Molecular systematics and biogeography of Crawfurdia, Metagentiana and Tripterospermum (Gentianaceae) based on nuclear ribosomal and plastid DNA sequences

Background and Aims The systematic position of the genus Metagentiana and its phylogenetic relationships with Crawfurdia, Gentiana and Tripterospermum have not been explicitly addressed. These four genera belong to one of two subtribes (Gentianinae) of Gentianeae. The aim of this paper is to examine the systematic position of Crawfurdia, Metagentiana and Tripterospermum and to clarify their phylogenetic affinities more clearly using ITS and trnL intron sequences.Methods Nucleotide sequences from the internal transcribed spacers (ITS) of nuclear ribosomal DNA and the plastid DNA trnL (UAA) intron were analysed phylogenetically. Ten of fourteen Metagentiana species were sampled, together with 40 species of other genera in the subtribe Gentianinae.Key Results The data support several previously published conclusions relating to the separation of Metagentiana from Gentiana and its closer relationships to Crawfurdia and Tripterospermum based on studies of gross morphology, floral anatomy, chromosomes, palynology, embryology and previous molecular data. The molecular clock hypothesis for the tested sequences in subtribe Gentianinae was not supported by the data (P < 0.05), so the clock-independent non-parametric rate smoothing method was used to estimate divergence time. This indicates that the separation of Crawfurdia, Metagentiana and Tripterospermum from Gentiana occurred about 11.4-21.4 Mya (million years ago), and the current species of these three genera diverged at times ranging from 0.4 to 6.2 Mya.Conclusions The molecular analyses revealed that Crawfurdia, Metagentiana and Tripterospermum do not merit status as three separate genera, because sampled species of Crawfurdia and Tripterospermum are embedded within Metagentiana. The speciation and rapid radiation of these three genera is likely to have occurred in western China as a result of upthrust of the Himalayas during the late Miocene and the Pleistocene.

Molecular phylogeny, recent radiation and evolution of gross morphology of the rhubarb genus Rheum (Polygonaceae) inferred from chloroplast DNA trnL-F sequences

Background and Aims Rheum, a highly diversified genus with about 60 species, is mainly confined to the mountainous and desert regions of the Qinghai-Tibetan plateau and adjacent areas. This genus represents a good example of the extensive diversification of the temperate genera in the Qinghai-Tibetan plateau, in which the forces to drive diversification remain unknown. To date, the infrageneric classification of Rheum has been mainly based on morphological characters. However, it may have been subject to convergent evolution under habitat pressure, and the systematic position of some sections are unclear, especially Sect. Globulosa, which has globular inflorescences, and Sect. Nobilia, which has semi-translucent bracts. Recent palynological research has found substantial contradictions between exine patterns and the current classification of Rheum. Two specific objectives of this research were (1) to evaluate possible relationships of some ambiguous sections with a unique morphology, and (2) to examine possible occurrence of the radiative speciation with low genetic divergence across the total genus and the correlation between the extensive diversification time of Rheum and past geographical events, especially the recent large-scale uplifts of the Qinghai-Tibetan Plateau.Methods The chloroplast DNA trnL-F region of 29 individuals representing 26 species of Rheum, belonging to seven out of eight sections, was sequenced and compared. The phylogenetic relationships were further constructed based on the sequences obtained.Key Results Despite the highly diversified morphology, the genetic variation in this DNA fragment is relatively low. The molecular phylogeny is highly inconsistent with gross morphology, pollen exine patterns and traditional classifications, except for identifying all samples of Sect. Palmata, three species of Sect. Spiciformia and a few species of Sect. Rheum as corresponding monophyletic groups. The monotypic Sect. Globulosa showed a tentative position within the clade comprising five species of Sect. Rheum. All of the analyses revealed the paraphyly of R. nobile and R. alexandrae, the only two species of Sect. Nobilia circumscribed by the possession of large bracts. The crude calibration of lineages based on trnL-F sequence differentiation implied an extensive diversification of Rheum within approx. 7 million years.Conclusions Based on these results, it is suggested that the rich geological and ecological diversity caused by the recent large-scale uplifts of the Qinghai-Tibetan Plateau since the late Tertiary, coupled with the oscillating climate of the Quaternary stage, might have promoted rapid speciation in small and isolated populations, as well as allowing the fixation of unique or rare morphological characters in Rheum. Such a rapid radiation, combined with introgressive hybridization and reticulate evolution, may have caused the transfer of cpDNA haplotypes between morphologically dissimilar species, and might account for the inconsistency between morphological classification and molecular phylogeny reported here.

