Transcriptome data analysis provides insights into the conservation of Michelia lacei, a plant species with extremely small populations distributed in Yunnan province, China

BACKGROUND

Michelia lacei W.W.Smith (Magnoliaceae), was classified as a Plant Species with Extremely Small Populations (PSESP) by the Yunnan Provincial Government in both action plans of 2012 and 2021. This evergreen tree is known for its high ornamental and scientific value, but it faces significant threats due to its extremely small population size and narrow geographical distribution. The study aims to understand the genetic structure, diversity, and demographic history of this species to inform its conservation strategies.

RESULTS

The analysis of transcriptome data from 64 individuals across seven populations of M. lacei identified three distinct genetic clusters and generated 104,616 single-nucleotide polymorphisms (SNPs). The KM ex-situ population, originating from Longling County, exhibited unique genetic features, suggesting limited gene flow. The genetic diversity was substantial, with significant differences between populations, particularly between the KM lineage and the OTHER lineage. Demographic history inferred from the data indicated population experienced three significant population declines during glaciations, followed by periods of recovery. We estimated the effective population size (Ne) of the KM and OTHER lineages 1,000 years ago were 85,851 and 416,622, respectively. Gene flow analysis suggested past gene flow between populations, but the KM ex-situ population showed no recent gene flow. A total of 805 outlier SNPs, associated with four environmental factors, suggest potential local adaptation and showcase the species' adaptive potential. Particularly, the BZ displayed 515 adaptive loci, highlighting its strong potential for adaptation within this group.

CONCLUSIONS

The comprehensive genomic analysis of M. lacei provides valuable insights into its genetic background and highlights the urgent need for conservation efforts. The study underscores the importance of ex-situ conservation methods, such as seed collection and vegetative propagation, to safeguard genetic diversity and promote population restoration. The preservation of populations like MC and BZ is crucial for maintaining the species' genetic diversity. In-situ conservation measures, including the establishment of in-situ conservation sites and community engagement, are essential to enhance protection awareness and ensure the long-term survival of this threatened plant species.

Tropical mountain ice core δ18O: A Goldilocks indicator for global temperature change

Very high tropical alpine ice cores provide a distinct paleoclimate record for climate changes in the middle and upper troposphere. However, the climatic interpretation of a key proxy, the stable water oxygen isotopic ratio in ice cores (δ18Oice), remains an outstanding problem. Here, combining proxy records with climate models, modern satellite measurements, and radiative-convective equilibrium theory, we show that the tropical δ18Oice is an indicator of the temperature of the middle and upper troposphere, with a glacial cooling of -7.35° ± 1.1°C (66% CI). Moreover, it severs as a "Goldilocks-type" indicator of global mean surface temperature change, providing the first estimate of glacial stage cooling that is independent of marine proxies as -5.9° ± 1.2°C. Combined with all estimations available gives the maximum likelihood estimate of glacial cooling as -5.85° ± 0.51°C.

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.

Paleochannel of the Yellow River within the Zoige Basin and its environmental significance on the NE Tibetan Plateau

Paleochannel sedimentary sequences can provide abundant information on regional environmental changes. A typical paleochannel (paleo-oxbow lake type) section of the Yellow River was identified within the Zoige Basin on the NE Tibetan Plateau. A multi-index approach was used to accurately identify sediments of different genetic types, such as riverbed deposits of the Yellow River, paleo-oxbow lake deposits, and overbank flood deposits (OFD) in the section. Based on optically stimulated luminescence (OSL) and AMS ¹⁴C dates, we examined the environmental evolution recorded by the section. The results show that: (1) The section is a record of environmental change since 4.17 ± 0.49 ka. During 4.17 ± 0.49 to 3.24 ± 0.26 ka, the ancient Yellow River occupied the channel. At 3.24 ± 0.26 ka, the paleochannel experienced a neck cutoff, and the fluvial environment began to change into the oxbow lake environment. After 2.45 ± 0.11 ka, the paleo-oxbow lake gradually disappeared. Subalpine meadow soil has developed at this site since 1.31 ± 0.05 ka. (2) Paleoenvironmental proxies indicate that the Zoige Basin was warmer and wetter before ~3.00 ka, and became drier and colder after ~3.00 ka, which may be mainly related to the weakening of the East Asian summer monsoon (EASM) and the strengthening of the Westerlies. (3) Two episodes of extreme overbank flooding occurred at 2.96 ± 0.24 to 2.87 ± 0.27 ka and 1.84 ± 0.20 to 1.70 ± 0.16 ka, correlated with climate shift period from the mid-Holocene climatic optimum to the late Holocene and the Dark Age Cold Period (DACP), respectively. Due to the relatively cold and dry climate in these periods, glaciers generally advanced on the Tibetan Plateau, and the contribution of snow and ice meltwater weakened. Therefore, the strong rainfall caused by the abnormal atmospheric circulation may be the main cause of these extreme overbank flooding.

