Taxonomy

Systematics

s.l. - “Systematics is the scientific study of the kinds and diversity of organisms and of any and all relationships among them” G.G. Simpson (1961)

s.s. – more or less equal to taxonomy

Taxonomy

Classification

Identification

Description

Nomenclature

Need for Classification

300,000 + or - spp. of plants

1.5 million + spp. of organisms

need for typological concepts (mental image)

Taxonomic Hierarchy

Distinction of taxa based on discontinuities of variation

Gaps are the result of extinction -- can only be bridged by the fossil record

Rank of taxa -- Judd, p. 5; Stace, p. 9 -- species as fundamental unit

Box in box "view of classification from above" -- Stace p. 11

Dendrogram "view of classification from the side" -- Stace p. 10

Characteristic endings denote rank in some cases -ales for order -aceae for family (exceptions to uniform family endings -- Leguminosae, Compositae, Umbelliferae, Guttiferae, Labiatae, Gramineae, Cruciferae, Palmae)

Names of higher categories – based on a shared feature e.g., angiosperms vs based on types, e.g., Magnoliophyta, cf. Judd, p. 5.

Kinds of Classification Systems

Artificial

Based on one or a few charactrers, e.g. habit or numbers of sexual parts (stamens and pistils)

Natural

According to Stace = phenetic = general purpose - high predictivity - multivariate approach - equal weight for each of many characters - weighting of characters or choice of diagnostic characters is done a posteriori (in light of experience) rather than a priori (according to basic assumption or deduction)

Phylogenetic

= phyletic (=special purpose classification according to Stace but cf. p. 14) - reflects only evolutionary pathways – may be less predictive than phenetic systems

Judd et al., p. 3, “…systematics is linked directly and centrally to the study of evolution in general, from the study of fossils to the study of genetic changes in local populations.”

A phylogenetic tree (phylogram) presents hypotheses bearing on the evolutionary relationships of the taxa (sing. – taxon) included, i.e. it presents a hypothesis of the evolutionary pathway leading to the origin of these taxa. Details related to the generation of phylograms will be discussed later (Judd, Chapter 2).

In Plant systematics: a phylogenetic approach, families and higher categories are generally formally recognized only if they are judged to be monophyletic, i.e. include all descendents of a common ancestor. Another simple way to identify monophyletic groups in a phylogram is that they can be “pruned” from the “tree” with a single snip (Figure 1.2, Judd, p. 4). For purposes of discussion or where no alternative formal name has yet been proposed, names of groups that are judged non-monophyletic by the authors are placed in “quotation marks.”

For clarification of the “Plants” covered by the text (Tracheophytes - aka vascular plants), see Judd, p. 2.

Show examples of mounted specimens

Refer to handout with example labels

Label elements

Genus and species name (not required in this course)

Family Name

Important information not discernable in preserved specimen, e.g. habit, size, distinctive odors, color of flowers, habitat

Location information - must include general and specific locality information sufficient to allow a third party (traveling from any location in the world) to relocate the population from which the specimen was collected

Collector’s Name

Collection Number

Collection Date

Herbaria – What are they and how do you find them? - Index Herbariorum

Utility of herbarium specimens

Document any and all kinds of research (voucher specimens)

Indicate the presence of a particular species at a particular place and time

Location data invaluable to systematic research

Conservation angle

Vegetation studies

Search for medicinal compounds – tie in with “predictivity”

Document biodiversity

Direct source of data for systematic and evolutionary studies

Potential source of materials for systematic research

Tissue fragments

Pollen

DNA, etc.

Collection Methods

Numbering

Notebook

Pruning shears, sampling of large plants

Plastic Bags

Labels

The Plant Press

Frame pieces

Spacers, blotters

Newspaper, keeping records

Preservation

Methods of drying

Special problems

Succulents

Thick, hard tissues, etc.

