Phylogenomic study of the subfamily Caprinae by cross-species chromosome painting with Chinese muntjac paints

Chromosomal homologies have been established between the Chinese muntjac (Muntiacus reevesi, MRE, 2n = 46) and five ovine species: wild goat (Capra aegagrus, CAE, 2n = 60), argall (Ovis ammon, OAM, 2n = 56), snow sheep (Ovis nivicola, ONI, 2n = 52), red goral (Naemorhedus cranbrooki, NCR, 2n = 56) and Sumatra serow (Capricornis sumatraensis, CSU, 2n = 48) by chromosome painting with a set of chromosome-specific probes of the Chinese muntjac. In total, twenty-two Chinese muntjac autosomal painting probes detected thirty-five homologous segments in the genome of each species. The chromosome X probe hybridized to the whole X chromosomes of all ovine species while the chromosome Y probe gave no signal. Our results demonstrate that almost all homologous segments defined by comparative painting show a high degree of conservation in G-banding patterns and that each speciation event is accompanied by specific chromosomal rearrangements. The combined analysis of our results and previous cytogenetic and molecular systematic results enables us to map the chromosomal rearrangements onto a phylogenetic tree, thus providing new insights into the karyotypic evolution of these species.

Genetic divergence of orangutan subspecies (Pongo pygmaeus)

Microsatellites and mitochondrial DNA sequences were studied for the two subspecies of orangutans (Pongo pygmaeus), which are located in Borneo (P. p, pygmaeus) and Sumatra (P. p. abelii), respectively. Both subspecies possess marked genetic diversity. Ge

热带印度洋低频Rossby波及其对上层热结构的影响

Rossby波是地球物理流体动力学中非常重要的一种波动，海洋斜压长Rossby波在海洋动力过程中起着相当重要的作用。它维持并影响强西边界流，是海盆内能量传播的主要机制，它所携带的变异信号从大洋的东边界传播到内部，对海气耦合系统起到很重要的作用。热带印度洋是季风爆发的源地，对季风的年际变化具有重要影响。研究热带印度洋对理解季风变率和提高季风预测水平有重要的科学和应用价值。 本文利用TOPEX/Poseidon等高度计资料、美国国家海洋数据中心（NODC）的世界海洋图集（WOA05）长期气候态水文资料、美国Scripps海洋研究所的上层海温资料、中国Argo资料中心提供的Argo资料、美国国家环境预测中心（NCEP）的海表面温度、FSU（Florida State University）月平均风场和海气界面热通量等观测数据，全面分析了热带印度洋低频Rossby波的基本特征，并深入研究了低频Rossby波的生成机制及其对上层海洋热结构的影响。 采用相关分析等统计方法，结合1.5层约化重力模式，研究了热带南印度洋低频Rossby波的生成机制。结果表明： （1）热带南印度洋低频Rossby波分为东边界扰动产生的Rossby波和南印度洋中部风强迫Rossby波；东边界激发的为自由Rossby波，沿12°S波速大约13 cm/s，向西最远传播到80°E左右，之后被局地变量调整；强迫Rossby波在西传的过程中不断加强，波速较快，沿12°S能超过20 cm/s； （2）东边界扰动由印度尼西亚贯通流（ITF）导致的地转调整过程引起；内区风强迫Rossby波生成和加强的关键区为（70°E–95°E，15°S–5°S）；显著的西传Rossby波同太平洋上的厄尔尼诺/南方涛动（ENSO）事件紧密相连，ENSO通过大气的遥驱动机制激发热带南印度洋低频Rossby波； （3）作为东边界低频变量扰动的一个重要因子，ITF的变化与ENSO事件密切相关，总的来讲，El Niño年ITF偏弱，La Niña年ITF偏强，这与前人的研究结果一致；但它在ENSO的不同位相时期，存在一定差异，并具有夏季锁相特征：El Niño事件发生年的春季到秋季，ITF偏强，夏季最强；从El Niño盛期（冬季）到次年秋季，ITF持续偏弱，夏季最弱。上述夏季锁相特征与夏季风的强弱变化相对应。La Niña期间情况相反。 西南印度洋（SWIO）（50°E–75°E，15°S–5°S）以及苏门答腊-爪哇沿岸地区是海表面高度异常（SSHA）和海表面温度异常（SSTA）相关显著的区域，表明内部海洋动力过程在次表层和表层变量的相互关系中起重要作用。本文以2006–2008年期间三个连续的同El Niño或者La Niña同时发生的正印度洋偶极子（IOD）事件为背景，基于Argo观测资料研究了表层和次表层IOD的演变以及二者的区别和联系，并首次采用垂直模态分解方法探讨了Rossby波对上层海洋热力结构影响的动力学特征，得到如下主要结论： （1）在热带印度洋，海洋动力过程一般主要由第一和第二低阶垂直斜压模态控制，而第一斜压模态处于主导地位——在SWIO海区，第一斜压模态运动的方差解释率为第二模态的2–3倍，在赤道和东南印度洋也达到2倍左右；另外，赤道印度洋地区高阶斜压模态运动对该地区的海洋动力过程也具有一定的贡献； （2）低频斜压Rossby波能影响海洋的垂直层结，尤其是强暖Rossby波使同第二斜压模态运动紧密相连的海洋上层层结减弱，加强第二斜压模态的贡献量，导致上层各等压线向下垂直位移增大，最终通过垂直混合过程调整上层海洋的热力结构；而低频斜压冷Rossby波会加强上层垂直层结，抑制该层内变量变化，因此第二斜压模态的贡献依然很小； （3）表层IOD和次表层IOD分布形态不同：表层东部冷异常主要集中在东南印度洋Sumatra-Java沿岸，次表层冷异常基本关于赤道对称；表层西部暖异常基本关于赤道对称，而在次表层赤道以南海温扰动强度远远大于赤道以北； （4）正IOD事件中，东南印度洋冷SSTA首先出现于Java沿岸，沿岸东南风引起的潜热释放增加以及沿岸上升流是该初始冷异常建立的主要机制，与之相关的SSTA东西梯度加强大气环流变化，并进一步强迫随后的海洋运动；1–2个月后，SST冷异常中心北跳到Sumatra沿岸并向西扩展，同时不断增强，其中Sumatra沿岸上升流、来自赤道印度洋的冷Kelvin波及其反射的西传冷Rossby波是这一演变过程的动力机制，而沿岸上升流起决定作用。

