Detection of copy number variations and their effects in Chinese bulls

BACKGROUND: Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. Here, with one pure-blooded Angus bull as reference, we describe a genome-wide analysis of CNVs based on comparative genomic hybridization arrays in 29 Chinese domesticated bulls and examined their effects on gene expression and cattle growth traits. RESULTS: We identified 486 copy number variable regions (CNVRs), covering 2.45% of the bovine genome, in 24 taurine (Bos taurus), together with 161 ones in 2 yaks (Bos grunniens) and 163 ones in 3 buffaloes (Bubalus bubalis). Totally, we discovered 605 integrated CNVRs, with more “loss” events than both “gain” and “both” ones, and clearly clustered them into three cattle groups. Interestingly, we confirmed their uneven distributions across chromosomes, and the differences of mitochondrion DNA copy number (gain: taurine, loss: yak & buffalo). Furthermore, we confirmed approximately 41.8% (253/605) and 70.6% (427/605) CNVRs span cattle genes and quantitative trait loci (QTLs), respectively. Finally, we confirmed 6 CNVRs in 9 chosen ones by using quantitative PCR, and further demonstrated that CNVR22 had significantly negative effects on expression of PLA2G2D gene, and both CNVR22 and CNVR310 were associated with body measurements in Chinese cattle, suggesting their key effects on gene expression and cattle traits. CONCLUSIONS: The results advanced our understanding of CNV as an important genomic structural variation in taurine, yak and buffalo. This study provides a highly valuable resource for Chinese cattle’s evolution and breeding researches. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-480) contains supplementary material, which is available to authorized users

Palynological evidence for the temporal stability of the plant community in the Yellow River Source Area over the last 7,400 years

The terrestrial ecosystem in the Yellow River Source Area (YRSA) is sensitive to climate change and human impacts, although past vegetation change and the degree of human disturbance are still largely unknown. A 170-cm-long sediment core covering the last 7,400 years was collected from Lake Xingxinghai (XXH) in the YRSA. Pollen, together with a series of other environmental proxies (including grain size, total organic carbon (TOC) and carbonate content), were analysed to explore past vegetation and environmental changes for the YRSA. Dominant and common pollen components—Cyperaceae, Poaceae, Artemisia, Chenopodiaceae and Asteraceae—are stable throughout the last 7,400 years. Slight vegetation change is inferred from an increasing trend of Cyperaceae and decreasing trend of Poaceae, suggesting that alpine steppe was replaced by alpine meadow at ca. 3.5 ka cal bp. The vegetation transformation indicates a generally wetter climate during the middle and late Holocene, which is supported by increased amounts of TOC and Pediastrum (representing high water-level) and is consistent with previous past climate records from the north-eastern Tibetan Plateau. Our results find no evidence of human impact on the regional vegetation surrounding XXH, hence we conclude the vegetation change likely reflects the regional climate signal

Assessing the impact of extreme droughts on dryland vegetation by multi-satellite solar-induced chlorophyll fluorescence

Satellite-estimated solar-induced chlorophyll fluorescence (SIF) is proven to be an effective indicator for dynamic drought monitoring, while the capability of SIF to assess the variability of dryland vegetation under water and heat stress remains challenging. This study presents an analysis of the responses of dryland vegetation to the worst extreme drought over the past two decades in Australia, using multi-source spaceborne SIF derived from the Global Ozone Monitoring Experiment-2 (GOME-2) and TROPOspheric Monitoring Instrument (TROPOMI). Vegetation functioning was substantially constrained by this extreme event, especially in the interior of Australia, in which there was hardly seasonal growth detected by neither satellite-based observations nor tower-based flux measurements. At a 16-day interval, both SIF and enhanced vegetation index (EVI) can timely capture the reduction at the onset of drought over dryland ecosystems. The results demonstrate that satellite-observed SIF has the potential for characterizing and monitoring the spatiotemporal dynamics of drought over water-limited ecosystems, despite coarse spatial resolution coupled with high-retrieval noise as compared with EVI. Furthermore, our study highlights that SIF retrieved from TROPOMI featuring substantially enhanced spatiotemporal resolution has the promising capability for accurately tracking the drought-induced variation of heterogeneous dryland vegetation

Human activities have reduced plant diversity in eastern China over the last two millennia

Understanding the history and regional singularities of human impact on vegetation is key to developing strategies for sustainable ecosystem management. In this study, fossil and modern pollen datasets from China are employed to investigate temporal changes in pollen composition, analogue quality, and pollen diversity during the Holocene. Anthropogenic disturbance and vegetation's responses are also assessed. Results reveal that pollen assemblages from non-forest communities fail to provide evidence of human impact for the western part of China (annual precipitation less than 400 mm and/or elevation more than 3000 m.a.s.l.), as inferred from the stable quality of modern analogues, principal components, and diversity of species and communities throughout the Holocene. For the eastern part of China, the proportion of fossil pollen spectra with good modern analogues increases from ca. 50% to ca. 80% during the last 2 millennia, indicating an enhanced intensity of anthropogenic disturbance on vegetation. This disturbance has caused the pollen spectra to become taxonomically less diverse over space (reduced abundances of arboreal taxa and increased abundances of herbaceous taxa), highlighting a reduced south–north differentiation and divergence from past vegetation between regions in the eastern part of China. We recommend that care is taken in eastern China when basing the development of ecosystem management strategies on vegetation changes in the region during the last 2000 years, since humans have significantly disturbed the vegetation during this period