The Development of Plant Taxonomy

Early Artificial Systems

Folk taxonomies

classification based on need - not influenced by science - rather precise vernacular names apply to families in some cases, e.g. grass and sedge or in other cases to taxa below the species level, e.g. broccoli, cauliflower, sprouts, cabbage, etc. for Brassica oleracea

Theophrastus c.375-285 B.C.

Outstanding Greek naturalist - student of Plato and Aristotle - became chief of Lyceum (univ.) at Athens

Historia Plantarum - 480 kinds of plants classified as trees, shrubs, undershrubs, and herbs

Dark ages - not much new and original

Age of Herbals

Sparked by the invention of the Gutenberg Press 1438 - at that time botany was largely synonymous with herbalism - the study of plants in relation to their value to man

Linnaeus' Artificial System

Carolus Linnaeus 1707-1778

Father of Taxonomic Botany

Born May 23, 1707 - Rashult, Sweden

While a student he published his first paper which dealt with sexuality of plants

Undertook an enumeration of plants in the Uppsala Botanical Garden and as the number of plants in the garden grew he became dissatisfied with earlier systems of classification and he began to classify plants according to his own sexual system

Published his Systema Naturae his "sexual system" 1735 - also classified all known animals and minerals

In Stockholm he became a prominent physician and was later appointed Professor of Medicine at Uppsala - this gave him the prestige and opportunity to teach botany which he did until 1775 when he was retired at his own request

He died January 10, 1778 after an illness of 2 years

Linnaeus' sexual system

24 classes based mainly on the number, union and length of stamens (Stace, p. 28)

The classes were subdivided into orders on the basis of the number of styles in each flower

Very artificial - related elements often fell in widely separated classes and some classes were very heterogeneous

Its strength was its simplicity - using the system the average botanist could not only classify but identify plants which were completely unknown to him

Species Plantarum 1753 Stace, p. 24

Starting point of botanical nomenclature

For each species the following was profided:

1. Generic name

2. Trivial name (specific epithet)

3. Specific phrase name (Latin polynomial which served as description of the species)

4. Abbreviated references to previous publications, location of specimens, and figures of species

5. Region where species is native

Natural Systems

With increased knowledge and understanding of the organography and functioning of plants came dissatisfaction with the artificiality of the sexual system of Linnaeus.

So-called natural systems were thought to reflect the "plan of the creator" - no implication of descent with modification or community of descent

Michel Adanson 1727-1806

Familles des Plantes 1763

Described 58 new families, 34 of which are still recognized under Adanson's names

Rejection of all artificial systems - description of taxa more or less equivalent to modern orders and families

Proposed multivariate system of classification in which he gave every character of the plant equal weight (father of numerical taxonomy?)

George Bentham 1800-1884

Wrote world monographs of the families Labiatae, Ericaceae, Polemoniaceae, Scrophulariaceae, Polygonaceae

Sir Joseph Dalton Hooker 1817-1911

Plant explorer, and plant geographer - Director of Royal Botanic Gardens, Kew

Bentham and Hooker

Genera Plantarum 1862-1883

Two-thirds written by Bentham

Each genus was studied anew

Classification was improved but still predicated on the dogma of immutability of species

The publication of Darwin's theories of evolution nearly coincided with the appearance of Bentham and Hooker's first volume -- Hooker then favored a complete reorganization of their classification, but Bentham refused because he did not yet accept Darwin's ideas, although he did so about a decade later

Bentham and Hooker's system was immediately adopted throughout the British Empire and in the U.S. -- the system is still retained by many British botanists and by British herbaria

QUOTE ALMIRA LINCOLN

Phylogenetic systems

Charles Darwin - 1809-1882 - origin of species - 1859

Gregor Mendel - 1822-1884 - laws of inheritance published 1866 - rediscovered 1900

Systems based on phylogeny - predicated on evolutionary theory- descent with modification - existing species are the products of evolutionary processes

Adolph Engler 1844-1930

Karl Prantl 1849-1893

Believed that evolutionary trends are always toward increasing complexity, not reduction - therefore, plants without petals always regarded as more primitive than plants with petals