A Tibetan ice core covering the past 1,300 years radiometrically dated with 39Ar

Ice cores from alpine glaciers are unique archives of past global and regional climate conditions. However, recovering climate records from these ice cores is often hindered by the lack of a reliable chronology, especially in the age range of 100 to 500 anni (a) for which radiometric dating has not been available so far. We report on radiometric ³⁹Ar dating of an ice core from the Tibetan Plateau and the construction of a chronology covering the past 1,300 a using the obtained ³⁹Ar ages. This is made possible by advances in the analysis of ³⁹Ar using the laser-based detection method atom trap trace analysis, resulting in a twofold increase in the upper age limit of ³⁹Ar dating. By measuring the anthropogenic ⁸⁵Kr along with ³⁹Ar we quantify and correct modern air contamination, thus removing a major systematic uncertainty of ³⁹Ar dating. Moreover, the ⁸⁵Kr data for the top part of the ice core provide information on firn processes, including the age difference between the ice and its enclosed gas. This first application of ³⁹Ar and ⁸⁵Kr to an ice core facilitates further ice cores from nonpolar glaciers to be used for recovering climate records of the Common Era, a period including pronounced anomalies such as the Little Ice Age and the Medieval Warm Period.

Denisovans and Homo sapiens on the Tibetan Plateau: dispersals and adaptations

Recent archaeological discoveries suggest that both archaic Denisovans and Homo sapiens occupied the Tibetan Plateau earlier than expected. Genetic studies show that a pulse of Denisovan introgression was involved in the adaptation of Tibetan populations to high-altitude hypoxia. These findings challenge the traditional view that the plateau was one of the last places on earth colonized by H. sapiens and warrant a reappraisal of the population history of this highland. Here, we integrate archaeological and genomic evidence relevant to human dispersal, settlement, and adaptation in the region. We propose two testable models to address the peopling of the plateau in the broader context of H. sapiens dispersal and their encounters with Denisovans in Asia.

Evolutionary history of two rare endemic conifer species from the eastern Qinghai-Tibet Plateau

BACKGROUND AND AIMS

Understanding the population genetics and evolutionary history of endangered species is urgently needed in an era of accelerated biodiversity loss. This knowledge is most important for regions with high endemism that are ecologically vulnerable, such as the Qinghai-Tibet Plateau (QTP).

METHODS

The genetic variation of 84 juniper trees from six populations of Juniperus microsperma and one population of Juniperus erectopatens, two narrow-endemic junipers from the QTP that are sister to each other, was surveyed using RNA-sequencing data. Coalescent-based analyses were used to test speciation, migration and demographic scenarios. Furthermore, positively selected and climate-associated genes were identified, and the genetic load was assessed for both species.

KEY RESULTS

Analyses of 149 052 single nucleotide polymorphisms showed that the two species are well differentiated and monophyletic. They diverged around the late Pliocene, but interspecific gene flow continued until the Last Glacial Maximum. Demographic reconstruction by Stairway Plot detected two severe bottlenecks for J. microsperma but only one for J. erectopatens. The identified positively selected genes and climate-associated genes revealed habitat adaptation of the two species. Furthermore, although J. microsperma had a much wider geographical distribution than J. erectopatens, the former possesses lower genetic diversity and a higher genetic load than the latter.

CONCLUSIONS

This study sheds light on the evolution of two endemic juniper species from the QTP and their responses to Quaternary climate fluctuations. Our findings emphasize the importance of speciation and demographic history reconstructions in understanding the current distribution pattern and genetic diversity of threatened species in mountainous regions.

Optical Excitation and Trapping of ^{81}Kr

We have realized optical excitation, trapping, and detection of the radioisotope ^{81}Kr with an isotopic abundance of 0.9 ppt. The 124 nm light needed for the production of metastable atoms is generated by a resonant discharge lamp. Photon transport through the optically thick krypton gas inside the lamp is simulated and optimized to enhance both brightness and resonance. We achieve a state-of-the-art ^{81}Kr loading rate of 1800  atoms/h, which can be further scaled up by adding more lamps. The all-optical approach overcomes the limitations on precision and sample size of radiokrypton dating, enabling new applications in the earth sciences, particularly for dating of polar ice cores.

Quaternary Permafrost in China: Framework and Discussions

The framework of Quaternary permafrost in China was reconstructed for the first time on the basis of available periglacial, glacial, and other proxies. During the Early Pleistocene (2.68–0.80 Ma BP), permafrost advanced southwards to 47–50° N in northern China and possibly occurred in alpine regions in western China. During the Middle Pleistocene (800–130 ka BP), permafrost occurred extensively on the Qinghai-Tibet Plateau (QTP) and in alpine or mountainous regions of northern, western, central, and northeastern China. The Great Interglacial occurred afterward and before the Last Glaciation, but the evidence of permafrost for this period has been seldom found. Permafrost evolution of the Last Glaciation (72–19 ka BP) in China is divided into: Expansion (72~50 ka BP), degradation (50–26 ka BP), and intensive expansion during the Last Permafrost Maximum (LPMax, 26–19 ka BP) with a permafrost extent of 5.3 × 106~5.4 × 106 km2, and when major features of present permafrost took shape. Permafrost fluctuated during the Younger Dryas (12.9–11.7 ka BP). Since the Holocene, permafrost in China expanded and retreated to lesser extents, forming the current permafrost environment. The Holocene evolution of permafrost was divided into: Unstable climate but stable permafrost during the early Holocene (11.7~8.5–7.0 ka BP); permafrost degradation during the Last Permafrost Minimum (LPMin, or the Holocene Megathermal; 8.5–7.0~4.0–3.0 ka BP) and the Medieval Warm Period (MWP; 1.0~0.5 ka BP); permafrost expansion during the Neoglaciation (4.0–3.0~1.0 ka BP) and the Little Ice Age (LIA; 0.5~0.1 ka BP); and recent permafrost degradation (20th century to the present). However, this review paper only provides the framework of Quaternary permafrost in China and some preliminary discussions. Many key questions await further investigations.