Observation of a large-scale filament eruption initiated by two small-scale erupting filaments pushing out from below

Filament eruptions often result in flares and coronal mass ejections (CMEs). Most studies attribute the filament eruptions to their instabilities or magnetic reconnection. In this study, we report a unique observation of a filament eruption whose initiation process has not been reported before. This large-scale filament, with a length of about 360 Mm crossing an active region, is forced to erupted by two small-scale erupting filaments pushing out from below. This process of multi-filament eruption results in an M6.4 flare in the active region NOAA 13229 on 25th February 2023. The whole process can be divided into three stages: the eruptions of two active-region filaments F1 and F2; the interactions between the erupting F1, F2, and the large-scale filament F3; and the eruption of F3. Though this multi-filament eruption occurs near the northwest limb of the solar disk, it produces a strong halo CME that causes a significant geomagnetic disturbance. Our observations present a new filament eruption mechanism, in which the initial kinetic energy of the eruption is obtained from and transported to by other erupting structures. This event provides us a unique insight into the dynamics of multi-filament eruptions and their corresponding effects on the interplanetary space.Comment: 16 pages, 10 figures. Accepted for publication in Solar Physic

Vegetation change and human-environment interactions in the Qinghai Lake Basin, northeastern Tibetan Plateau, since the last deglaciation

The nature of the interaction between prehistoric humans and their environment, especially the vegetation, has long been of interest. The Qinghai Lake Basin in North China is well-suited to exploring the interactions between prehistoric humans and vegetation in the Tibetan Plateau, because of the comparatively dense distribution of archaeological sites and the ecologically fragile environment. Previous pollen studies of Qinghai Lake have enabled a detailed reconstruction of the regional vegetation, but they have provided relatively little information on vegetation change within the Qinghai Lake watershed. To address the issue we conducted a pollen-based vegetation reconstruction for an archaeological site (YWY), located on the southern shore of Qinghai Lake. We used high temporal-resolution pollen records from the YWY site and from Qinghai Lake, spanning the interval since the last deglaciation (15.3 kyr BP to the present) to quantitatively reconstruct changes in the local and regional vegetation using Landscape Reconstruction Algorithm models. The results show that, since the lateglacial, spruce forest grew at high altitudes in the surrounding mountains, while the lakeshore environment was occupied mainly by shrub-steppe. From the lateglacial to the middle Holocene, coniferous woodland began to expand downslope and reached the YWY site at ∼ 7.1 kyr BP. The living environment of the local small groups of Paleolithic-Epipaleolithic humans (during 15.3–13.1 kyr BP and 9–6.4 kyr BP) changed from shrub-steppe to coniferous forest–steppe. The pollen record shows no evidence of pronounced changes in the vegetation community corresponding to human activity. However, based on a comparison of the local and regional vegetation reconstructions, low values of biodiversity and a significant increase in two indicators of vegetation degradation, Chenopodiaceae and Rosaceae, suggest that prehistoric hunters-gatherers likely disturbed the local vegetation during ∼ 9.0–6.4 kyr BP. Our findings are a preliminary attempt to study human-environment interactions at Paleolithic-Epipaleolithic sites in the region, and they contribute to ongoing environmental archaeology research in the Tibetan Plateau

Can we detect coronal mass ejections through asymmetries of Sun-as-a-star extreme-ultraviolet spectral line profiles?

Coronal mass ejections (CMEs) are the largest-scale eruptive phenomena in the solar system. Associated with enormous plasma ejections and energy release, CMEs have an important impact on the solar-terrestrial environment. Accurate predictions of the arrival times of CMEs at the Earth depend on the precise measurements on their three-dimensional velocities, which can be achieved using simultaneous line-of-sight (LOS) and plane-of-sky (POS) observations. Besides the POS information from routine coronagraph and extreme ultraviolet (EUV) imaging observations, spectroscopic observations could unveil the physical properties of CMEs including their LOS velocities. We propose that spectral line asymmetries measured by Sun-as-a-star spectrographs can be used for routine detections of CMEs and estimations of their LOS velocities during their early propagation phases. Such observations can also provide important clues for the detection of CMEs on other solar-like stars. However, few studies have concentrated on whether we can detect CME signals and accurately diagnose CME properties through Sun-as-a-star spectral observations. In this work, we constructed a geometric CME model and derived the analytical expressions for full-disk integrated EUV line profiles during CMEs. For different CME properties and instrumental configurations, full disk-integrated line profiles were synthesized. We further evaluated the detectability and diagnostic potential of CMEs from the synthetic line profiles. Our investigations provide important constraints on the future design of Sun-as-a-star spectrographs for CME detections through EUV line asymmetries.Comment: 28 pages, 13 figures. Accepted for publication in ApJS. Comments welcome