probed by study of ODP Site 1208 North Pacific marine sediments. Herein, we present magnetic proxy data that indicate a 4-fold increase of dust between ~ 2.73 and ~ 2.72 Ma, with subsequent increases at the start of glacials thereafter, indicating a strengthening of the mid-latitude westerlies. Moreover, a permanent shift in dust composition after 2.72 Ma is observed, consistent with drier conditions in the source region and/or the incorporation of material which could not have been transported via the weaker Pliocene winds. The sudden increase in our dust proxy data, a coeval rapid rise in dust recorded by proxy dust data in the North Atlantic (Site U1313), and the Site 1208 shift in dust composition, suggest that the iNHG represents a permanent crossing of a climate threshold toward global cooling and ice sheet growth, ultimately driven by lower atmospheric CO₂.

Late Miocene Tarim desert wetting linked with eccentricity minimum and East Asian monsoon weakening

Periodic wetting is an inherent feature of many monsoon marginal region deserts. Previous studies consistently demonstrate desert wetting during times of Earth's high orbital eccentricity and strong summer monsoon. Here we report the first evidence demonstrating desert wetting during Earth's low orbital eccentricity from the late Miocene strata of the northwestern Tarim Basin of northern China, which is commonly thought to be beyond the range of Asian monsoon precipitation. Using mechanisms for modern Tarim wetting as analogs, we propose that East Asian summer monsoon weakening enhanced westward moisture transport and caused opposite desert wetting pattern to that observed in monsoon marginal region deserts. This inference is supported by our model simulations. This result has far-reaching implications for understanding environmental variations in non-monsoonal deserts in the next few thousands of years under high atmospheric CO₂ content and low eccentricity.

Eccentricity forcing of East Asian monsoonal systems over the past 3 million years

The East Asian summer monsoon and the precipitation it brings are relevant for millions of people. Because of the monsoon's importance, there has been a substantial amount of work attempting to describe the driving mechanisms behind its past variability. However, discrepancies exist, with speleothem-based East Asian monsoon reconstructions differing from those based on loess records from the Chinese Loess Plateau during the late Quaternary. The periodicity of wet and dry phases experienced by desert areas that lie on the periphery of the East Asian monsoon's influence offer another independent view of monsoonal variability. Here, we provide environmental records based on magnetic parameters for the last 3 million years from the Tengger Desert, China, one such marginal arid region. Our results reveal wet-dry cycles at a dominant frequency of 405 kiloyears, with drier intervals corresponding to eccentricity minima. These findings are consistent with previous reconstructions of East Asian summer and North African summer monsoon precipitation variability. Our records emphasize the dominant role of eccentricity in forcing East Asian monsoonal precipitation as well as monsoonal-derived environmental fluctuations experienced in peripheral desert areas. These results challenge the traditional view that high-latitude ice sheets are the primary driver of East Asian monsoon precipitation during the Quaternary based on Chinese loess records.

Poleward and weakened westerlies during Pliocene warmth

The prevailing mid-latitude westerly winds, known as the westerlies, are a fundamental component of the climate system because they have a crucial role in driving surface ocean circulation¹ and modulating air-sea heat, momentum and carbon exchange^1-3. Recent work suggests that westerly wind belts are migrating polewards in response to anthropogenic forcing^4,5. Reconstructing the westerlies during past warm periods such as the Pliocene epoch, in which atmospheric carbon dioxide (CO₂) was about 350 to 450 parts per million⁶ and temperatures were about 2 to 4 degrees Celsius higher than today⁷, can improve our understanding of changes in the position and strength of these wind systems as the climate continues to warm. Here we show that the westerlies were weaker and more poleward during the warm Pliocene than during glacial periods after the intensification of Northern Hemisphere glaciation (iNHG), which occurred around 2.73 million years ago⁸. Our results, which are based on dust and export productivity reconstructions, indicate that major ice sheet development during the iNHG was accompanied by substantial increases in dust fluxes in the mid-latitude North Pacific Ocean, especially compared to those in the subarctic North Pacific. Following this shift, changes in dust and productivity largely track the glacial-interglacial cycles of the late Pliocene and early Pleistocene epochs. On the basis of this pattern, we infer that shifts in the westerlies were primarily driven by variations in Plio-Pleistocene thermal gradients and ice volume. By combining this relationship with other dust records^9-11 and climate modelling results¹², we find that the proposed changes in the westerlies were globally synchronous. If the Pliocene is predictive of future warming, we posit that continued poleward movement and weakening of the present-day westerlies in both hemispheres can be expected.