Die natürlichen Pflanzenfamilien

Many volumes 1887-1915 - provided means of identification of all known plant genera from algae to seed plants on a world-wide basis - modern keys and illustrations provided

Considered existing angiosperms to be composed of many fragmentary lines of evolution

Groups with no perianth considered most primitive > sepals only > sepals and separate petals > sepals and coalescent petals

Ironwood, willows, birches > sandlewood, oaks > buttercups, roses, violets > primroses, cucurbits, daisies

Ovary position considered as secondary criteria

Charles E. Bessey 1845-1915

The first American to make a significant contribution to the knowledge of plant relationships

Besseyan system of 1915

Most realistic arrangement of plants up to that time

Presented a series of "dicta" or statements which he used to judge the primitiveness of plant groups - these provide as modified and expanded the theoretical basis for most current systems of classification

32 orders were recognized in his scheme - the sequence of presentation was determined by his dicta

He gave primary emphasis to ovary position, secondary emphasis to perianth features

Duration and Habit

Annual

Biennial

Perennial

Herb

Shrub

Tree

Vine

Liana

Succulent

Roots

Tap root

Fibrous root

Adventitious

Stems

Node

Internode

Axillary bud

Terminal Bud

Rhizomes

Stolon

Bulb

Tuber

Corm

Phyllotaxy

Alternate

Opposite

Whorled

Basal

Distichous

Decussate

Leaf Parts

Stipules

Leaflets

Petiole

Rachis

Leaf Composition

Simple

Compound

Pinnate

Palmate

Leaf Blade Shape

Needle-like

Awl-like

Linear

Lanceolate

Oblanceolate

Ovate

Obovate

Elliptical

Deltoid

Orbicular

Leaf Attachment

Sessile

Petiolate

Decurrent

Perfoliate

Sheathing

Cuneate

Leaf Apex

Acute

Acuminate

Obtuse

Mucronate

Truncate

Emarginate

Leaf Blade Base

Rounded

Truncated

Oblique

Cordate

Sagittate

Hastate

Leaf Margin

Entire

Serrate

Dentate

Crenate

Lobed

Divided

Pinnatifid

Ciliate

Leaf Surface

Glaucous

Glabrous

Glandular-punctate

Leaf Venation

Pinnate

Palmate

Parallel

Leaf Ptyxis

Revolute

Involute

Leaf Vernation

Imbricate

Valvate

Vestiture

Pubescent

Tomentose

Pilose

Hispid

Stellate

Glandular

Scabrous

Special Modifications

Tendrils

Scales

Phyllodes

Aug 2000

NOMENCLATURE

ICBN adopted at each IBC every 6 years - Berlin 1987

Latin binomial = generic term + specific epithet

Generic term may be taken from any source

Reflect botanical character - Trifolium, Cephalanthus

Commemorative - Dioscorea, Jeffersonia

Latinized form of common name - Tsuga, (Japanese) Ginkgo (Chinese)

Specific epithets from similar sources

Trifolium repens, T. virginicum, Asarum lewisii

Even derived from generic names e.g. Aureolaria pedicularia

Same specific name may be used in any number of genera

No latin binomial is complete without reference to the original author of the name, e.g. Trifolium repens L.

Priority of name is established by date of valid publication

Starting point for nomenclature of seed plants, ferns, liverworts, sphagnum mosses, lichens, most algae and the myxomycetes is Linnaeus' Species Plantarum 1753 - for the rest of the mosses Hedwig's Species Muscorum 1801 - Fungi Fries Systema Mycologicum (1821 - 1832)

International agreement can result in conservation of a generic or family name that otherwise lacks priority - criterion for this - general usage for over 50 years after publication

