1. 樹木學及實習 Dendrology and Practice 植物型態 Plant Morphology
國立臺灣大學 森林環境暨資源學系 鍾國芳 (Kuo-Fang Chung)
School of Forestry and Resource Conservation, National Taiwan University
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2. How to classify plants? How do we put different plants in groups?
What is species? How to recognition and delimitate species? (物種的描述)
Classification (分門別類)

3. What is a plant species?
Since the ancient Greek, a species, such as particular species of oak, was considered the manifestation of a unique, unchangeable essence (本質). Any deviations from this essence were regarded as unimportant.
Darwin’s “Origin of Species”
Darwin’s observations and inferences leading to the Evolution theories
Superfecundity
Variation
Ernst Mayr “One long argument” p72
Over many generations,
evolution & speciation
Steady state of natural populations
Differential survival (natural selection)
Struggle for existence
Limited resource
Heritability of variation

4. Modern corn—a miracle of artificial selection (人擇)

5. What should we do with the species problems?
Different groups of organisms differ widely in morphology, genes, ecology, geographic distribution, pollination ……
The lack of consensus on species definition can partly attribute to idiosyncratic nature of the biodiversity.
Each lineage is unique.
Morphology is the most accessible source of data about evolutionary relationship and is the only basis for the easy recognition of most species today.
Taxa are hypotheses, open to repeat testing as new data or methods of analysis become available (e.g., DNA barcoding).

6. Darwin placed Linneaus scheme of classification within an evolutionary framework—Descent with modification
“… species are nested within genera, genera within families, and so forth because of a history of descent with modification within evolutionary lineages—“…the view that an arrangement (hierarchical taxonomic system) is only so far natural as it is genealogical (evolutionary)”

7. The importance of (organism) classification
Organizing knowledge of the natural world into a system aids communication and helps us to understand better the organisms that surround us and upon which we depend. ……. The basic function of words is that of naming (Lyons 1977), and in the human mind nothing really exists or can be communicated without a name.
Christenhusz et al. (2011) Preface to “Linear sequence, classification, synonymy, and bibliography of vascular plants: Lycophytes, ferns, gymnosperms and angiosperms” Phytotaxa 19: 4-6.

8. Classification: naming (命名), grouping (歸類), and naming the groups
Names:
Purposes of classification:
Easy to use
Stable
An aid to memory
Predictive
concise
The logic of classification:
Hierarchical, groups nested within groups

9. The hierarchical (階層) natural of classification— groups nested within groups

10. Classification: naming and grouping
Effective and efficient communication
Think about the amount of information a name carries!
The degree of confidence on a classification system.
Reducing the heterogeneity of a group of objects
Increase our understanding and ability to predict the characteristics of any one of the objects.
Scale, hierarchical
Purpose-driven (no single best classification)
Not a static, once-and-for-all activity
Anything can be classified, but modern biological classification is different because it involves evolutionary relationships.

11. 植物分類學 Plant Classification/Taxonomy/Systematics
Classification (分類學): classifying
Taxonomy (命名學): Naming (taxon/taxa: 分類群)
Systematics (系統分類學): classification + taxonomy + phylogenetics (親緣關係、譜系關係)
植物辨識 (plant identification)
野外工作、標本館、形態學
植物命名 (nomenclature, taxonomy)
植物命名法規 (International Code of Botanical Nomenclature)
分類文獻 (priority)
植物親緣關係的重建 (phylogenetics, systematics)
穩定且能反映物種演化的分類架構 (Classification)
Angiosperm Phylogeny Group Classification (APG III)

12. How to classify plants?
Hierarchical taxonomic system is so far natural only as it is genealogical (evolutionary)
How do we put different plants in groups?