Machine Learning Models of Groundwater Arsenic Spatial Distribution in Bangladesh: Influence of Holocene Sediment Depositional History

Recent advances in machine learning methods offer the opportunity to improve risk assessment and to decipher factors influencing the spatial variability of groundwater arsenic ([As]_gw). A systematic comparison reveals that boosted regression trees (BRT) and random forest (RF) outperform logistic regression. The probability of [As]_gw exceeding 5 μg/L (approximate median value of Bangladesh [As]_gw), 10 μg/L (WHO provisional guideline value), and 50 μg/L (Bangladesh drinking water standard) is modeled by BRT and RF methods for Bangladesh and its four subregions demarcated by major rivers. Of the 109 geo-environmental and hydrochemical predictor variables, phosphorus and iron emerge as the most important across spatial scales, consistent with known As mobilization mechanisms. Well depth is significant only when hydrochemical parameters are not considered, consistent with prior studies. A peak of probability of [As]_gw exceedance at ∼30 m depth is evident in the partial dependence plots (PDPs) for spatial-parameter-only models but not in the equivalent all-parameter models, suggesting that sediment depositional history explains interdependent spatial patterns of groundwater As-P-Fe in Holocene aquifers. The South region exhibits a decrease of probability of [As]_gw exceedance below 150 m depth in PDPs for spatial-parameter-only and all-parameter models, supporting that the deeper Pleistocene aquifer is a low-As water resource.

Population Genetic Structure Reveals Two Lineages of Amynthas triastriatus (Oligochaeta: Megascolecidae) in China, with Notes on a New Subspecies of Amynthas triastriatus

Amynthas triastriatus (Oligochaete: Megascolecidae) is a widely distributed endemic species in Southern China. To shed light on the population genetic diversity and to elucidate the population differentiation and dispersal of A. triastriatus, a population genetic structure study was undertaken based on samples from 35 locations collected from 2010 to 2016. Two exclusive lineages within A. triastriatus-lineage A and lineage B-were revealed. Lineage A was mainly distributed at high altitudes while lineage B was mainly distributed at low altitudes in Southeast China. The genetic diversity indices indicated that the populations of A. triastriatus had a strong genetic structure and distinct dispersal histories underlying the haplogroups observed in this study. Combined with morphological differences, these results indicated a new cryptic subspecies of A. triastriatus. Lineage A was almost degenerated to parthenogenesis and lineage B had a trend to parthenogenesis, which suggested that parthenogenesis could be an internal factor that influenced the differentiation and dispersal of A. triastriatus. The divergence time estimates showed that A. triastriatus originated around Guangxi and Guangdong provinces and generated into two main lineages 2.97 Ma (95%: 2.17-3.15 Ma) at the time of Quaternary glaciation (2.58 Ma), which suggested that the Quaternary glaciation may have been one of main factors that promoted the colonization of A. triastriatus.

Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms

Microorganisms in glacier ice provide tens to hundreds of thousands of years archive for a changing climate and microbial responses to it. Analyzing ancient ice is impeded by technical issues, including limited ice, low biomass, and contamination. While many approaches have been evaluated and advanced to remove contaminants on ice core surfaces, few studies leverage modern sequencing to establish in silico decontamination protocols for glacier ice. Here we sought to apply such “clean” sampling techniques with in silico decontamination approaches used elsewhere to investigate microorganisms archived in ice at ∼41 (D41, ∼20,000 years) and ∼49 m (D49, ∼30,000 years) depth in an ice core (GS3) from the summit of the Guliya ice cap in the northwestern Tibetan Plateau. Four “background” controls were established – a co-processed sterile water artificial ice core, two air samples collected from the ice processing laboratories, and a blank, sterile water sample – and used to assess contaminant microbial diversity and abundances. Amplicon sequencing revealed 29 microbial genera in these controls, but quantitative PCR showed that the controls contained about 50–100-times less 16S DNA than the glacial ice samples. As in prior work, we interpreted these low-abundance taxa in controls as “contaminants” and proportionally removed them in silico from the GS3 ice amplicon data. Because of the low biomass in the controls, we also compared prokaryotic 16S DNA amplicons from pre-amplified (by re-conditioning PCR) and standard amplicon sequencing, and found the resulting microbial profiles to be repeatable and nearly identical. Ecologically, the contaminant-controlled ice microbial profiles revealed significantly different microorganisms across the two depths in the GS3 ice core, which is consistent with changing climate, as reported for other glacier ice samples. Many GS3 ice core genera, including Methylobacterium, Sphingomonas, Flavobacterium, Janthinobacterium, Polaromonas, and Rhodobacter, were also abundant in previously studied ice cores, which suggests wide distribution across glacier environments. Together these findings help further establish “clean” procedures for studying low-biomass ice microbial communities and contribute to a baseline understanding of microorganisms archived in glacier ice.