Authority modification and rank changes

Pedicularis mogollonica Greene

Pedicularis parryi Gray ssp. mogollonica (Greene) Carr

Associated Parts

Scape

Peduncle

Bract

Pedicel

Receptacle

Involucre

Nectary

Hypanthium

Perigynous zone

Epigynous zone

Fusion of Parts

Adnation

Coalescence

Connation

Perianth

-parts

Calyx

Sepals

Corolla

Petals

Tepals

-descriptive

Apetalous

Sympetalous

Apopetalous-

Synsepalous

Androecium

-parts

Stamen

Staminode

Filament

Anther

Locule - Cell

Connective

-descriptive

Monadelphous

Hypogynous

Perigynous

Epigynous

Gynoecium

-parts

Carpel

Pistil

Pistillode

Simple pistil

Compound pistil

Stigma

Style

Ovary

Superior ovary

Inferior ovary

Locule

Septum

Placenta

-descriptive

Apocarpous

Monocarpous

Syncarpous

Placentation

Parietal

Axile

Free central

Apical

Basal

Flower Types

Complete

Incomplete

Perfect – Bisexual-

Hermaphrodite

Imperfect – Unisexual

Carpellate-Pistillate

Sexual Expression ofTaxa

Monoecious

Dioecious

Synoecious

Flower Symmetry

Actinomorphic - Radial

Zygomorphic – Bilateral

Asymmetric

Inflorescence

Solitary

Indeterminate

(Racemose)

Determinate

(Cymose)

Spike

Raceme

Panicle

Catkin

Corymb

Umbel

Head

Cyme

Fruit Types

Accessory

Aggregate

Multiple

Fleshy

Berry

Drupe

Pome

Dry Indehiscent

Achene

Caryopsis

Samara

Schizocarp

Dry Dehiscent

Capsule

Follicle

Legume

Seeds

Aril

Ruminate Endosperm

Perisperm

Aug 2000

The Phylogenetic Approach - Phylogeny (Evolutionary history)

Divergence of lineages (illustrated as though observed during the process – Judd, p 10-11, Figs. 2.1-2.3.

Characters

Flower color, Stem structure, etc.

Character states

White, Red; Herbaceous, Woody, etc.

Derived characters

New characteristics relative to ancestral population, Red flowers, Woody stems, e.g.

Monophyletic group

An ancestor and all of its descendants

Synapomorphies

Shared derived characters (characters that have arisen in the ancestor of a group and are present in all of its members)

Determining Evolutionary History (Reconstructing past events)

Selection of characters – they must be heritable

Homology of characters – can’t compare apples and oranges

Judd et al. avoid any precise definition of homology but imply that homologous characters are specified by a common gene or set of genes such that mutation in these results in different character states of the homologous character

Recording and organizing observations on character states

Venn diagram (Judd, p. 12, Fig. 2.4A)

Network (Judd, p. 12, Fig. 2.4B

Matrix (taxon by character with character states defining clusters) (Judd, p. 12, Fig. 2.4C)

These are not phylogenies as no timeline is implied

Producing evolutionary trees (cladograms)

Rooting

Specifies the ancestral character states and causes subsequent changes to be polarized (given direction)

Effected by including one or more outgroups in the analysis. The necessary assumption is that members of the group under study (ingroup) are more similar to each other than they are to the outgroup (i.e., the outgroup separated from the ingroup lineage prior to diversification of the ingroup).

Does not change the length of the cladogram but will often dramatically affect the order of events and polarity of characters, as well as the general appearance of the tree.

Guiding principles

Ockham’s razor – guiding rule of simplicity in science that suggests it is unwise to create a hypothesis more complicated than necessary to account for the observed data

Parsimony – rule of simplicity following Ockham’s razor – the simplest explanation (shortest number of steps in a phylogeny) is the most desirable

Complicating factors in phylogenetic analyses

Homoplasy (evolutionary noise)

Parallelism – appearance of similar character states in unrelated organisms

Reversal – derived character state changes back to ancestral state

Hybridization – divergent lineages fuse into one – will not be reflected in a cladogram – phylogenetic analysis assumes that evolution can be diagrammed as a branching tree – hybridization produces a reticulated topography more like a macramé

Measurements of homoplasy for entire tree or individual characters

Consistency Index – number of character states (genetic switches) divided by the actual number of changes (tree length)

Retention Index – maximum length minus the actual length divided by the maximum length minus the minimum length [(Max-L)/(Max-Min)]

Measurements of homoplasy for parts of trees

Decay index – the number of extra steps required to produce a tree in which the branch in question collapses (next distal group is lost)

Bootstrap analysis – character states from an initial data matrix are randomly selected to fill each of at least 100 new matrices that are subsequently used to generate a minimum of 100 most parsimonious trees. The bootstrap value of a particular clade may then be expressed as the percentage of the trees generated in the analysis in which that clade is supported.