13. How will you classify? Which plants should be classified as groups?

14. How will you classify? Which plants should be classified as groups?
Plant habit is important? (woody vs. herbaceous plants)

15. How will you classify? Which plants should be classified as groups?
Plant habit is important? (woody vs. herbaceous plants)
Leaf shape is more important? (elliptic vs. linear)

16. How will you classify? Which plants should be classified as groups?
Plant habit is important? (woody vs. herbaceous plants)
Leaf shape is more important? (elliptic vs. linear)
Number of petals is more important (5 vs. 4)

17. How will you classify? Which plants should be classified as groups?
Plant habit is important? (woody vs. herbaceous plants)
Leaf shape is more important? (elliptic vs. linear)
Number of petals is more important (5 vs. 4)
Color of petals is more important (yellow vs. red)

18. How will you classify? Which plants should be classified as groups?
Plant habit is important? (woody vs. herbaceous plants)
Leaf shape is more important? (elliptic vs. linear)
Number of petals is more important (5 vs. 4)
Color of petals is more important (yellow vs. red)
Number of stamen is more important (5 vs. 4 vs. 2)

19. How will you classify? Which plants should be classified as groups?
Plant habit is important? (woody vs. herbaceous plants)
Leaf shape is more important? (elliptic vs. linear)
Number of petals is more important (5 vs. 4)
Color of petals is more important (yellow vs. red)
Number of stamen is more important (5 vs. 4 vs. 2)
Pollen surface is more important (smooth vs. spiny)

20. How will you classify? Which plants should be classified as groups?
Why should I believe you?
A deeper understanding of morphological characters
developmental, ontongenetic studies

21. The tradition of taxonomy……
“Young taxonomists are trained like performing monkeys, almost wholly by imitation, and that only in the rarest cases are they given any instruction in taxonomy theory” —Cain (1959) “…… because of the subjective nature of the problem, it is difficult to lay down any hard and fast procedure for attaining satisfactory results……” —Mayr, Linsley, and Usinger (1953)

22. Giants in plant taxonomy and their classification systems
Carolus Linnaeus (L.) ( )
Species plantarum (1753), starting point of plant taxonomy
de Jussieu
Genera plantarum (1789)—the idea of family
Augustin Pyramus de Candolle (DC.)
Prodromus systematis naturalis regni vegetabilis ( )
George Bentham and Joseph D. Hooker
Genera plantarum ( )

23. Giants in plant taxonomy and their classification systems (cont.)
Engler and Prantl—Die Naturlichen Pflanzenfamilien ( )
C. E. Bessey—The Essentials of Botany (1884)
J. Hutchinson—The Families of Flowering Plants (1973)
A. Takhtajan—Outline of the Classification of Flowering Plants (1980)
A. Croquist—An Integrated System of Classification of Flowering Plants (1981)
Angiosperm Phylogeny Group (1998- )
Hopefully, from now on, this is the only system we have to remember and follow!

24. 分類學原理 (Principles of Classification)
How to classify plants? How do we put different plants in groups?
By comparing characters possessed by different plants and then placing them in groups, guided by trained intuition, almost by instinct, taxonomy is largely still practicing this way (～1960’s)
By calculating the overall similarity of all (as many as possible) characters that you can observed—phenetics (數值分類學/相似性分類學) (1960’s～)
By tracking the transformation of character state series and find the shortest possible trajectory (among the numerous possibilities) of all character transformations—cladistics [支序(分類)學] (1960’s～)

25. Numerical Phenetics (numerical taxonomy) 數值分類、表形學派
P.H.A. Sneath (bacteriologists) and R.R. Sokal (biostatistist, anthropologist)
Searching for objective classification based on purely numerical (phenetic), overall similarity among taxa.
Hope to recover history but did not intend to reconstruct phylogenetic relationship.