Industrial-age doubling of snow accumulation in the Alaska Range linked to tropical ocean warming

Future precipitation changes in a warming climate depend regionally upon the response of natural climate modes to anthropogenic forcing. North Pacific hydroclimate is dominated by the Aleutian Low, a semi-permanent wintertime feature characterized by frequent low-pressure conditions that is influenced by tropical Pacific Ocean temperatures through the Pacific-North American (PNA) teleconnection pattern. Instrumental records show a recent increase in coastal Alaskan precipitation and Aleutian Low intensification, but are of insufficient length to accurately assess low frequency trends and forcing mechanisms. Here we present a 1200-year seasonally- to annually-resolved ice core record of snow accumulation from Mt. Hunter in the Alaska Range developed using annual layer counting and four ice-flow thinning models. Under a wide range of glacier flow conditions and layer counting uncertainty, our record shows a doubling of precipitation since ~1840 CE, with recent values exceeding the variability observed over the past millennium. The precipitation increase is nearly synchronous with the warming of western tropical Pacific and Indian Ocean sea surface temperatures. While regional 20^th Century warming may account for a portion of the observed precipitation increase on Mt. Hunter, the magnitude and seasonality of the precipitation change indicate a long-term strengthening of the Aleutian Low.

A global multiproxy database for temperature reconstructions of the Common Era

Reproducible climate reconstructions of the Common Era (1 CE to present) are key to placing industrial-era warming into the context of natural climatic variability. Here we present a community-sourced database of temperature-sensitive proxy records from the PAGES2k initiative. The database gathers 692 records from 648 locations, including all continental regions and major ocean basins. The records are from trees, ice, sediment, corals, speleothems, documentary evidence, and other archives. They range in length from 50 to 2000 years, with a median of 547 years, while temporal resolution ranges from biweekly to centennial. Nearly half of the proxy time series are significantly correlated with HadCRUT4.2 surface temperature over the period 1850-2014. Global temperature composites show a remarkable degree of coherence between high- and low-resolution archives, with broadly similar patterns across archive types, terrestrial versus marine locations, and screening criteria. The database is suited to investigations of global and regional temperature variability over the Common Era, and is shared in the Linked Paleo Data (LiPD) format, including serializations in Matlab, R and Python.

Contrasting the complexity of the climate of the past 122,000 years and recent 2000 years

The complexity of the climate of the past 122;000 years and recent 2000 years was investigated by analyzing the δ¹⁸O records of ice cores based on the sample entropy (SampEn) method and Lempel-Ziv (LZ) complexity. In using SampEn method, the climate complexity is measured by the sample entropy, which is a modified approximate entropy defined in terms of the occurring probability of new modes in a record. A larger sample entropy reflects a higher probability to spot a new mode in the data, and in this sense signals a larger complexity of the sample. The δ¹⁸O record of the past 122,000-year is found to have smaller SampEn than the recent 2000-year. This result suggests that the climate of the past 122;000-year has less complexity than that of the recent 2000 years, even though the record for the former exhibits stronger fluctuations and multifractality than the latter. This diagnosis is additionally supported by calculations of LZ complexity, which has smaller value for the record of the past 122;000 years than the recent 2000 years. Our theoretical findings may further contribute to ongoing explorations into the nonlinear statistical character of the climate change.

Holocene carbon dynamics at the forest-steppe ecotone of southern Siberia

The forest-steppe ecotone in southern Siberia is highly sensitive to climate change; global warming is expected to push the ecotone northwards, at the same time resulting in degradation of the underlying permafrost. To gain a deeper understanding of long-term forest-steppe carbon dynamics, we use a highly resolved, multiproxy, palaeolimnological approach, based on sediment records from Lake Baikal. We reconstruct proxies that are relevant to understanding carbon dynamics including carbon mass accumulation rates (CMAR; g C m^-2  yr^-1 ) and isotope composition of organic matter (δ¹³ C_TOC ). Forest-steppe dynamics were reconstructed using pollen, and diatom records provided measures of primary production from near- and off-shore communities. We used a generalized additive model (GAM) to identify significant change points in temporal series, and by applying generalized linear least-squares regression modelling to components of the multiproxy data, we address (1) What factors influence carbon dynamics during early Holocene warming and late Holocene cooling? (2) How did carbon dynamics respond to abrupt sub-Milankovitch scale events? and (3) What is the Holocene carbon storage budget for Lake Baikal. CMAR values range between 2.8 and 12.5 g C m^-2  yr^-1 . Peak burial rates (and greatest variability) occurred during the early Holocene, associated with melting permafrost and retreating glaciers, while lowest burial rates occurred during the neoglacial. Significant shifts in carbon dynamics at 10.3, 4.1 and 2.8 kyr bp provide compelling evidence for the sensitivity of the region to sub-Milankovitch drivers of climate change. We estimate that 1.03 Pg C was buried in Lake Baikal sediments during the Holocene, almost one-quarter of which was buried during the early Holocene alone. Combined, our results highlight the importance of understanding the close linkages between carbon cycling and hydrological processes, not just temperatures, in southern Siberian environments.

Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing

The effects of Quaternary climatic oscillations on the demography of organisms vary across regions and continents. In taxa distributed in Europe and North America, several paradigms regarding the distribution of refugia have been identified. By contrast, less is known about the processes that shaped the species' spatial genetic structure in areas such as the Himalayas, which is considered a biodiversity hotspot. Here, we investigated the phylogeographic structure and population dynamics of Primula tibetica by combining genomic phylogeography and species distribution models (SDMs). Genomic data were obtained for 293 samples of P. tibetica using restriction site-associated DNA sequencing (RADseq). Ensemble SDMs were carried out to predict potential present and past distribution ranges. Four distinct lineages were identified. Approximate Bayesian computation analyses showed that each of them have experienced both expansions and bottlenecks since their divergence, which occurred during or across the Quaternary glacial cycles. The two lineages at both edges of the distribution were found to be more vulnerable and responded in different ways to past climatic changes. These results illustrate how past climatic changes affected the demographic history of Himalayan organisms. Our findings highlight the significance of combining genomic approaches with environmental data when evaluating the effects of past climatic changes.