Phylogenetic analyses of Saussurea sect. Pseudoeriocoryne (Asteraceae : Cardueae) based on chloroplast DNA trnL-F sequences

The genus Saussurea is distributed mainly in the temperate and subarctic regions of Eurasia and consists of about 300 species classified into six subgenera and 20 sections. Sect. Pseudoeriocoryne in the subgenus Eriocoryne comprises four species, and is delimited mainly by acaulescence and an inflorescence with congested capitula surrounded by a rosette of leaves. All of these species are endemic to the and Qinghai-Tibet Plateau. Sequences from the chloroplast DNA trnL-F region were obtained for the four species in this section and 26 other species from four subgenera of Saussurea to resolve phylogenetic relationships among these species and to determine whether the shared characters that define sect. Pseudoeriocoryne are synapomorphic or were acquired by convergent evolution. The resulting phylogenies indicated that Saussurea sect. Pseudoeriocoryne as traditionally defined does not constitute a monophyletic group and that each of its species belongs to separate clades. Furthermore, none of these species showed a close relationship with the other species of subgenus Eriocoryne. Our results further indicated that none of the investigated subgenera are monophyletic, and that species from different subgenera clustered together. All these conclusions are provisional and their confirmation would require stronger phylogenetic support. Two possible explanations are suggested for low sequence divergence, poor resolution of internal clades and clustering of species with the rather distinct morphology of Saussurea detected in the present study. The first is rapid radiation and diversification triggered by fast habitat fragmentation due to the recent lifting of the Qinghai-Tibet Plateau and the Quaternary climate oscillations. This could have led to rapid morphological divergence while sequences diverged very little, and also caused the convergent acquisition of similar characteristics in unrelated lineages due to similar selection pressures. The second possible explanation is that both introgressive hybridization and reticulate evolution might have caused the transferring of cpDNA sequences between morphologically dissimilar species, thus leading to homogenization of sequences between lineages. (C) 2004 Elsevier Ltd. All rights reserved.

Molecular phylogeny and biogeography of the Qinghai-Tibet Plateau endemic Nannoglottis (Asteraceae)

All taxa endemic to the Qinghai-Tibet Plateau are hypothesized to have originated in situ or from immediately adjacent areas because of the relatively recent formation of the plateau since the Pliocene, followed by the large-scaled biota extinction and recession caused by the Quaternary ice sheet. However, identification of specific progenitors remains difficult for some endemics, especially some endemic genera. Nannoglottis, with about eight species endemic to this region, is one such genus. Past taxonomic treatments have suggested its relationships with four different tribes of Asteraceae. We intend to identify the closest relatives of Nannoglottis by evaluating the level of monophyly, tribal delimitation, and systematic position of the genus by using molecular data from ndhF gene, trnL-F, and ITS region sequences. We find that all sampled species of Nannoglottis are a well-defined monophyly. This supports all recent taxonomic treatments of Nannoglottis, in which all sampled species were placed in one broadly re-circumscribed genus. Nannoglottis is most closely related to the Astereae, but stands as an isolated genus as the first diverging lineage of the tribe, without close relatives. A tentative relationship was suggested for Nannoglottis and the next lineage of the tribe was based on the ITS topology, the "basal group," which consists of seven genera from the Southern Hemisphere. Such a relationship is supported by some commonly shared plesiomorphic morphological characters. Despite the very early divergence of Nannoglottis in the Astereae, the tribe must be regarded to have its origin in Southern Hemisphere rather than in Asia, because based on all morphological, molecular, biogeographical, and fossil data, the Asteraceae and its major lineages (tribes) are supposed to have originated in the former area. Long-distance dispersal using Southeast Asia as a steppingstone from Southern Hemisphere to the Qinghai-Tibet Plateau is the most likely explanation for this unusual biogeographic link of Nannoglottis. The 23-32-million-year divergence time between Nannoglottis and the other Astereae estimated by DNA sequences predated the formation of the plateau. This estimation is further favored by the fossil record of the Asteraceae and the possible time of origin of the Astereae. Nannoglottis seems to have reached the Qinghai-Tibet area in the Oligocene-Eocene and then re-diversified with the uplift of the plateau. The molecular infragenetic phylogeny of the genus identifies two distinct clades, which reject the earlier infrageneric classification based on the arrangement of the involucral bracts and the length of the ligules, but agree well with the habits and ecological preferences of its current species. The "alpine shrub" vs. "coniferous forest" divergence within Nannoglottis was estimated at about 3.4 million years ago when the plateau began its first large-scale uplifting and the coniferous vegetation began to appear. Most of the current species at the "coniferous forest" clade of the genus are estimated to have originated from 1.02 to 1.94 million years ago, when the second and third uprisings of the plateau occurred, the climate oscillated and the habitats were strongly changed. The assumed evolution, speciation diversity, and radiation of Nannoglottis based on molecular phylogeny and divergence times agree well with the known geological and paleobotanical histories of the Qinghai-Tibet Plateau. (C) 2002 Elsevier Science (USA). All rights reserved.

