methods of taxonomic studies 分类学研究方法 [课件]

Methods of Taxonomic Studies分類學研究方法,教師：蘇夢淮Email: .twWeb Site: .tw/class,Tools of Studies,Although taxonomy is the basis for all botanical subjects, those subjects provide tools (the ways) for taxonomic studies.“How to find and compare the variant characters” is the basic concept of a taxonomic study.,Traditional procedures,Collections (採集)Observations (觀察)Comparisons (比較)Taxonomic treatments (分類處理),Subjectivity (主觀性) is the biggest problem to the traditional taxonomy.,Numerical Taxonomy; Phenetics數值分類學,Definition,The numerical evaluation of the affinity or similarity between taxonomic units (or operational taxonomic units; OTU) and the ordering of these units into taxa on the basis of their affinities.,Phenetic procedures,Transforming descriptive characters to data matrix (量化).Computing the similarity / dissimilarity index (相似/相異性指數).Clustering to produce a dendrogram (樹狀圖).Validation (驗證): More statistics and test.Taxonomic treatments.,(R. R. Sokal. 1986. Phenetic Taxonomy: Theory and Methods. Annu. Rev. Ecol. Syst. 17: 423-442.),Statistics of Phenetics,Two categories：Clustering methods (聚類法) 。Ordination methods (排序法) 。Methods and data type (資料型態)。Ex. PCA不能使用命名式 (nominal)資料。Statistical tests (檢定): Testing the robustness of statistics results.,An example of data matrix,An example of clustering result,An example of ordination result,Question. Whats the deficiencies in phenetics?,Cytology: karyotype細胞學: 核型,Haploid, diploid and polyploid,Expression: X (基數) vs. n (套數).Ex. In Camellia, X = 15. If Chromosome number of C. brevistyla is 45, then we can say its 3X or triploid.Ex. When we count the chromosome from reproductive cell of Camellia, we say “n = 15”. When we count the chromosome from somatic cell, we say “2n = 30”.Polyploid is common in plants. However, it is usually lethal in animals. Polyploid plays a important role in the speciation. Autopolyploid (同源多倍體) vs. allopolyploid (異源多倍體).,Chromosome number is meaningful in taxonomy. Even in a same taxon, the chromosome number might be varied in different populations.The chromosome numbers of angiosperms range from 2n = 4 (Asteraceae 菊科的某些種) to 2n = ca. 250 (Crassulaceae景天科的燈籠草)Ophioglossaceae (瓶爾小草科) and Polypodiaceae (水龍骨科) show unusually high chromosome numbers, the highest being 2n = 1260 in Ophioglossum reticulatum.,Chromosome number,Chromosome structure,Question.,Why the polyploid is important in the speciation?Whats the advantages of polyploid?How to evaluate the phylogeny between population by chromosomes?,Anatomy解剖學,Leaf cross sections,Stoma morphology,Stoma morphology,vs.,vs.,Palynology 孢粉學,Palynology is the study of pollen and spores. The outer layer of pollen and spores often contains a special compound, sporopollenin, which resists degradation by various chemicals, bacteria, and fungi and contributes to the long persistence of pollen in sediments. Pollen, therefore, has been important in paleobotanical (古植物) studies.,The two most important structural features of pollen grains are the apertures (孔) and the outer wall. The surface of the pollen wall, or exine (外壁), may be more or less smooth, as in many wind-pollinated species, or variously sculptured by spines, striations, reticulating ridges, knobs, and other features. These surface projections, which attach the pollen grain to animal pollinators, are a rich source of systematic characters.,Pollen structure, variability, and methods of study,Strobilanthes rankanensis,S. fauriei,Molecular Biology分子生物學,Progressing of the molecular tools,Inorganic molecules = Chemotaxonomy (化學分類學).Proteins （蛋白質）： Amino acid sequencing（氨基酸定序） 、 Isozyme electrophoresis（同功酶電泳）.Restriction fragment length polymorphism ( RFLP ): DNA + Restriction enzyme.PCR（Polymerase Chain Reaction；聚合酶連鎖反應）-based dominant marker (顯性遺傳標記) ：RAPD (Random Amplified Polymorphic DNA)、AFLP (Amplified Fragment Length Polymorphism)、ISSR (Inter-Simple Sequence Repeat)、 MicrosatelliteDNA sequencing （DNA定序）.,(D. J. Crawford. 2000. Plant macromolecular systematics in the past 50 years: one view. Taxon 49: 479-501.),Chemotaxonomy,Common used for economic or medical plants, especially for the microorganisms.,/fig/0701060904003.png,RAPD,/content/vol280/issue21/images/large/zbc0220505800001.jpeg,Sequence alignment,Parsimony analysis,1956 bps x 33 OTUs Total 3768 treesTree length = 212CI = 0.84, 南投 嘉義至屏東 台東,Summary,Traditional procedures are not suitable in the present taxonomic studies, because the remaining problems usually are complex. Its better that m