26. 特徵 (character) 與特徵狀態 (character state)
莖: 木本 (woody) vs. 草本 (herbaceous)
葉形: 橢圓形 (elliptic) vs. 線形 (linear)
花瓣數目: 5 vs. 4
花瓣顏色: 黃 (yellow) vs. 紅 (red)
雄蕊數目: 5 vs. 4. vs. 2
花粉表面: 平滑 (smooth) vs. 有刺 (spiny)

27. 特徵資料矩陣 Character data matrix
莖: 木本 (woody) vs. 草本 (herbaceous)
葉形: 橢圓形 (elliptic) vs. 線形 (linear)
花瓣數目: 5 vs. 4
花瓣顏色: 黃 (yellow) vs. 紅 (red)
雄蕊數目: 5 vs. 4. vs. 2
花粉表面: 平滑 (smooth) vs. 有刺 (spiny) 葉形 莖
花瓣數目
花瓣顏色
雄蕊數目
花粉表面
X. alba E W 5 R 4 Sp
X. lutea H Sm
X. nigra L Y 2
X. purpurea
X. rubens
X. elliptica

28. From data matrix to distance table葉形 莖
花瓣數目
花瓣顏色
雄蕊數目
花粉表面
A- X. alba E W 5 R 4 Sp
B- X. lutea H Sm
C- X. nigra L Y 2
D- X. purpurea
E- X. rubens
F- X. elliptica
Calculate the differences between two plants
X. alba: E W 5 R 4 Sp
X. lutea:E H 5 R 4 Sm
difference = 2
X: nigra:L W 4 Y 2 Sm
difference = 5
Fill the matrix A B C D E F 2 5 4 3 6 1

29. Unweighted Pair Group Method with Arithmatic Mean (UPGMA) (無權重群組算數平均法)
clustering the pair of plants (operational taxonomic units/OTUs) with the smallest distance (and divided by 2)
re-calculating the distance matrix
Dist (A,CD) = [(DistAC + DistAD)]/2 =[(5+4)/2] = 4.5
Dist (B,CD) = [(DistBC + DistBD)]/2 =[(5+6)/2] = 5.5
Dist (CD,E) = [(DistCE + DistDE)]/2 =[(1+2)/2] = 1.5
Dist (CD,F) = [(DistCF + DistDF)/2] = =[(3+4)/2] = 3.5 A B C D E F 2 5 4 3 6 1 C D
0.5 A B CD E F 2
4.5 4 3
5.5
1.5
3.5

30. Unweighted Pair Group Method with Arithmatic Mean (UPGMA)
re-clustering the pair of OTUs with the smallest distance
re-calculating the distance matrix
Dist(A,CDE)=[(DistA,CD)+(DistAE)]/2 =[(4.5+4)/2]=4.25
Dist (B,CDE) =[(DistB.CD)+(DistBE)]/2 =[(5.5+4)/2]=4.75
Dist (CDE,F) =[(DistCD.F)+(DistEF)]/2 =[(3.5+3)/2]=3.25 A B CD E F 2
4.5 4 3
5.5
1.5
3.5 CD E
0.75
1.5/2 = 0.75 A B
CDE F 2
4.25 3
4.75
3.25

31. Unweighted Pair Group Method with Arithmatic Mean (UPGMA)
re-clustering the pair of OTUs with the smallest distance
re-calculating the distance matrix
Dist(AB,CDE)=[(DistA,CDE)+(DistB.CDE)]/2 =[( )/2]=4.5
Dist (AB,F) =[(DistAF)+(DistBF)]/2 =[(3+3)/2]=3 A B
CDE F 2
4.25 3
4.75
3.25
2/2 = 1 A B 1 AB
CDE F
4.5 3
3.25

32. Unweighted Pair Group Method with Arithmatic Mean (UPGMA)
re-clustering the pair of OTUs with the smallest distance
re-calculating the distance matrix
Dist(ABF,CDE)=[(DistAB,CDE)+(DistF.CDE)]/2 =[( )/2]=3.875 AB
CDE F
4.5 3
3.25
3/2 = 1.5 AB F 1
ABF
CDE
3.875
C- X. nigra
D- X. purpurea
E- X rubens
F- X. elliptica
A- X. alba
B- X. lutea
0.0
0.5
1.0
1.5
2.0
3.875/2 =