中高层大气对低层大气声重波响应的分析

Acoustic Gravity waves (AGW) play an important role in balancing the atmospheric energy and momentum budget. Propagation of gravity wave in the atmosphere is one of the important factors of changing middle and upper atmosphere and ionosphere. The purpose of this dissertation is to study the propagation of gravity wave in a compression atmosphere whit means of numerical simulation and to analyze the response of middle and upper atmosphere to pulse disturbance from lower atmosphere. This work begins with the establishment of 2-D fully nonlinear compressible atmospheric dynamic model in polar coordinate, which is used ton numerically study gravity wave propagation. Then the propagation characteristics of acoustic gravity wave packets are investigated and discussed. We also simulate the response of middle and upper atmosphere to pulse disturbance of lower atmosphere in background winds or without background winds by using this model and analyze the data we obtained by using Fourier Transform (FT), Short-time Fourier Transform (STFT) and Empirical Mode Decomposition (EMD) method which is an important part of Hilbert-Huang Transform (HHT). The research content is summarized in the following: 1. By using a two-dimensional full-implicit-continuous-Eulerian (FICE) scheme and taking the atmospheric basic motion equations as the governing equations, a numerical model for nonlinear propagation of acoustic gravity wave disturbance in two-dimensional polar coordinates is solved. 2. Then the propagation characteristics of acoustic gravity wave packets are investigated and discussed. Results of numerical simulation show that the acoustic gravity wave packets propagate steadily upward and keep its shape well after several periods. 3. We simulate the response of middle and upper atmosphere to pulse disturbance of lower atmosphere in background winds or without background winds by using this model, and obtain the distribution of a certain physical quantity in time and space from earth’s surface to 300km above. The results reveal that the response of ionosphere occurs at a large horizontal distance from the source and the disturbance becomes greater with increasing of height. The situation when the direction of the background wind is opposite to or the same as the direction of disturbed velocity of gravity-wave is studied. The results show that gravity wave propagating against winds is easier than those propagating along winds and the background wind can accelerate gravity wave propagation. Just upon the source, an acoustic wave component with period of 6 min can be found. These images of simulation are similar to observations of the total electron content (TEC) disturbances caused by the great Sumatra-Andaman earthquake on December 26 in 2004. 4. Using the EMD method the disturbed velocity data of a certain physical quantity in time and space can be decomposed into a series of intrinsic mode function (IMF) and a trend mode respectively. The results of EMD reveal impact of the gravity wave frequency under the background winds.

