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Plant taxonomy (植物分類学)

Mount Usu / Sarobetsu post-mined peatland
From left: Crater basin in 1986 and 2006. Cottongrass / Daylily

[scientific name, synonym, books , specimen, plant morphology, plant anatomy]

When I was a high school student, I wanted to be a plant taxonomist. But now ... That is why this page is made.

(Mayr et al. 1953)

The developmental stages of taxonomy
1. α-taxonomy (analytical, flora)

≈ descriptive taxonomy, typological taxonomy, and faunistic or floristic taxonomy

2. β-taxonomy (classificated)

≈ phylogenetic taxonomy, phylogeny, systematics

3. γ-taxonomy (biosystematic)

≈ iosystematics, evolution

[History of natural sciences]

History of taxonomy (分類学史)

Prior to Linnaeus
Aristoteles BC384-BC322, "Historia Animalium (動物誌)"

Enaima (有血類) ≈ vertebrates and Anaima (無血類) ≈ invertebrates

Theophrastes BC372-BC288 or BC370-285

"Historia Plantarum (植物誌)", "De cauris plantarum (植物の起源)"
introduced the concept of plant taxonomy

plant = tree + shrub + under-shrub or semi-shrub + herb
tree = clearly distinguished between stem and branch
↔ shrub-herb = unclear difference between them

Pliny AD 23-79, Rome: Geology - "Natural history (自然誌)"

mints, legumes, umbels, etc. → classified based on human use

e.g., flavor/smell, medicine, food, bean = artificial taxonomy

→ roughly consistent with family (科) in the modern taxonomy

Dioscorides Ca. 50: artificial taxonomy
The Dark Age
the effects of the Christian faith = deny evolution and speciation → mainly progress of (artificial) morphological taxonomy
Albert Magnus 1193?-1280, Germany, "De vegetabilibus (植物について)"

plant = 1) leafy plant (a. monocotyledon, b. dicotyledon), 2) leafless plant (= cryptogam)

1400-1700: The ages of medicinal herbs

fashion of folk remedy or therapy

Brunfels O 1464-1534
Bock H 1498-1554
Fuchs L 1501-1566
Caesalpinus A 1519-1603: 1583 "De plantis libri"
Bauhin G 1560-1624
Jung J 1587-1657
Pitton de Tourefort J 1656-1708: "Methodus plantarum nova (1682)"

Plants: described approximately 18,000 species
I Herbae (herbs)

A: Imperfectae (flowerless)
B: Perfectae (flower)

a: Dicotyledons
b: Monocotyledons

II Arbores (trees)

A: Monocotyledons
B: Dicotyledons

From Linnaeus to Darwin
Carl von Linnaeus (Linné) 1707-1778, Sweden, natural history
Bufforn (1707-1788)

Taxonomy + Morphology + Ecological technique, habit and competition

Darwin E 1731-1802, Engl. (the grandfather of Darwin C)


Humboldt, Alexander von 1769.9.14 -1859.5.6 (Gr): Naturalist

"Essai sur la geographie des plantes (1805)"
"Ansichten der Natur 2 vols (1808)"
"Voyage aux regions equinoxiales du nouveau continent 30 vols (1811-26)"
"Kosmos (1845-62)"

Lamarck JB 1744-1829, France: naturalist

considering hierarchical evolution - related to taxonomical order

1789 de Jussieu, Antoine Laurent: de Jussieu system
1813 de Candolle, Anguste Pyramus: de Candolle system
1838 Endlicher, Stephan Ladislaus: Endlicher system
1843 Brongniart, Adolphe-Théodore: Brongniart system
→ the classification keys are different among these, because of criteria are different
von Baer 1792-1876
Haeckel Ernst Heinrich 1834-1919: phylogenetic taxonomy - dendrogram

fundamental law of biogenesis or recapitulation theory

1879-1962 → classical syllabi of plant taxa
1892 Engler's syllabus

Species concept (種概念)

Syngameon: syngameon and biological species are distinguished by the differences in the innter structures

Ex. Pinus, Quercus, Geum, Iris → the West Coast of USA: syngameon is more common than biological species (Grant 1981)
Antirirhium majus × A. glutinosum (snap dragon flower)
Rhinanthus: accidentaly becoming snap dragon flower
Diogitalia: abruptly developing spur
→ macro-recombination

Relationships between biological and taxonomical species
Table. Biological species vs taxonomic species
    Biological Sibling  Semi-    Micro-  → evolutionary
    species    species  species  species
    Taxonomic           ×       ×      → no time scale
Sibling species (同形異種): regarded as sibling species complex on taxonomy

Ex. Drosphila pseudoobscura, D. persimilis
→ they are homomorphic but do not corss under natural conditions
a slight morphological difference in male petasma when observed in detail
→ impossible to identify them only based on morphological species (形態種) ↔ differences in physiological and genetical characteristics
Grand (1981) proposed that sibling species complex is treated as one taxonomic species