33. 0.0 0.5 1.0 1.5 2.0 C- X. nigra D- X. purpurea E- X rubens
F- X. elliptica
A- X. alba
B- X. lutea
0.0
0.5
1.0
1.5
2.0

34. Advantages and pitfalls of phenetic approaches
Easy to operate
Computationally fast
Most alike ≠ most closely related (parallel and convergent evolution; e.g. Euphorbia vs. cacti)
Aiming for objective, but difficult to achieve
Selection of characters
Phenetic approaches are now widely used in ecology

36. Phylogenetic Systematics/Cladistics (支序學)
Willi Hennig (German entomologist)
Hennig recognized the logical consequences of evolutionary constraint—new structure and functions resulting from modification of existing ones.
Evolution is recognized as changes from a preexisting ancestral (primitive, plesiomorphic) condition to a new, derived (advanced, apomorphic) condition.
Reconstructing history of lineage diversification (cladogensis) by tracing the character transformation

37. The concept of Characters and Homology (特徵與同源性)
Homology (同源性): character shared by a group of organisms or taxa due to inheritance from a common ancestor.
Homoplasy (同塑性、非同源相似性): character that appears similar among a group of organism or taxa, but the similarity is due to parallel or convergent evolution rather than inheritance from a common ancestor (wings of bats, birds, flying squirrel, butterflies, etc. .

38. Homoplasy
Convergent evolution (趨同演化): evolution of similar features independent in different evolutionary lineages, usually from different antecedent features or by different development pathways. (e.g., 仙人 掌的刺 vs. 小檗的刺；鳥、蝙蝠、翼手龍的翅膀)
Parallel evolution (平行演化): the evolution of similar or identical features independently in related lineage, though usually to be based on similar modification of the same developmental pathway. (e.g., 寄 生或腐生植物在不同分類群獨立演化)

39. Cladogram (phylogenetic tree)

40. cladogram (支序圖): depicting relationships only
diagonal lines
perpendicular lines
Unrooted tree (無根樹)
phylogram (譜系圖):
relationships with branch lengths

41. Anatomy of Cladistics 1. Monophyletic (Holo-) group (單系/源群)
Grouping (clade 支序群) includes all descendant taxa and their common ancestor
All taxonomic groups (taxa) should be monophyletic.

42. Paraphyletic group (並/側系群)
Grouping includes an ancestor and some but not all of its descendents

43. Paraphyletic group (並/側系群)
Grouping includes an ancestor and some but not all of its descendents

44. Monophyly and paraphyly
Grouping includes an ancestor and some but not all of its descendents
The problem with ranked taxonomy!

45. Angiosperm phylogeny

46. Polyphyletic group (多源群)
Grouping includes taxa that trace back through two or more separate ancestors before reaching a common ancestor.

47. Chirita 唇柱苣苔屬, a polyphyletic taxon

48. Cladogram (支序樹), ingroup (內群), sister group (姊妹群), outgroup (外群)
Ingroup: focal set of taxa within a monophyletic group.
Sister group: outgroup that most close to the ingroup
Outgroup is use to root the tree and provide an ancestor-descendent orientation of characters.
Additional
outgroups
Sister
Ingroups
X Y Z

49. 葉形 莖
花瓣數目
花瓣顏色
雄蕊數目
花粉表面
X. alba E W 5 R 4 Sp
X. Lutea H Sm
X. Nigra L Y 2
X. Purpurea
X. Rubens
X. elliptica
Outgroup
E↔L W ↔ H ↔ Y ↔ R → 4 → 2 Sp ↔ Sm

50. 1 2 3 4 5 6
X. alba
X. lutea
X. nigra
X. purpurea
X. rubens
Outgroup

51. homoplasious character1 2 3 4 5 6
X. alba
X. lutea
X. nigra
X. purpurea
X. rubens
Outgroup
homoplasious character

52. Tree length (樹長) = 8

53. Tree length (樹長) = 8
Tree length (樹長) = 11

54. Parsimony methods The goal is to find the most parsimonious tree (MP)
The criteria are to calculate the changes of character states, i.e. the evolutionary steps
First, we have to know the way to evaluate a given tree