Autoapomorphy – a character that changes once in only one taxon – uninformative of relationships

Polyphyletic – said of groups that have two or more ancestral sources in which the parallel similarities evolved – sometimes simply referred to as non-monophyletic (Petal fusion – Judd, p. 17, Fig. 2.8B)

Paraphyletic – said of a group including a common ancestor and some, but not all of its decendents – sometimes simply referred to as non-monophyletic (Judd, p. 14, diamonds plus squares in Fig. 2.5B)

Metaphyletic – said of a group that cannot be positively determined to be either paraphyletic or monophyletic (Judd, p. 14, circles in Fig 2.5C)

Plesiomorphic – refers to ancestral character states

Symplesiomorphic – refers to sharing of ancestral character states

Consensus tree – a cladogram reflecting the groups defined by all methods of analysis or among different kinds of character matrices (Judd, p. 8, Fig. 2.9)

The Phylogenetic Approach and Classification

Naming is straightforward – only monophyletic groups are given names

Not all monophyletic groups are given names – if they were, a tremendous proliferation of ranks and a very cumbersome classification would result

Determination of ranks is arbitrary

The family is the lowest category considered in our text

In most cases existing family circumscriptions have been found to be monophyletic and therefore existing names are still applied

Several existing families were found to be non-monophyletic and they were combined or divided to produce monophyletic units, e.g., legume families Mimosaceae, Caesalpiniaceae, and Fabaceae become Fabaceae; the previously large non-monophyletic family Scrophulariaceae was made monophyletic by transferring the bulk of the family to Plantaginaceae and Orobanchaceae

If existing formal names were available for these units then those names were adopted

In some cases where formal names were not yet available for smaller units, non-monophyletic families are still recognized but their names are placed in quotation marks.

Monophyletic groups above the rank of family are not all formally recognized in our text, in part because formal names have not yet been proposed for them. For convenience and discussion some of these have been given informal designations, e. g. Tricolpates, corresponding to a large monophyletic assemblage of families previously lumped into a still larger but non-monophyletic group called dicots. I a few cases the monophyletic groups above the family level correspond to previously recognized entities, e.g., the monocots.

Phenetics – classification based on overall similarity – forerunner of cladistic methodology – may also be referred to as Numerical Taxonomy or Taximetrics (P. H. Sneath & R. R. Sokal - text - Numerical Taxonomy)

Select OTU (operational taxonomic unit – any level in the hierarchy) for comparison

Define and codify characters to be used (generally at least 100 characters)

Score each OTU for each character in a data matrix table [t (taxon) x n (character)]

Measure Similarity of all Pairs of O.T.U.'s (S = n_s/[n_s + n_d])

Perform cluster analysis or generate similarity matrix (t x t)

Generate phenogram based on similarity matrix

Not designed to retrieve evolutionary history and do not distinguish between synapomorphy and convergent or parallel evolution.

SIMILARITY MATRIX

A	x
B	9	x
C	6	6	x
D	5	5	5	x
E	9	9	6	5	x
F	6	6	8	5	6	x
G	6	6	8	5	6	8	x
H	5	5	5	9	5	5	5	x
	A	B	C	D	E	F	G	H

CLUSTER ANALYSIS

A	x
E	9	x
B	9	9	x
G	6	6	6	x
C	6	6	6	8	x
F	6	6	6	8	8	x
D	5	5	5	5	5	5	x
H	5	5	5	5	5	5	9	x
	A	E	B	G	C	F	D	H