Allopolyploidy (異質倍数体): AA/BB → AABB - factors determining discontinuity (not identified by the common maneuver)

Taxon (pl. taxa) (タクソン, 分類群)


The fundamental concept of taxonomy

Taxonomic rank (分類階級)

Domain (ドメイン): = formerly empire or superkingdom


Kingdom (regnum, regna (pl.), 界)
Phylum (phyla (pl.) 門): nucleus, chlorophyll, mode of body plan, etc = formerly division (prior to 1993)

→ five kingdoms proposed by Whittaker (ホイッタカー)

Class (網): there is no exact agreement on the criteria of identical characteristics between the classes

Ex. Class Dinophyta (鞭毛植物): Desmophyceae and Dinophyceae are established by the locations, directions and flagella of canaliform structure on cell wall
Rhodophyta (紅色植物): Protoflorideae and Florideae are established by cell tethering

Order (ordo, ordes (pl.) 目): natural taxonomic group in many cases, as compared with class
Family (familia, familiae (pl.) 科): roughly consisting of natural groups
Tribe (連): below ranks with names derived from family. Family consists of subfamily andtribe when the discontinuous morphological changes are large and small, respectively, between the subgroups of species, as a practical problem
Genus, genera (pl.) (属): species name is determined by genus name due to the binomial nomenclature, although the standard unit is species on taxnomy
Section (節): summarizing species bewteen genus and species if needed
Species (): the standard unit for biological taxonomy

Macro-evolution (大進化) →→ Micro-evolution (小進化)
Kingdom - Phylum - Class - Order - Family - Genus - Species

Macro-evolution: long-term

body plan, micro-organism, reproductive organ, alternation of nuclear phases, alternation of generation → important character for clarifying macro-evolution

Micro-evolution: short-term at species or lower level

[ Mount Koma { preparing specimen | floral diagram | floral formula | references ]

Specimen (標本)

An individual or a part of plant(s), used for measuring the properties of the species for long time
Perfect specimen (完全標本)
A specimen keeps the most of all characteristics of the species, i.e., roots, stems, leaves, and flowers or fruits
Table 1. Unanticipated, post hoc functions of herbarium specimens. See Appendix S1 for an extended version that includes bibliography of published studies that validate these applications, when available (Heberling & Isaac 2017).
Specimen use: Description of potential applications
Genetics: genetic diff erences among species, populations, and individuals
Interspecific variation:

archival DNA for taxonomic identifi cation (DNA barcoding), molecular systematics, and evolutionary biology

Genotypic variation:

"Gene bank" for measuring variation within and among population across species' ranges and through time
archived propagules ("seed vault") for "resurrection" studies

Functional trait ecophysiology: intraspecifi c phenotypic shifts through time, space and across environmental gradients

plant height
leaf morphometrics (area, thickness, leaf mass per area, shape, dissection, toothiness)
leaf anatomy (stomatal, trichome, and vein densities)
belowground anatomy and morphology

Tissue chemistry:

nutrient chemistry (leaf N, C, P)
stable isotopes (Δ13C, δ13C, δ15N, δ18O)
deuterium isotopomer ratios (carbon metabolism proxy)
bioaccumulation or other eff ects of natural chemicals or anthropogenic pollutants (heavy metals, N deposition, particulates, smog, ozone)
protein, fatty acid, and amino acid composition
secondary metabolites in roots, leaves, or seeds

Reproductive biology:

flower or fruit number, morphology, size, anatomy
pollen transport networks


flowering time
leaf-out time


insect damage
effects of overabundant, large herbivores


disease presence and damage


taxonomic or genotypic diversity of mycorrhizal fungi or bacterial symbionts in rhizosphere and roots
endophyte presence and taxonomy

Nontarget specimen research: utilization of specimens preserved unintentionally with target collection originally of interest
Soil science:

soil preserved with specimen roots as source of edaphic or belowground microbial information through space and time

Invertebrate zoology:

insects or other organisms pressed with leaves for understanding plant-insect interactions, insect taxonomy, and invasion ecology

[ checklist ]

Specimens collected from Mount Koma

Specimens stored in the Hokkaido University Museum (SAPS)

Chimaphila umbellata (L.) W. Barton Drosera rotundifolia L. Campanula lasiocarpa Cham.
Chimaphila Drosera Campanula
Collected from a rocky bare land at 550 m elevation on the southwest slope of Mount Koma on August 3 2000. The species were distributed patchily. The capsules were developed. In an gravel area at 850 m elevation on the SW slope on August 13 2000. At 850 m elevation on the SW slope on August 3 2000.

Scale bar = 2 cm

Preparing specimen (標本作成法)

Objectives of preparing plant specimen
  • identifying the plant
  • checking plant characteristics and variations, including seasonal variations
  • understanding habitats and their diversity
  • type specimen for taxonomy
  • voucher (research proof)
1. Initial preparations
2. Pressing and drying
3. Identification
4. Labeling
5. Mounting
Specimen labels (標本ラベル)