55. Molecular (DNA) data
Molecular data are particular suitable for cladistic analyses
The number of characters is theoretically unlimited
Everyone interprets the data in the same way
Easier to assess homology
Less subject to selection; independent of the morphological data and thus can be used to test previous taxonomic hypotheses.
Better in keeping the signature of the evolutionary history of organisms

56. Character optimization (特徵最佳化)
Sp_1: TCAGACGATTGTCAGACCATTG
Sp_2: TCAGTCGACTGTCAAACCATTG
Sp_3: TCGGTCAATTGTCAAACGATTG
Sp_4: TCGGTCAATTGTCAAACGATTG
Sp_1 is outgroup. Three different tree topologies.

57. Character optimization: character 3
Sp_1 TCAGACGATTGTCAGACCATTG
Sp_2 TCAGTCGACTGTCAAACCATTG
Sp_3 TCGGTCAATTGTCAAACGATTG
Sp_4 TCGGTCAATTGTCAAACGATTG
Step=2
Step=1
A→G
G→A 1 2 3 A G
Character optimization: character 3

58. Sp_1 TCAGACGATTGTCAGACCATTG Sp_2 TCAGTCGACTGTCAAACCATTG
Sp_1 TCAGACGATTGTCAGACCATTG
Sp_2 TCAGTCGACTGTCAAACCATTG
Sp_3 TCGGTCAATTGTCAAACGATTG
Sp_4 TCGGTCAATTGTCAAACGATTG
Unrooted trees
A→G
G →A A G
Step=1
Step=2
A→G
A←G

59. Character optimization: character 7
Sp_1 TCAGACGATTGTCAGACCATTG
Sp_2 TCAGTCGACTGTCAAACCATTG
Sp_3 TCGGTCAATTGTCAAACGATTG
Sp_4 TCGGTCAATTGTCAAACGATTG G A G A G A
Character optimization: character 7
Step=2
Step=2
Step=1 1 2 3 G A
G→A
Step=2
A→G 1

60. Most parsimonious tree1 2 3
Step=6
Step=9
Step=9
Most parsimonious tree

61. How many trees out there are we dealing with?
3 OTUs
Root

62. Unrooted trees
3 trees
Rooted trees
15 trees
Four taxa

63. How many trees we need to search?
The number of unrooted trees:
The number of rooted trees:

64. All possible unrooted tree number
Taxon number
All possible unrooted tree number 3 1 4 5 15 6
105 7
945 8
10,395 9
135,135 10
2,027,025 11
34,459,425 12
654,729,075 13
13,749,310,575 14
316,234,143,225
7,905,853,580,625 16
213,458,046,676,875 17
6,190,283,353,629,375 18
191,898,783,962,510,625 19
6,332,659,870,762,850,625 20
221,643,095,476,699,771,875 21
8,200,794,532,637,891,559,375 22
319,830,986,772,877,770,815,625 23
13,113,070,457,687,988,603,440,625 24
563,862,029,680,583,509,947,946,875 25
25,373,791,335,626,257,947,657,609,375 >1029 -
etc.

65. In real world, how many trees can we search?
Say a computer can evaluate 106 trees per second.
If we want to evaluate all of the trees for 25 taxa, we will need x = 1029/106/60/60/24/365 = 3.17x1015 >三千兆年
Many ways to get-by this problems
faster computer, software……..