Responses of the summer Asian-Pacific zonal thermal contrast and the associated evolution of atmospheric circulation to transient orbital changes during the Holocene

This study investigates the response of large-scale atmospheric circulation over the Asian-Pacific sector and precipitation over eastern China to transient orbital changes during the Holocene summer using an intermediate-complexity climate model. Corresponding to variations in the incoming solar radiation, the eddy sea level pressure (SLP) exhibited an out-of-phase relationship between the North Pacific and the Eurasian landmass that was similar to the present-day Asia-Pacific Oscillation (APO) pattern and was defined as the paleo-APO. Its index presented an increasing trend, which implies the enhancement of a zonal thermal contrast between Asia and the North Pacific. Associated with the strengthening of the paleo-APO was the westward shift in North Pacific high pressure. Accordingly, there was less/more summer precipitation over both the middle reach of the Yangtze River and Southwest China/over North China. The high-resolution stalagmite δ¹⁸O records further support this decrease in the model precipitation. Along with the strengthening of paleo-APO from the early Holocene to the present, the eddy SLP anomalies exhibited a decreasing/increasing trend over the Eurasian landmass/the North Pacific, with a phase change of approximately 4.5 ka BP, and they both moved westward. Meanwhile, a less rainfall belt over eastern China exhibited northward propagation from southern China.

Satellite measurements reveal strong anisotropy in spatial coherence of climate variations over the Tibet Plateau

This study uses high-resolution, long-term satellite observations to evaluate the spatial scales of the climate variations across the Tibet Plateau (TP). Both land surface temperature and precipitation observations of more than 10 years were analysed with a special attention to eight existing ice-core sites in the TP. The temporal correlation for the monthly or annual anomalies between any two points decreases exponentially with their spatial distance, and we used the e-folding decay constant to quantify the spatial scales. We found that the spatial scales are strongly direction-dependent, with distinctive patterns in the west-east and south-north orientations, for example. Meanwhile, in the same directions the scales are largely symmetric backward and forward. Focusing on the west-east and south-north directions, we found the spatial coherence in the first is generally stronger than in the second. The annual surface temperature had typical spatial scales of 302–480 km, while the annual precipitation showed smaller scales of 111–182 km. The majority of the eight ice-core sites exhibit scales much smaller than the typical scales over the TP as a whole. These results provide important observational basis for the selection of appropriate downscaling strategies, deployment of climate-data collection networks, and interpreting paleoclimate reconstructions.

Population dynamics of Agriophyllum squarrosum, a pioneer annual plant endemic to mobile sand dunes, in response to global climate change

Climate change plays an important role in the transition of ecosystems. Stratigraphic investigations have suggested that the Asian interior experienced frequent transitions between grassland and desert ecosystems as a consequence of global climate change. Using maternally and bi-parentally inherited markers, we investigated the population dynamics of Agriophyllum squarrosum (Chenopodiaceae), an annual pioneer plant endemic to mobile sand dunes. Phylogeographic analysis revealed that A. squarrosum could originate from Gurbantunggut desert since ~1.6 Ma, and subsequently underwent three waves of colonisation into other deserts and sandy lands corresponding to several glaciations. The rapid population expansion and distribution range shifts of A. squarrosum from monsoonal climate zones suggested that the development of the monsoonal climate significantly enhanced the population growth and gene flow of A. squarrosum. These data also suggested that desertification of the fragile grassland ecosystems in the Qinghai-Tibetan Plateau was more ancient than previously suggested and will be aggravated under global warming in the future. This study provides new molecular phylogeographic insights into how pioneer annual plant species in desert ecosystems respond to global climate change, and facilitates evaluation of the ecological potential and genetic resources of future crops for non-arable dry lands to mitigate climate change.

Abrupt sand-dune accumulation at the northeastern margin of the Tibetan Plateau challenges the wet MIS3a inferred from numerous lake-highstands

Over the Tibetan Plateau and adjacent regions, numerous ¹⁴C-based lake records revealed a ubiquitous wet climatic period during 40–25 ka (late MIS 3), which is in contradiction with the global pattern of generally cold and dry climates. This paper focuses on OSL dating results of a large set of sand dunes and alluvial sediments (50 OSL ages) from the Qinwangchuan (QWC) Basin at the northeast edge of the Tibetan Plateau, with the aim to test the validity of the anomalous wet condition for the late MIS 3 interval, evidenced by numerous lake highstands. The abrupt sand dune accumulation as indication of increased aridity in the study area was OSL dated to ~40–13 ka. This dry climatic inference of the sand dune system from QWC apparently shows no wet MIS 3a event. Thus, the anomalous wet conditions revealed by high lake levels for the late MIS 3 phase may not be a universal phenomena across entire western China.

