Seismic imaging of a mid-crustal low-velocity layer beneath the northern coast of the South China Sea and its tectonic implications

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Deep seismic structure across the southernmost Mariana trench: Implications for arc rifting and plate hydration

Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research-Solid Earth 124(5), (2019): 4710-4727, doi:10.1029/2018JB017080.The southernmost Mariana margin lacks a mature island arc and thus differs significantly from the central‐north Mariana and Izu‐Bonin margins. This paper presents a new P wave velocity model of the crust and uppermost mantle structure based on a 349‐km‐long profile of wide‐angle reflection/refraction data. The active source seismic experiment was conducted from the subducting Pacific plate to the overriding Philippine plate, passing through the Challenger Deep. The subducting plate has an average crustal thickness of ~6.0 km with Vp of 7.0 ± 0.2 km/s at the base of the crust and low values of only 5.5–6.9 km/s near the trench axis. The uppermost mantle of the subducting plate is characterized by low velocities of 7.0–7.3 km/s. The overriding plate has a maximum crustal thickness of ~18 km beneath the forearc with Vp of ~7.4 km/s at the crustal bottom and 7.5–7.8 km/s in the uppermost mantle. A zone of slight velocity reduction is imaged beneath the Southwest Mariana Rift that is undergoing active rifting. The observed significant velocity reduction in a near‐trench crustal zone of ~20–30 km in the subducting plate is interpreted as a result of faulting‐induced porosity changes and fracture‐filling fluids. The velocity reduction in the uppermost mantle of both subducting and overriding plates is interpreted as mantle serpentinization with fluid sources from dehydration of the subducting plate and/or fluid penetration along faults.Data acquisition and sample collections were supported by the Mariana Trench Initiative of the Chinese Academy of Sciences (CAS). We are grateful to the science parties and crews of R/V Shiyan 3 of the South China Sea Institute of Oceanology, CAS, for contributions to data acquisition. Constructive reviews by Robert Stern, Martha Savage, and anonymous reviewers significantly improved the manuscript. We thank Gaohua Zhu, Fan Zhang, Chunfeng Li, Zhen Sun, Zhi Wang, and Minghui Zhao for helpful discussion. The bathymetric maps were plotted using GMT (Wessel & Smith, 1995). Digital files of the velocity models and selected raw data are deposited and accessible online (at https://pan.baidu.com/s/1AbDJOgLZhYn1C‐3sg7S9Xw). This work was supported by the Strategic Priority Program of CAS (XDA13010101), CAS (Y4SL021001, QYZDY‐SSW‐DQC005, and 133244KYSB20180029), Key Laboratory of Ocean and Marginal Sea Geology, CAS (OMG18‐03), National Natural Science Foundation of China (41890813, 41676042, U1701641, 91628301, 41576041, and U1606401), and HKSAR Research Grant Council grants (14313816).2019-10-0

Study on closing and cracking stress calculation method of fractured rock

Determining the characteristic stress intensity according to the rock stress-strain curve is significant significance for rock engineering. Nowadays, there are relatively mature methods for determining peak stress and damage stress. However, the crack volume strain method, axial strain method, and strain response method are more subjective to determine rock’s closure stress and initiation stress. The closure rock stress and crack initiation stress refined value method are proposed based on these methods, which are based on the discreteness of the rock stress and strain point. Through optimizing the stress characteristics by an objective function (variance function), the subjectivity of artificial observation is avoided; Based on the trend of rock stress-strain curve, an empirical method for determining rock closure stress and crack initiation stress is proposed. The test results indicate that the two proposed methods that calculate closure rock stress and crack initiation stress can obtain reasonable results. These methods can be used as a supplement to the characteristics of the rock stress determination method and can be used in actual engineering

Paternal chromosome elimination of inducer triggers induction of double haploids in Brassica napus