Phylogeny, Taxonomy, and Biogeography of Pterocarya (Juglandaceae)

Relict species play an important role in understanding the biogeography of intercontinental disjunctions. Pterocarya (a relict genus) is the valuable model taxon for studying the biogeography of East Asian versus southern European/West Asian disjunct patterns. This disjunction has not been as well studied as others (e.g., between Eastern Asia and North America). Several phylogenetic studies on Pterocarya have been conducted, but none have provided a satisfactory phylogenetic resolution. Here, we report the first well-resolved phylogeny of Pterocarya using restriction site-associated DNA sequencing data based on the sampling of all taxa across the entire distribution area of the genus. Taxonomic treatments were also clarified by combining morphological traits. Furthermore, fossil-calibrated phylogeny was used to explore the biogeography of Pterocarya. Our results support the existence of two sections in Pterocarya, which is in accordance with morphological taxonomy. Section Platyptera comprises three species: P. rhoifolia, P. macroptera, and P. delavayi. Section Pterocarya also comprises three species: P. fraxinifolia, P. hupehensis, and P. stenoptera. The divergence between the two sections took place during the early Miocene (20.5 Ma). The formation of the Gobi Desert and climate cooling of northern Siberia in the Middle Miocene (15.7 Ma) might have caused the split of the continuous distribution of this genus and the formation of the East Asian versus southern European/West Asian disjunct pattern. Lastly, the divergence between P. hupehensis and P. stenoptera as well as between P. rhoifolia and P. macroptera/P. delavayi (10.0 Ma) supports the late Miocene diversification hypothesis in East Asia.

Genome resequencing reveals demographic history and genetic architecture of seed salinity tolerance in Populus euphratica

Populus euphratica is a dominant tree species in desert riparian forests and possesses extraordinary adaptation to salinity stress. Exploration of its genomic variation and molecular underpinning of salinity tolerance is important for elucidating population evolution and identifying stress-related genes. Here, we identify approximately 3.15 million single nucleotide polymorphisms using whole-genome resequencing. The natural populations of P. euphratica in northwest China are divided into four distinct clades that exhibit strong geographical distribution patterns. Pleistocene climatic fluctuations and tectonic deformation jointly shaped the extant genetic patterns. A seed germination rate-based salinity tolerance index was used to evaluate seed salinity tolerance of P. euphratica and a genome-wide association study was implemented. A total of 38 single nucleotide polymorphisms were associated with seed salinity tolerance and were located within or near 82 genes. Expression profiles showed that most of these genes were regulated under salt stress, revealing the genetic complexity of seed salinity tolerance. Furthermore, DEAD-box ATP-dependent RNA helicase 57 and one undescribed gene (CCG029559) were demonstrated to improve the seed salinity tolerance in transgenic Arabidopsis. These results provide new insights into the demographic history and genetic architecture of seed salinity tolerance in desert poplar.

Phylogeography and ecological niche modeling unravel the evolutionary history of the Yarkand hare, Lepus yarkandensis (Mammalia: Leporidae), through the Quaternary

Background

The Taklimakan Desert in China is characterized by unique geological and historical dynamics and endemic flora and fauna, but the influence of historical climate oscillations on the evolutionary history of endemic animals is poorly understood. Lepus yarkandensis is an oases-dependent Near Threatened species that lives in fragmented oasis habitats in the Taklimakan Desert, China. We investigated the geological and climatic impacts on its geographical differentiation, demographic history and influence of Pleistocene glacial-interglacial cycles on the evolutionary history of L. yarkandensis. Further, studied the impact of climatic oscillation based modification on phylogeography, distribution and diversification pattern of Yarkand hare by using Cytb (1140 bp), MGF (592 bp) and SPTBN1 (619 bp) markers. Ecological niche modeling (ENM) revealed the evolutionary history of this species in response to climate change during the Quaternary. Paleodistribution modeling was used to identify putative refugia and estimate their historical distributions.