66. Phenetics vs. Cladistics
Phentics: Algorithm—by defining a specific sequence of steps that leads to the determination of tree (UPGMA, NJ)—fast and you get one tree
Cladistics: Optimality criteria—by defining a (optimal) criterion for comparing alternative phylogenies to one another and deciding which is better (parsimony, maximum likelihood, Bayesian)—slow and you can get many trees

67. Which method is better in reflecting true evolutionary relationship?
Phenogram-UPGMA
Maximum Parsimony Tree

68. Angiosperm families with nodular nitrogen-fixing symbioses and the frequency of this association in each family
Prokaryote
Angiosperm family [Genera having root nodules/Approx. total genera] Bold, family/genus in Taiwan
Rhizobiaceae
Fabaceae 豆科 [530/730]
Cannabaceae 大麻科 (Trema) [1/11]
Frankia (Actinorhizal plants, 放線根瘤植物)
Betulaceae (Alnus) 樺木科 [1/6]
Cassuarinacedae 木麻黃科 (Allocasuarina, Casuarina, Gymnostoma) [4/4]
Elaeagnaceae 胡頹子科 (Elaeagnus, Hippophae, Shepherdia) [3/3]
Myricaceae 楊梅科 (Morella, Myrica, Comptonia) [2/3]
Rhamnaceae 鼠李科 (Ceanothus, Colletia, Discaria, Kentrothamnus, Retanilla, Trevoa) [7/55]
Rosaceae 薔薇科 (Cercocarpus, Chamaebatia , Purshia, Dryas) [5/100]
Datiscaceae 疣柱花科 (Datisca) [1/1]
Coriariacaee 馬桑科 (Coriaria) [1/1]

69. fabids 豆類 Cucurbitales 瓜目 Nitrogen-fixing clade Fagales 殼斗目
Rosales 薔薇目
Fabales 豆目
Celastrales 衛矛目
Oxalidales 酢醬草目
Malpighiales 黃褥花目
Zygophyllales 蒺藜目
Nitrogen-fixing clade
維管束植物約400個科中，僅有分屬於10個科的少數植物在根瘤與固氮細菌共生具固氮的能力，這10個科在APG的分類中，分屬於瓜目、殼斗目、薔薇目及豆目。 These orders share a genetic predisposition for nitrogen fixation via root nodules, and this condition represents a possible synapomorphy for this group of four orders.

70. 版權聲明 3 4 6 7 9 頁碼 作品 版權標示 作者/來源 製表：國立臺灣大學 鍾國芳
參考來源：Charles Darwin, On the Origin of Species by Natural Selection, 1859. 4
Wikimedia Commons / Author: John Doebley
。本作品採創用CC 「姓名標示」3.0未本地化授權釋出。 6
Wikimedia Commons / illustration by Charles Darwin, SVG file by Inductiveload
。本作品屬公共領域之著作。
“…the view that an arrangement is only so far natural as it is genealogical”
Charles Darwin, On the Origin of Species by Natural Selection, 本作品屬公共領域之著作。 7
Organizing knowledge …be communicated without a name.
Christenhusz et al. (2011) Preface to “Linear sequence, classification, synonymy, and bibliography of vascular plants: Lycophytes, ferns, gymnosperms and angiosperms” Phytotaxa 19: 4-6.
瀏覽日期：2014/08/23。本作品依據著作權法第 46、52、65 條合理使用。 9
圖表繪製：國立臺灣大學 鍾國芳

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15, 16 17 18 19 20

72. 版權聲明 21 25、26、27、49、50、67 27 28 頁碼 作品 版權標示 作者/來源
“Young taxonomists…in taxonomy theory”
Cain, A.J. (1959) The post-Linnaean development of taxonomy. Proceedings of the Linnean Society, London, 170, 234–244.本作品依據著作權法第 46、52、65 條合理使用。
“because of the subjective nature …results…”
Mayr, Ernst, Linsley, E. Gorton and Usinger, Robert L Methods and Principles of Systematic Zoology. p. 168; also pp. 176–177. McGraw-Hill. 本作品依據著作權法第 46、52、65 條合理使用。
25、26、27、49、50、67
繪製：國立臺灣大學 鍾國芳 27 28

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Wikimedia Commons / Author: Petter Bøckman
。本作品屬公共領域之著作。 40
繪製：國立臺灣大學 鍾國芳
41、42、46
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繪製：國立臺灣大學 鍾國芳 61 62 64 67

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繪製：國立臺灣大學 鍾國芳