A synthetic octoploid rapeseed, Y3380, induces maternal doubled haploids when used as a pollen donor to pollinate plant. However, the mechanism underlying doubled haploid formation remains elusive. We speculated that double haploid induction occurs as the inducer line’s chromosomes pass to the maternal egg cell, and the zygote is formed through fertilization. In the process of zygotic mitosis, the paternal chromosome is specifically eliminated. Part of the paternal gene might have infiltrated the maternal genome through homologous exchange during the elimination process. Then, the zygote haploid genome doubles (early haploid doubling, EH phenomenon), and the doubled zygote continues to develop into a complete embryo, finally forming doubled haploid offspring. To test our hypothesis, in the current study, the octoploid Y3380 line was back bred with the 4122-cp4-EPSPS exogenous gene used as a marker into hexaploid Y3380-cp4-EPSPS as paternal material to pollinate three different maternal materials. The fertilization process of crossing between the inducer line and the maternal parent was observed 48 h after pollination, and the fertilization rate reached 97.92% and 98.72%. After 12 d of pollination, the presence of cp4-EPSPS in the embryo was detected by in situ PCR, and at 13–23 d after pollination, the probability of F1 embryos containing cp4-EPSPS gene was up to 97.27%, but then declined gradually to 0% at 23–33 d. At the same time, the expression of cp4-EPSPS was observed by immunofluorescence in the 3rd to 29th day embryo. As the embryos developed, cp4-EPSPS marker genes were constantly lost, accompanied by embryonic death. After 30 d, the presence of cp4-EPSPS was not detected in surviving embryos. Meanwhile, SNP detection of induced offspring confirmed the existence of double haploids, further indicating that the induction process was caused by the loss of specificity of the paternal chromosome. The tetraploid-induced offspring showed infiltration of the induced line gene loci, with heterozygosity and homozygosity. Results indicated that the induced line chromosomes were eliminated during embryonic development, and the maternal haploid chromosomes were synchronously doubled in the embryo. These findings support our hypothesis and lay a theoretical foundation for further localization or cloning of functional genes involved in double haploid induction in rapeseed

Lineage-specific accelerated sequences underlying primate evolution

Understanding the mechanisms underlying phenotypic innovation is a key goal of comparative genomic studies. Here, we investigated the evolutionary landscape of lineage-specific accelerated regions (LinARs) across 49 primate species. Genomic comparison with dense taxa sampling of primate species significantly improved LinAR detection accuracy and revealed many novel human LinARs associated with brain development or disease. Our study also yielded detailed maps of LinARs in other primate lineages that may have influenced lineage-specific phenotypic innovation and adaptation. Functional experimentation identified gibbon LinARs, which could have participated in the developmental regulation of their unique limb structures, whereas some LinARs in the Colobinae were associated with metabolite detoxification which may have been adaptive in relation to their leaf-eating diet. Overall, our study broadens knowledge of the functional roles of LinARs in primate evolution

The Genomic Footprints of the Fall and Recovery of the Crested Ibis

Human-induced environmental change and habitat fragmentation pose major threats to biodiversity and require active conservation efforts to mitigate their consequences. Genetic rescue through translocation and the introduction of variation into imperiled populations has been argued as a powerful means to preserve, or even increase, the genetic diversity and evolutionary potential of endangered species [1-4]. However, factors such as outbreeding depression [5, 6] and a reduction in available genetic diversity render the success of such approaches uncertain. An improved evaluation of the consequence of genetic restoration requires knowledge of temporal changes to genetic diversity before and after the advent of management programs. To provide such information, a growing number of studies have included small numbers of genomic loci extracted from historic and even ancient specimens [7, 8]. We extend this approach to its natural conclusion, by characterizing the complete genomic sequences of modern and historic population samples of the crested ibis (Nipponia nippon), an endangered bird that is perhaps the most successful example of how conservation effort has brought a species back from the brink of extinction. Though its once tiny population has today recovered to >2,000 individuals [9], this process was accompanied by almost half of ancestral loss of genetic variation and high deleterious mutation load. We furthermore show how genetic drift coupled to inbreeding following the population bottleneck has largely purged the ancient polymorphisms from the current population. In conclusion, we demonstrate the unique promise of exploiting genomic information held within museum samples for conservation and ecological research.© 2018 The Author(s). Published by Elsevier Ltd. This is an open access article available to all published under a Creative Commons Attribution – NonCommercial – NoDerivs (CC BY-NC-ND 4.0). The attached file is the published pdf

Dense sampling of bird diversity increases power of comparative genomics

© 2020, The Author(s). Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species