Results

Both historical demographic analyses and climatic niche modeling revealed strong effects of glacial climate changes, suggesting recurrent range contractions and expansions. The EBSP results indicated clear population expansion of L. yarkandensis since the Pleistocene. In the “early Pleistocene”, the demographic expansion continued from 0.83 MYA to the last glacial period. The ENM analysis supported a wide distribution of Lepus yarkandensis at high altitudes during the last interglacial (LIG) period. During the last glacial maximum (LGM), the suitable climate was reduced and restricted to the western part of the Taklimakan Desert.

Conclusions

Inland aridification, oasis evolution and river flow played major roles in the population differentiation and demographic history of Yarkand hares. Historically, the large, continuous oases in the Taklimakan Desert contained a viable and unique population of L. yarkandensis. The fragmented desert environment might have caused low gene flow between individuals or groups, thus leading to predominant genetic differentiation. The Pleistocene climatic cycles triggered the diversification and expansion of this species during cold and warm periods, respectively, leading to multiple colonization events within the Taklimakan Desert. These events might be due to the expansion of the Taklimakan Desert during the Middle Pleistocene. Yarkand hare previously occupied vast areas at low and intermediate altitudes in Xinjiang, Gansu, Shanxi, Henan and Shaanxi Provinces in China. The past aridification, climate change-induced oasis modifications, changes in river volumes and flow directions, and human activities all affected the population demography and phylogeography of the Yarkand hare.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1426-z) contains supplementary material, which is available to authorized users.

Oxygen and Carbon Stable Isotope Composition of Cretaceous to Pliocene Calcareous Paleosols in the Tian Shan Region (Central Asia): Controlling Factors and Paleogeographic Implications

The Late Mesozoic–Cenozoic topographic and climate evolution of Central Asia remains highly debated. The final retreat of the proto-Paratethys Sea from the western Tarim Basin is thought to correspond in time with the onset of tectonic uplift in the Pamir, Tian Shan and Altai ranges, as well as with regional aridification. The oxygen and carbon isotope compositions of the sediment deposits in the various Central Asian basins have already been used to decipher both the topographic and climatic changes that occurred in that region during the Cenozoic, generally concentrating on one sedimentary section and/or on a limited time range and either using multiple-type samples including sandstone calcitic cements, marine carbonates, fossils, or paleosols. In order to get a homogeneous dataset, minimizing variations in the isotopic composition of the material depending on its type and/or depositional environment, we selected only calcareous paleosols sampled in several continuous sections covering a wide time range from the Late Jurassic to the Pliocene. Our sampling also covers a wide area encompassing the whole Tian Shan region, which allows detecting regional variations in the δ18O and δ13C values. We show that the influence of the distance to the proto-Paratethys Sea on the paleosol δ18O record was not significant. Besides local factors such as the occurrence of large lakes that can have a significant effect on the isotopic composition of the calcareous paleosols, the long-term evolution of both the δ18O and δ13C values possibly reflects the hypsometry of the river drainage systems that bring water to the basins. However, as it is commonly accepted that the δ18O of soil carbonates is controlled by the δ18O of in-situ precipitation, this last conclusion remains to be further investigated.

First long-term detection of paleo-oceanic signature of dust aerosol at the southern marginal area of the Taklimakan Desert

We firstly conducted a long-term in-situ field measurement at a marginal area (Hotan) of the southern Taklimakan Desert covering all four seasons. Detailed chemical characterization of dust aerosol over Hotan showed several unconventional features, including (1) ubiquity of high Na⁺ and Cl⁻ abundances in the Taklimakan dust aerosol and its Cl⁻/Na⁺ ratio close to seawater; (2) high Ca content in the Taklimakan dust (7.4~8.0%) which was about two times of that in the natural crust; (3) high abundance of soluble sulfate concentrations and strong correlations between sulfate and Na⁺ and Cl⁻ as well as typical mineral tracers such as Al and Ca. Our results collectively indicated that the dust aerosol from the Taklimakan Desert was characterized of evident paelo-oceanic signature as the Taklimakan Desert was found as an ocean in the ancient times from the perspective of paleogeology. It was estimated that primary sources dominated the total abundances of sulfate during the dust seasons while previous climate modeling works had seldom considered the cooling effects of sulfate from the Taklimakan Desert.