Lake sediment records on climate change and human activities in the Xingyun Lake catchment, SW China

Sediments from Xinyun Lake in central Yunnan, southwest China, provide a record of environmental history since the Holocene. With the application of multi-proxy indicators (total organic carbon (TOC), total nitrogen (TN), δ13C and δ15N isotopes, C/N ratio, grain size, magnetic susceptibility (MS) and CaCO3 content), as well as accelerator mass spectrometry (AMS) 14C datings, four major climatic stages during the Holocene have been identified in Xingyun's catchment. A marked increase in lacustrine palaeoproductivity occurred from 11.06 to 9.98 cal. ka BP, which likely resulted from an enhanced Asian southwest monsoon and warm-humid climate. Between 9.98 and 5.93 cal. ka BP, a gradually increased lake level might have reached the optimum water depth, causing a marked decline in coverage by aquatic plants and lake productivity of the lake. This was caused by strong Asian southwest monsoon, and coincided with the global Holocene Optimum. During the period of 5.60-1.35 cal. ka BP, it resulted in a warm and dry climate at this stage, which is comparable to the aridification of India during the mid- and late Holocene. The intensifying human activity and land-use in the lake catchment since the early Tang Dynasty (∼1.35 cal. ka BP) were associated with the ancient Dian culture within Xingyun's catchment. The extensive deforestation and development of agriculture in the lake catchment caused heavy soil loss. Our study clearly shows that long-term human activities and land-use change have strongly impacted the evolution of the lake environment and therefore modulated the sediment records of the regional climate in central Yunnan for more than one thousand years.

Evidence for solar cycles in a late Holocene speleothem record from Dongge Cave, China

The association between solar activity and Asian monsoon (AM) remains unclear. Here we evaluate the possible connection between them based on a precisely-dated, high-resolution speleothem oxygen isotope record from Dongge Cave, southwest China during the past 4.2 thousand years (ka). Without being adjusted chronologically to the solar signal, our record shows a distinct peak-to-peak correlation with cosmogenic nuclide ¹⁴C, total solar irradiance (TSI), and sunspot number (SN) at multi-decadal to centennial timescales. Further cross-wavelet analyses between our calcite δ¹⁸O and atmospheric ¹⁴C show statistically strong coherence at three typical periodicities of ~80, 200 and 340 years, suggesting important roles of solar activities in modulating AM changes at those timescales. Our result has further indicated a better correlation between our calcite δ¹⁸O record and atmospheric ¹⁴C than between our record and TSI. This better correlation may imply that the Sun–monsoon connection is dominated most likely by cosmic rays and oceanic circulation (both associated to atmospheric ¹⁴C), instead of the direct solar heating (TSI).

Microrefugia and Shifts of Hippophae tibetana (Elaeagnaceae) on the north side of Mt. Qomolangma (Mt. Everest) during the last 25000 years

Microrefugia at high altitudes or high latitudes are thought to play an important role in the post-glacial colonization of species. However, how populations in such microrefugia have responded to climate changes in alternating cold glacial and warm interglacial stages remain unclear. Here we present evidence to indicate the Rongbuk Valley of the Mt. Qomolangma (Mt. Everest) area, the highest region on earth, had microrefugia for Hippophae tibetana and discuss how this low shrub was adapted to the extreme climate fluctuations of the last 25,000 years by shifts. By integrating geological, glaciological, meteorological, and genetic information, we found that the Rongbuk Valley was not only a glacial microrefugium but also an interglacial microrefugium for H. tibetana: the former was located on the riverbank below 4800 m above sea level (asl) or lower area and the latter at ∼5000 m asl. Our results show that after the Last Glacial Maximum (LGM), H. tibetana in the valley has undergone upward and downward migrations around ∼5000 m driven by climate fluctuations and the population in the glacial microrefugium has suffered extinction or extreme contraction. Moreover, with the rise of temperature in the last four decades, the upper limit of H. tibetana has shifted at least 30 m upward. Combining population history and recent range shift of this species is important in predicting the fate of this endemic species to future climate changes.

The impacts of climate change and human activities on biogeochemical cycles on the Qinghai-Tibetan Plateau

With a pace of about twice the observed rate of global warming, the temperature on the Qinghai-Tibetan Plateau (Earth's 'third pole') has increased by 0.2 °C per decade over the past 50 years, which results in significant permafrost thawing and glacier retreat. Our review suggested that warming enhanced net primary production and soil respiration, decreased methane (CH(4)) emissions from wetlands and increased CH(4) consumption of meadows, but might increase CH(4) emissions from lakes. Warming-induced permafrost thawing and glaciers melting would also result in substantial emission of old carbon dioxide (CO(2)) and CH(4). Nitrous oxide (N(2)O) emission was not stimulated by warming itself, but might be slightly enhanced by wetting. However, there are many uncertainties in such biogeochemical cycles under climate change. Human activities (e.g. grazing, land cover changes) further modified the biogeochemical cycles and amplified such uncertainties on the plateau. If the projected warming and wetting continues, the future biogeochemical cycles will be more complicated. So facing research in this field is an ongoing challenge of integrating field observations with process-based ecosystem models to predict the impacts of future climate change and human activities at various temporal and spatial scales. To reduce the uncertainties and to improve the precision of the predictions of the impacts of climate change and human activities on biogeochemical cycles, efforts should focus on conducting more field observation studies, integrating data within improved models, and developing new knowledge about coupling among carbon, nitrogen, and phosphorus biogeochemical cycles as well as about the role of microbes in these cycles.