Molecular evidence for the sister relationship of the eastern Asia-North American intercontinental species pair in the Podophyllum group (Berberidaceae)

The presumed pair relationships of intercontinental vicariad species in the Podophyllum group (Sinopodophyllum hexandrum vs. Podophyllum pelatum and Diphylleia grayi vs. D. cymosa) were recently, considered to be paraphyletic. In the present paper, the trnL-F and ITS gene sequences of the representatives were used to examine the sister relationships of these two vicariad species. A heuristic parsimony analysis based on the trnLF data identified Diphylleia as the basal clade of the other three genera, but provided poor resolution of their inter-relationships. High sequence divergence was found in the ITS data. ITS1 region, more variable but parsimonyuninformative. has no phylogenetic value, Sequence divergence of the ITS2 region provided abundant, phylogenetically informative variable characters. Analysis of ITS2 sequences confirmeda sister relationship between the presumable vicariad species, in spite of a low bootstrap support for Sinopodophyllum hexandrum vs. Podophyllum pelatum. The combined ITS2 and trnL-F data enforced a sister relationship between Sinopodophyllum hexandrum and Podophyllum pelatum with an elevated bootstrap support of 100%. Based on molecular phylogeny, the morphological evolution of this group was discussed. The self-pollination might have evolved from cross-fertilization two times in this group. The different pollination and seed dispersal systems of Sinopodophyllum hexandrum and Podophlyllum pelatum resulted from their adaptations to different ecological habitats. The divergence time of Sinopodophyllum hexandrum-Podophyllum pelatum is estimated to be 6.52+/-1.89 myr based on the ITS divergence. The divergence of this species pair predated or co-occurred with the recent uplift of the Himalayas 4-3 myr during the late Miocene and the formation of the alpine habitats. Sinopodophyllum hexandrum developed a host of specialized characters in its subsequent adaptation to the arid alpine surroundings. The present study confirmed the different patterns of species relationship between Asian-North American disjuncts. The isolation of plant elements between North America and eastern Asia must have been a gradual process, resulting in the different phylogenetic patterns and divergence times of the disjuncts.

Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences

The phylogenetic relationships among worldwide species of genus Ochotona were investigated by sequencing mitochondrial cytochrome b and ND4 genes. Parsimony and neighbor-joining analyses of the sequence data yielded congruent results that strongly indicated three major clusters: the shrub-steppe group, the northern group, and the mountain group. The subgeneric classification of Ochotona species needs to be revised because each of the two subgenera in the present classification contains species from the mountain group. To solve this taxonomic problem so that each taxon is monophyletic, i.e., represents a natural clade, Ochotona could be divided into three subgenera, one for the shrub-steppe species, a second for the northern species, and a third for the mountain species. The inferred tree suggests that the differentiation of this genus in the Palearctic Region was closely related to the gradual uplifting of the Tibet (Qinghai-Xizang) Plateau, as hypothesized previously, and that vicariance might have played a major role in the differentiation of this genus on the Plateau, On the other hand, the North American species, O. princeps, is most likely a dispersal event, which might have happened during the Pliocene through the opening of the Bering Strait. The phylogenetic relationships within the shrub-steppe group are worth noting in that instead of a monophyletic shrub-dwelling group, shrub dwellers and steppe dwellers are intermingled with each other. Moreover, the sequence divergence within the sister tars of one steppe? dweller and one shrub dweller is very low. These findings support the hypothesis that pikes have entered the steppe environment several times and that morphological similarities within steppe dwellers were due to convergent evolution. (C) 2000 Academic Press.

Variation in mitochondrial DNA and phylogeny of six species of pikas (Ochotona)

Phylogenetic relationships of six species of Ochotona were investigated using mitochondrial DNA (mtDNA) restriction-site analysis. The phylogenetic tree constructed using PAUP was based on 62 phylogenetically informative sites with O. erythrotis designated as an outgroup. Two clades were evident. One contained O. curzoniae, O. huangensis, and O. thibetana. in the second, O. daurica was a sister taxon of O. cansus. The five species appear to come from different maternal lineages. The branching structure of the tree and sequence divergence confirm that huangensis and cansus are distinct species, and that mol-osa is a synonym of O. cansus rather than O. thibetana. Divergence time, estimated from genetic distances, indicates that the ancestors of the two maternal lineages diverged ca. 6.5 x 10(6) years ago. O. curzoniae diverged from O. huangensis, and O. daurica diverged from O. cansus, at about the same time (ca. 3.4 x 10(6) years ago). These data suggest a period of rapid radiation of the genus Ochotona in China, perhaps during the late Pliocene. These calculations correspond roughly to tectonic events and environmental changes in China throughout this period, and appear to be substantiated by the fossil record.

Phylogenetic relationships of five pika species (genus Ochotona) based on mitochondrial DNA restriction maps

Restriction site mapping of mitochondrial DNA (mtDNA) with 16 restriction endonucleases was used to examine the phylogenetic relationships of Ochotona cansus, O. huangensis, O. thibetana, O. curzoniae and O. erythrotis. A 1-kb length variation between O. erythrotis of subgenus Pika and other four species of subgenus Ochotona was observed, which may be a useful genetic marker for identifying the two subgenera. The phylogenetic tree constructed using PAUP based on 61 phylogenetically informative sites suggests that O. erythrotis diverged first, followed by O. cansus, while O. curzoniae and O. huangensis are sister taxa related to O. thibetana, The results indicate that both O. cansus and O. huangensis should be treated as independent species. If the base substitution rate of pikas mtDNA was 2% per million years, then the divergence time of the two subgenera, Pika and Ochotana, is about 8.8 Ma ago of late Miocence, middle Bao-dian of Chinese mammalian age, and the divergence of the four species in subgenus Ochotona would have occurred about 2.5 - 4.2 Ma ago, Yushean of Chinese mammalian age. This calculation appears to be substantiated by the fossil record.

基于测角的自主移动机器人定位算法

给出了自主移动机器人定位的两种算法：解析算法和数值算法。解析法公式较以往的简洁。数值算法结合解析法和高斯－牛顿算法，不仅能避免因初值选取不合理而导致求解过程发散的问题，而且能提高运算精度和速度，通过对两种算法的计算机仿真，表明了解析算法具有运算速度快，而数值算法精度高的特点。其结果已用于自主移动机器人的研制中。