特大地震激发地球自由振荡的数值模拟研究

Large earthquakes, such as the Chile earthquake in 1960 and the Sumatra-Andaman earthquake on Dec 26, 2004 in Indonesia, have generated the Earth’s free oscillations. The eigenfrequencies of the Earth’s free oscillations are closely related to the Earth’s internal structures. The conventional methods, which mainly focus on calculating the eigenfrequecies by analytical ways, and the analysis on observations can not easily study the whole processes from earthquake occurrence to the Earth’s free oscillation inspired. Therefore, we try to use numerical method incorporated with large-scale parallel computing to study on the Earth’s free oscillations excited by giant earthquakes. We first give a review of researches and developments of the Earth’s free oscillation, and basical theories under spherical coordinate system. We then give a review of the numerical simulation of seismic wave propagation and basical theories of spectral element method to simulate global seismic wave propagation. As a first step to study the Earth’s free oscillations, we use a finite element method to simulate the propagation of elastic waves and the generation of oscillations of the chime bell of Marquis Yi of Zeng, by striking different parts of the bell, which possesses the oval crosssection. The bronze chime bells of Marquis Yi of Zeng are precious cultural relics of China. The bells have a two-tone acoustic characteristic, i.e., striking different parts of the bell generates different tones. By analysis of the vibration in the bell and the spectrum analysis, we further help the understanding of the mechanism of two-tone acoustic characteristics of the chime bell of Marquis Yi of Zeng. The preliminary calculations have clearly shown that two different modes of oscillation can be generated by striking different parts of the bell, and indicate that finite element numerical simulation of the processes of wave propagation and two-tone generation of the chime bell of Marquis Yi of Zeng is feasible. These analyses provide a new quantitative and visual way to explain the mystery of the two-tone acoustic characteristics. The method suggested by this study can be applied to simulate free oscillations excited by great earthquakes with complex Earth structure. Taking into account of such large-scale structure of the Earth, small-scale low-precision numerical simulation can not simply meet the requirement. The increasing capacity in high-performance parallel computing and progress on fully numerical solutions for seismic wave fields in realistic three-dimensional spherical models, Spectral element method and high-performance parallel computing were incorporated to simulate the seismic wave propagation processes in the Earth’s interior, without the effects of the Earth’s gravitational potential. The numerical simulation shows that, the results of the toroidal modes of our calculation agree well with the theoretical values, although the accuracy of our results is much limited, the calculated peaks are little distorted due to three-dimensional effects. There exist much great differences between our calculated values of spheroidal modes and theoretical values, because we don’t consider the effect the Earth’ gravitation in numerical model, which leads our values are smaller than the theoretical values. When , is much smaller, the effect of the Earth’s gravitation make the periods of spheroidal modes become shorter. However, we now can not consider effects of the Earth’s gravitational potential into the numerical model to simulate the spheroidal oscillations, but those results still demonstrate that, the numerical simulation of the Earth’s free oscillation is very feasible. We make the numerical simulation on processes of the Earth’s free oscillations under spherically symmetric Earth model using different special source mechanisms. The results quantitatively show that Earth’s free oscillations excited by different earthquakes are different, and oscillations at different locations are different for free oscillation excited by the same earthquake. We also explore how the Earth’s medium attenuation will take effects on the Earth’s free oscillations, and take comparisons with the observations. The medium attenuation can make influences on the Earth’s free oscillations, though the effects on lower-frequency fundamental oscillations are weak. At last, taking 2008 Wenchuan earthquake for example, we employ spectral element method incorporated with large-scale parallel computing technology to investigate the characteristics of seismic wave propagation excited by Wenchuan earthquake. We calculate synthetic seismograms with one-point source model and three-point source model respectively. Full 3-D visualization of the numerical results displays the profile of the seismic wave propagation with respect to time. The three-point source, which was proposed by the latest investigations through field observation and reverse estimation, can better demonstrate the spatial and temporal characteristics of the source rupture processes than one-point source. Primary results show that those synthetic signals calculated from three-point source agree well with the observations. This can further reveal that the source rupturing process of Wenchuan earthquake is a multi-rupture process, which is composed by at least three or more stages of rupture processes. In conclusion, the numerical simulation can not only solve some problems concluding the Earth’s ellipticity and anisotropy, which can be easily solved by conventional methods, but also finally solve the problems concluding topography model and lateral heterogeneity. We will try to find a way to fully implement self-gravitation in spectral element method in future, and do our best to continue researching the Earth’s free oscillations using the numerical simulations to see how the Earth’ lateral heterogeneous will affect the Earth’s free oscillations. These will make it possible to bring modal spectral data increasingly to bear on furthering our understanding of the Earth’s three-dimensional structure.