Natural variation of C-repeat-binding factor (CBFs) genes is a major cause of divergence in freezing tolerance among a group of Arabidopsis thaliana populations along the Yangtze River in China

We used a monophyletic group of four natural populations of Arabidopsis thaliana expanded from a single ancestor along the Yangtze River c. 90,000 yr ago to study the molecular mechanism of the divergence in their freezing tolerance, in order to gain an insight into the genetic basis of their local adaption to low temperatures. Freezing tolerance assays, measurements of metabolites in the raffinose biosynthesis pathway and transactivation-activity assays of variation in forms of cold-responsive transcription factors were conducted on the four populations. Quantitative trait locus mapping was adopted with F₂ populations of the most- and least freezing-tolerant populations. The degree of freezing tolerance among the four populations was negatively correlated with the lowest monthly average temperature of January in their native habitats, and positively correlated to the expression level of some cold-regulated genes. We identified a major locus harboring three cold-responsive transcription factor genes CBF1-3, and found a nucleotide insertion in CBF2 in all populations except SXcgx, which generated a dysfunctional CBF2 protein. The CBF2 in SXcgx experienced a stronger natural selection in the cooler environment after CBF3 lost its response to low temperature, which possibly reflects a local adaptation of these populations during the expansion from a common ancestor.

High regional climate sensitivity over continental China constrained by glacial-recent changes in temperature and the hydrological cycle

The East Asian monsoon is one of Earth's most significant climatic phenomena, and numerous paleoclimate archives have revealed that it exhibits variations on orbital and suborbital time scales. Quantitative constraints on the climate changes associated with these past variations are limited, yet are needed to constrain sensitivity of the region to changes in greenhouse gas levels. Here, we show central China is a region that experienced a much larger temperature change since the Last Glacial Maximum than typically simulated by climate models. We applied clumped isotope thermometry to carbonates from the central Chinese Loess Plateau to reconstruct temperature and water isotope shifts from the Last Glacial Maximum to present. We find a summertime temperature change of 6-7 °C that is reproduced by climate model simulations presented here. Proxy data reveal evidence for a shift to lighter isotopic composition of meteoric waters in glacial times, which is also captured by our model. Analysis of model outputs suggests that glacial cooling over continental China is significantly amplified by the influence of stationary waves, which, in turn, are enhanced by continental ice sheets. These results not only support high regional climate sensitivity in Central China but highlight the fundamental role of planetary-scale atmospheric dynamics in the sensitivity of regional climates to continental glaciation, changing greenhouse gas levels, and insolation.

Seasonal variations, speciation and possible sources of mercury in the snowpack of Zhadang glacier, Mt. Nyainqêntanglha, southern Tibetan Plateau

Ten snowpits were sampled at the Zhadang glacier during 2008 and 2011 to investigate the seasonal variations, speciation, and sources of mercury (Hg) in the southern Tibetan Plateau. In the 2008 snowpit, total Hg (Hg(T)), particulate matter, most of major ions were found in higher concentrations during the non-monsoon season than in the monsoon season. Analysis of Hg speciation indicated that Hg(T) in the 2011 snowpits was dominated by particulate-bound Hg (Hg(P)). Most of particulate matter in the 2008 snowpit was dominated by fine particulates, indicating that the influx of particulate matter and Hg(P) was probably occurring by long-range transportation via general atmospheric circulation. Analysis of dominant ion Ca²⁺ and alkaline pH values has suggested that the long-range transported Hg(P), originating from dust storm activities, may be the most important source for Hg in the Zhadang glacier snowpit during the non-monsoon season. Backward-trajectory analysis indicates the majority of the air masses arriving at the Zhandang glacier originated from the arid regions of northwestern India (e.g., Thar Desert), confirming that arid regions in central and southern Asia are likely the main sources of Hg being deposited in the Zhadang glacier snowpit. This study also suggests that ice core records from the Tibetan Plateau may be useful tools for interpreting long-term historical records of atmospheric Hg deposition, and reconstructing Hg biogeochemical cycling.

Mercury distribution and deposition in glacier snow over western China

Western China is home to the largest aggregate of glaciers outside the polar regions, yet little is known about how the glaciers in this area affect the transport and cycling of mercury (Hg) regionally and globally. From 2005 to 2010, extensive glacier snow sampling campaigns were carried out in 14 snowpits from 9 glaciers over western China, and the vertical distribution profiles of Hg were obtained. The Total Hg (THg) concentrations in the glacier snow ranged from <1 to 43.6 ng L(-1), and exhibited clear seasonal variations with lower values in summer than in winter. Spatially, higher THg concentrations were typically observed in glacier snows from the northern region where atmospheric particulate loading is comparably high. Glacier snowpit Hg was largely dependent on particulate matters and was associated with particulate Hg, which is less prone to postdepositional changes, thus providing a valuable record of atmospheric Hg deposition. Estimated atmospheric Hg depositional fluxes ranged from 0.74 to 7.89 μg m(-2) yr(-1), agreeing very well with the global natural values, but are one to two orders of magnitude lower than that of the neighboring East Asia. Elevated Hg concentrations were observed in refrozen ice layers in several snowpits subjected to intense melt, indicating that Hg can be potentially released to meltwater.