叠前时间偏移: 基于波动方程的架构、发展和应用

This dissertation starts from the point that the prestack time migration can been considered as an approximation of the prestack depth migration, giving a wave equation based prestack time migration approach. The new approach includes: analytically getting the travel time and amplitude based on the one way wave equation and the stationary-phase theory, using ‘spread’ imaging method and imaging following the prestack depth migration, updating the velocity model with respect to the flats of the events in CRP gathers. Based on this approach, we present a scheme that can image land seismic data without field static correction. We may determine the correct near surface velocities and stack velocities by picking up the residual correction of the events in the CRP gathers. We may get the rational migration section based on the updated velocities and correct the migration section from a floating datum plane to a universal datum plane. We may adaptively determine the migration aperture according to the dips of the imaging structures. This not only speed up the processing, but may suppress the migration noise produce by the extra aperture. We adopt the deconvolution imaging condition of wave equation migration. It may partially compensate the geometric divergence. In this scheme, we use the table-driven technique which may enhance the computational efficiency. If the subsurface is much more complicated, it may be impossible to distinguish the DTS curve. To solve this problem, we proposed a technique to determine the appropriate range of the DTS curve. We synthesize DTS panel in this range using different velocities and depths, and stack the amplitude around the zero time. Determine the correct velocity and location of the considered grid point by comparing the values.

叠前时间偏移：各向异性、多次波衰减及应用

At present, in order to image complex structures more accurately, the seismic migration methods has been developed from isotropic media to the anisotropic media. This dissertation develops a prestack time migration algorithm and application aspects for complex structures systematically. In transversely isotropic media with a vertical symmetry axis (VTI media), the dissertation starts from the theory that the prestack time migration is an approximation of the prestack depth migration, based on the one way wave equation and VTI time migration dispersion relation, by combining the stationary-phase theory gives a wave equation based VTI prestack time migration algorithm. Based on this algorithm, we can analytically obtain the travel time and amplitude expression in VTI media, as while conclude how the anisotropic parameter influence the time migration, and by analyzing the normal moveout of the far offset seismic data and lateral inhomogeneity of velocity, we can update the velocity model and estimate the anisotropic parameter model through the time migration. When anisotropic parameter is zero, this algorithm degenerates to the isotropic time migration algorithm naturally, so we can propose an isotopic processing procedure for imaging. This procedure may keep the main character of time migration such as high computational efficiency and velocity estimation through the migration, and, additionally, partially compensate the geometric divergence by adopting the deconvolution imaging condition of wave equation migration. Application of this algorithm to the complicated synthetic dataset and field data demonstrates the effectiveness of the approach. In the dissertation we also present an approach for estimating the velocity model and anisotropic parameter model. After analyzing the velocity and anisotropic parameter impaction on the time migration, and based on the normal moveout of the far offset seismic data and lateral inhomogeneity of velocity, through migration we can update the velocity model and estimate the anisotropic parameter model by combining the advantages of velocity analysis in isotropic media and anisotropic parameter estimation in VTI media. Testing on the synthetic and field data, demonstrates the method is effective and very steady. Massive synthetic dataset、2D sea dataset and 3D field datasets are used for VTI prestack time migration and compared to the stacked section after NMO and prestack isotropic time migration stacked section to demonstrate that VTI prestack time migration method in this paper can obtain better focusing and less positioning errors of complicated dip reflectors. When subsurface is more complex, primaries and multiples could not be separated in the Radon domain because they can no longer be described with simple functions (parabolic). We propose an attenuating multiple method in the image domain to resolve this problem. For a given velocity model，since time migration takes the complex structures wavefield propagation in to account, primaries and multiples have different offset-domain moveout discrepancies, then can be separated using techniques similar to the prior migration with Radon transform. Since every individual offset-domain common-reflection point gather incorporates complex 3D propagation effects, our method has the advantage of working with 3D data and complicated geology. Testing on synthetic and real data, we demonstrate the power of the method in discriminating between primaries and multiples after prestack time migration, and multiples can be attenuated in the image space considerably.