Cenozoic aridization in Central Eurasia shaped diversification of toad-headed agamas (Phrynocephalus; Agamidae, Reptilia)

We hypothesize the phylogenetic relationships of the agamid genus Phrynocephalus to assess how past environmental changes shaped the evolutionary and biogeographic history of these lizards and especially the impact of paleogeography and climatic factors. Phrynocephalus is one of the most diverse and taxonomically confusing lizard genera. As a key element of Palearctic deserts, it serves as a promising model for studies of historical biogeography and formation of arid habitats in Eurasia. We used 51 samples representing 33 of 40 recognized species of Phrynocephalus covering all major areas of the genus. Molecular data included four mtDNA (COI, ND2, ND4, Cytb; 2,703 bp) and four nuDNA protein-coding genes (RAG1, BDNF, AKAP9, NKTR; 4,188 bp). AU-tests were implemented to test for significant differences between mtDNA- and nuDNA-based topologies. A time-calibrated phylogeny was estimated using a Bayesian relaxed molecular clock with nine fossil calibrations. We reconstructed the ancestral area of origin, biogeographic scenarios, body size, and the evolution of habitat preference. Phylogenetic analyses of nuDNA genes recovered a well-resolved and supported topology. Analyses detected significant discordance with the less-supported mtDNA genealogy. The position of Phrynocephalus mystaceus conflicted greatly between the two datasets. MtDNA introgression due to ancient hybridization best explained this result. Monophyletic Phrynocephalus contained three main clades: (I) oviparous species from south-western and Middle Asia; (II) viviparous species of Qinghai–Tibetan Plateau (QTP); and (III) oviparous species of the Caspian Basin, Middle and Central Asia. Phrynocephalus originated in late Oligocene (26.9 Ma) and modern species diversified during the middle Miocene (14.8–13.5 Ma). The reconstruction of ancestral areas indicated that Phrynocephalus originated in Middle East–southern Middle Asia. Body size miniaturization likely occurred early in the history of Phrynocephalus. The common ancestor of Phrynocephalus probably preferred sandy substrates with the inclusion of clay or gravel. The time of Agaminae radiation and origin of Phrynocephalus in the late Oligocene significantly precedes the landbridge between Afro-Arabia and Eurasia in the Early Miocene. Diversification of Phrynocephalus coincides well with the mid-Miocene climatic transition when a rapid cooling of climate drove progressing aridification and the Paratethys salinity crisis. These factors likely triggered the spreading of desert habitats in Central Eurasia, which Phrynocephalus occupied. The origin of the viviparous Tibetan clade has been associated traditionally with uplifting of the QTP; however, further studies are needed to confirm this. Progressing late Miocene aridification, the decrease of the Paratethys Basin, orogenesis, and Plio–Pleistocene climate oscillations likely promoted further diversification within Phrynocephalus. We discuss Phrynocephalus taxonomy in scope of the new analyses.

Resilience of the Asian atmospheric circulation shown by Paleogene dust provenance

The onset of modern central Asian atmospheric circulation is traditionally linked to the interplay of surface uplift of the Mongolian and Tibetan-Himalayan orogens, retreat of the Paratethys sea from central Asia and Cenozoic global cooling. Although the role of these players has not yet been unravelled, the vast dust deposits of central China support the presence of arid conditions and modern atmospheric pathways for the last 25 million years (Myr). Here, we present provenance data from older (42-33 Myr) dust deposits, at a time when the Tibetan Plateau was less developed, the Paratethys sea still present in central Asia and atmospheric pCO2 much higher. Our results show that dust sources and near-surface atmospheric circulation have changed little since at least 42 Myr. Our findings indicate that the locus of central Asian high pressures and concurrent aridity is a resilient feature only modulated by mountain building, global cooling and sea retreat.

The abrupt onset of the modern South Asian Monsoon winds

The South Asian Monson (SAM) is one of the most intense climatic elements yet its initiation and variations are not well established. Dating the deposits of SAM wind-driven currents in IODP cores from the Maldives yields an age of 12. 9 Ma indicating an abrupt SAM onset, over a short period of 300 kyrs. This coincided with the Indian Ocean Oxygen Minimum Zone expansion as revealed by geochemical tracers and the onset of upwelling reflected by the sediment’s content of particulate organic matter. A weaker ‘proto-monsoon’ existed between 12.9 and 25 Ma, as mirrored by the sedimentary signature of dust influx. Abrupt SAM initiation favors a strong influence of climate in addition to the tectonic control, and we propose that the post Miocene Climate Optimum cooling, together with increased continentalization and establishment of the bipolar ocean circulation, i.e. the beginning of the modern world, shifted the monsoon over a threshold towards the modern system.