Global climate evolution during the last deglaciation

Deciphering the evolution of global climate from the end of the Last Glacial Maximum approximately 19 ka to the early Holocene 11 ka presents an outstanding opportunity for understanding the transient response of Earth's climate system to external and internal forcings. During this interval of global warming, the decay of ice sheets caused global mean sea level to rise by approximately 80 m; terrestrial and marine ecosystems experienced large disturbances and range shifts; perturbations to the carbon cycle resulted in a net release of the greenhouse gases CO(2) and CH(4) to the atmosphere; and changes in atmosphere and ocean circulation affected the global distribution and fluxes of water and heat. Here we summarize a major effort by the paleoclimate research community to characterize these changes through the development of well-dated, high-resolution records of the deep and intermediate ocean as well as surface climate. Our synthesis indicates that the superposition of two modes explains much of the variability in regional and global climate during the last deglaciation, with a strong association between the first mode and variations in greenhouse gases, and between the second mode and variations in the Atlantic meridional overturning circulation.

Phylogeographic study of Apodemus ilex (Rodentia: Muridae) in Southwest China

BACKGROUND

The Mountains of southwest China have complex river systems and a profoundly complex topography and are among the most important biodiversity hotspots in the world. However, only a few studies have shed light on how the mountains and river valleys promote genetic diversity. Apodemus ilex is a fine model for investigating this subject.

METHODOLOGY/PRINCIPAL FINDINGS

To assess the genetic diversity and biogeographic patterns of Apodemus ilex, the complete cytochrome b gene sequences (1,140 bp) were determined from 203 samples of A. draco/ilex that were collected from southwest China. The results obtained suggested that A. ilex and A. draco are sistergroups and diverged from each other approximately 2.25 million years ago. A. ilex could be divided into Eastern and Western phylogroups, each containing two sub-groups and being widespread in different geographical regions of the southern Hengduan Mountains and the western Yunnan - Guizhou Plateau. The population expansions of A. ilex were roughly from 0.089 Mya to 0.023 Mya.

CONCLUSIONS

Our result suggested that A. ilex is a valid species rather than synonym of A. draco. As a middle-high elevation inhabitant, the phylogenetic pattern of A. ilex was strongly related to the complex geographical structures in southwest China, particularly the existence of deep river valley systems, such as the Mekong and Salween rivers. Also, it appears that the evolutionary history of A. ilex, such as lineage divergences and population expansions were strongly affected by climate fluctuation in the Late Pleistocene.

Incision rate of the Yellow River in Northeastern Tibet constrained by 10Be and 26Al cosmogenic isotope dating of fluvial terraces: implications for catchment evolution and plateau building

Unlike other large rivers flowing out of Tibet, the Yellow River escapes from the plateau towards the NE crossing no less than five NW–SE striking, actively growing ranges and intervening basins. Thick Plio-Quaternary deposits and fluvial terraces testify to a phase of aggradation and sediment infill up to the average surface elevation (3200–3250 m a.s.l.) of the Gonghe, Guide and Qinghai Lake basins. A set of seven main terraces across the Gonghe Basin suggests progressive down-cutting of the Yellow River carving the 500 m deep Longyang gorge at the basin exit. 10Be and 26Al concentrations in quartz of surface and sub-surface samples of four terraces constrain the timing of incision by determining the burial age of the deposit and the exposure age of its surface. Modelling the depth dependence of the 10Be concentration and the 26Al/10Be ratio allows us to constrain the onset of the ongoing phase of incision to 120–250 ka. These ages suggest long-term incision rates between 2–6 mm a−1. Together with the present morphology of the Yellow River terraces across the Gonghe basin and the Longyang gorge, our results imply rapid river catchment evolution and interaction between river dynamics, tectonic and climate in northeastern Tibet.

Climate change: the evidence and our options

Glaciers serve as early indicators of climate change. Over the last 35 years, our research team has recovered ice-core records of climatic and environmental variations from the polar regions and from low-latitude high-elevation ice fields from 16 countries. The ongoing widespread melting of high-elevation glaciers and ice caps, particularly in low to middle latitudes, provides some of the strongest evidence to date that a large-scale, pervasive, and, in some cases, rapid change in Earth's climate system is underway. This paper highlights observations of 20th and 21st century glacier shrinkage in the Andes, the Himalayas, and on Mount Kilimanjaro. Ice cores retrieved from shrinking glaciers around the world confirm their continuous existence for periods ranging from hundreds of years to multiple millennia, suggesting that climatological conditions that dominate those regions today are different from those under which these ice fields originally accumulated and have been sustained. The current warming is therefore unusual when viewed from the millennial perspective provided by multiple lines of proxy evidence and the 160-year record of direct temperature measurements. Despite all this evidence, plus the well-documented continual increase in atmospheric greenhouse gas concentrations, societies have taken little action to address this global-scale problem. Hence, the rate of global carbon dioxide emissions continues to accelerate. As a result of our inaction, we have three options: mitigation, adaptation, and suffering.

Population increase and environmental deterioration correspond with microlithic innovations in South Asia ca. 35,000 years ago

Genetic studies of South Asia's population history have led to postulations of a significant and early population expansion in the subcontinent, dating to sometime in the Late Pleistocene. We evaluate this argument, based on new mtDNA analyses, and find evidence for significant demographic transition in the subcontinent, dating to 35-28 ka. We then examine the paleoenvironmental and, particularly, archaeological records for this time period and note that this putative demographic event coincides with a period of ecological and technological change in South Asia. We document the development of a new diminutive stone blade (microlithic) technology beginning at 35-30 ka, the first time that the precocity of this transition has been recognized across the subcontinent. We argue that the transition to microlithic technology may relate to changes in subsistence practices, as increasingly large and probably fragmented populations exploited resources in contracting favorable ecological zones just before the onset of full glacial conditions.