波动方程偏移速度分析

On the subject of oil and gas exploration, migration is an efficacious technique for imagining structures underground. Wave-equation migration (WEM) dominates over other migration methods in accuracy, despite of higher computational cost. However, the advantages of WEM will emerge as the progress of computer technology. WEM is sensitive to velocity model more than others. Small velocity perturbations result in grate divergence in the image pad. Currently, Kirrchhoff method is still very popular in the exploration industry for the reason of difficult to provide precise velocity model. It is very urgent to figure out a way to migration velocity modeling. This dissertation is mainly devoted to migration velocity analysis method for WEM: 1. In this dissertation, we cataloged wave equation prestack depth migration. The concept of migration is introduced. Then, the analysis is applied to different kinds of extrapolate operator to demonstrate their accuracy and applicability. We derived the DSR and SSR migration method and apply both to 2D model. 2. The output of prestack WEM is in form of common image gathers (CIGs). Angle domain common image gathers (ADCIGs) gained by wave equation are proved to be free of artifacts. They are also the most potential candidates for migration velocity analysis. We discussed how to get ADCIGs by DSR and SSR, and obtained ADCIGs before and after imaging separately. The quality of post stack image is affected by CIGs, only the focused or flattened CIGs generate the correct image. Based on wave equation migration, image could be enhanced by special measures. In this dissertation we use both prestack depth residual migration and time shift imaging condition to improve the image quality. 3. Inaccurate velocities lead to errors of imaging depth and curvature of coherent events in CIGs. The ultimate goal of migration velocity analysis (MVA) is to focus scattered event to correct depth and flatten curving event by updating velocities. The kinematic figures are implicitly presented by focus depth aberration and kinetic figure by amplitude. The initial model of Wave-equation migration velocity analysis (WEMVA) is the output of RMO velocity analysis. For integrity of MVA, we review RMO method in this dissertation. The dissertation discusses the general ideal of RMO velocity analysis for flat and dipping events and the corresponding velocity update formula. Migration velocity analysis is a very time consuming work. Respect to computational convenience, we discus how RMO works for synthetic source record migration. In some extremely situation, RMO method fails. Especially in the areas of poorly illuminated or steep structure, it is very difficult to obtain enough angle information for RMO. WEMVA based on wave extrapolate theory, which successfully overcome the drawback of ray based methods. WEMVA inverses residual velocities with residual images. Based on migration regression, we studied the linearized scattering operator and linearized residual image. The key to WEMVA is the linearized residual image. Residual image obtained by Prestack residual migration, which based on DSR is very inefficient. In this dissertation, we proposed obtaining residual migration by time shift image condition, so that, WEMVA could be implemented by SSR. It evidently reduce the computational cost for this method.

人工源频率域大地电磁法正反演研究

The CSAMT method is playing an important role in the exploration of geothermal and the pre-exploration in tunnel construction project recently. In order to instruct the interpretation technique for the field data, the forward method from ID to 3D and inversion method in ID and 2D are developed in this paper for the artificial source magnetotelluric in frequency domain. In general, the artificial source data are inverted only after the near field is corrected on the basis of the assumption of half-homogeneous space; however, this method is not suitable for the complex structure because the assumption is not valid any more. Recently the new idea about inversion scheme without near field correction is published in order to avoid the near field correction error. We try to discuss different inversion scheme in ID and 2D using the data without near field correction.The numerical integration method is used to do the forward modeling in ID CSAMT method o The infinite line source is used in the 2D finite-element forward modeling, where the near-field effect is occurred as in the CSAMT method because of using artificial source. The pseudo-delta function is used to modeling the source distribution, which reduces the singularity when solving the finite-element equations. The effect on the exploration area is discussed when anomalous body exists under the source or between the source and exploration area; A series of digital test show the 2D finite element method are correct, the results of modeling has important significant for CSAMT data interpretation. For 3D finite-element forward modeling, the finite-element equation is derived by Galerkin method and the divergence condition is add forcedly to the forward equation, the forward modeling result of the half homogeneous space model is correct.The new inversion idea without near field correction is followed to develop new inversion methods in ID and 2D in the paper. All of the inversion schemes use the data without near field correction, which avoid introducing errors caused by near field correction. The modified grid parameter method and the layer-by-layer inversion method are joined in the ID inversion scheme. The RRI method with artificial source are developed and finite-element inversion method are used in 2D inversion scheme. The inversion results using digital data and the field data are accordant to the model and the known geology data separately, which means the inversion without near field correction is accessible. The feasibility to invert the data only in exploration area is discussed when the anomalous body exists between the source and the exploration area.