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.

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

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

Sources of systematic information – (Judd, Chapters 4 & 5)

Recall morphology of vegetative and reproductive structures already covered in lab

Pollination Biology

Wind and Water Pollination

Animal Pollination (Judd, p 59-60, Table 4-1)

Deception – Carrion flowers, Aristolochia, Stapelia, Rafflesia, Aroids

Coevolution – Yucca/Tegiticula and Ficus

Pseudocopulation – Ophrys orchids

Anatomy

Light microscopy

Transmission electron microscopy (TEM) - ultrastructure

Scanning electron microscopy (SEM) – micromorphology

Vascular tissue

Secondary xylem - evolutionary sequence of tracheids to vessel elements (Judd, p. 70, Fig. 4.31)

Secondary phloem – Sieve-element plastids of two major types S-type with starch accumulation; P-type with protein accumulation – found only in Caryophyllales (Judd, p.71, Fig. 4.32.

Nodal anatomy (Judd, p. 72, Fig. 4.33)

Leaf Anatomy

Indumentum (Judd, p. 52, Fig. 4.15)

Cuticle deposits (waxes) (Judd, p. 73, Fig. 4.34)

Stomates (Judd, p.73, Fig. 4.35

C3 vs C4 (Kranz) anatomy (vascular bundle sheaths with chloroplasts) (Judd, p. 73)

Petiolar vascular traces (Judd, p. 74, Fig. 4.36)

Secretory structures

Latex – Apocynaceae, Euphorbiaceae, Campanulaceae

Essential oils – Rutaceae, Lamiaceae

Pellucid dots – Rutaceae, Myrtaceae

Crystals (Judd, p. 74, Fig 4.37

Raphides – Araceae

Cystolith – Moraceae, Urticaceae

Stem Anatomy (Judd, p. 75, Fig. 4.38)

Scattered vascular bundles - Monocots

Bicollateral vascular bundles – Cucurbitaceae

Internal phloem – Myrtales, Gentianales, Solanales

Concentric rings of vascular tissue, each with xylem and phloem - Caryophyllales

Floral Anatomy

Vascular traces in gynoecium – especially helpful to determine number of carpels in obscure cases

Initiation of stamen primordia – Centripetal vs Centrifugal

Spores, Gametophytes, and Gametangia (Judd, p. 76, Table 4.2)

Homospory – only one kind of sporangium producing one kind of spore – the gametophytes are free living, macroscopic (potentially consisting of millions of cells), and produce both antheridia and archegonia (Lycopodiaceae, Equisetaceae, Psilotaceae, and most Ferns)

Heterospory – two kinds of sporangia (microsporangia and megasporangia) produce two kinds of spores (microspores and megaspores, respectively) – the gametophytes are dependent on the sporophyte, small (3 to a few thousand cells) and contained within the spore – gametangia are lacking in angiosperms, “gymnosperms” have only archegonia, both archegonia and antheridia are present in Selaginellaceae, Isoetaceae, and the small group of heterosporous ferns

Ovules and megagametophytes

Orientation of ovule (Judd, p. 77, Fig. 4.39)

Number of integuments

Unitegmic

Bitegmic

Megasporangium wall

Crassinucellate

Tenuinucellate

Megagametophyte (embryo sac) (Judd, p. 77, Fig. 4.40)

Embryo and Endosperm (Judd p. 78, Fig. 4.42)

Monocot

Dicot

Endosperm present or absent when seed ripe

Chromosomes – Cytotaxonomy (systematic application of chromosomal information)

Number (Judd, p. 79, Table 4.3)

Diploid number = 2n -- range in plants 2n=4 (Haplopappus gracilis, Bracycome sp.) to 2n=1260 (Ophioglossum reticulatum)

Haploid number = n

Known for less than 25% of flowering plant species

Base number = x (for flowering plants x=7, for Caryophyllales x=9)

Aneuploidy (Dysploidy)

Polyploidy (Judd, p. 80, Table 4.4) (Stace, p. 113)

(based on x=15, O. reticulatum is 84 ploid)

Autopolyploidy

Allopolyploidy

About 70% of flowering plants are considered to be polyploids

Size - Stace, p. 120 -- Agavaceae 5 large, 25 small, asymmetrical karyotype

Structure Judd, p. 81-82, Fig 4.44-45)

Centromere position - Metacentric, Telocentric, Stace, p. 128.

Secondary constrictions & satellites

Special stains, can emphasize certain structural features, e.g. Giemsa

Karyotype (combines size, number and structural aspects of chromosomes for the entire genome) (idiogram --Stace, p. 119)

Pairing behavior during meiosis – can help interpret aneuploid and polyploid changes and also identify other structural modifications that are commonly involved in chromosome evolution (deletions, duplications, inversions, and translocations)

Palynology (Judd, p. 83, Fig. 4.46-47)

Condition at time of release

Monads, Diads, Tetrads, Pollinia

Binucleate, Trinucleate

Size (10 µm – 350 µm)

Shape (spherical to rod-shaped – up to 520 µm)

Apertures (number, shape, and position varies)

Colpate – Sulcate (long, narrow apertures)

Porate – round apertures

Wall (exine) features (thick, thin, smooth, spiny)

Secondary Plant Compounds

Alkaloids – (Judd, p. 84, Fig. 4.49) generally amino acid derivatives, commonly physiologically active in animals, often used medicinally (cocaine, morphine, atropine, colchicine, quinine, strychnine) – certain types are limited in taxonomic distribution and therefore are of systematic value

Betalains and Anthocyanins – (Judd, p. 85, Fig. 4.50) Two mutually exclusive categories of plant pigments important in defining colors of flowers and fruits with obvious implications related to pollination and fruit dispersal. Betalains are distinguished by their incorporation of nitrogen and their limited taxonomic distribution in the Caryophyllales.

Glucosinolates (Mustard oil glucosides (Judd, p. 85, Fig. 4.51) – source of hot mustard oils) – with one exception, confined to the order Brassicales

Cyanogenic glycosides (Judd, p. 85, Fig. 4.52) – defensive compounds of wide occurrence produced through a variety of biosynthetic pathways, some of which are of limited taxonomic distribution.

Polyacetylenes (Judd, p. 86, Fig. 4.53) – a group of non-nitrogenous compounds produced by linkage of acetate units via fatty acids – found in several closely related asterid families, including Asteraceae and Apiaceae

Terpenoids (Judd, p. 86-87, Figs 4.54-57) – a large and very diverse group of compounds formed in the mevalonic acid pathway, many having primary physiological functions (examples include monterpenoids and sequiterpenoids as major components of essential oils, and various iridoid compounds that characterize the asterid clade.

Flavonoids (Judd, p. 87, Fig. 4.58)– Phenolic compounds of widespread taxonomic occurrence, probably of some importance in plant defense against herbivores, usually most helpful in assessing infraspecific variation or relationships among closely related species

Proteins – Exceedingly diverse group of molecules formed by the linkage of amino acids into a polypeptide chain – functions include enzymes, storage molecules, transport molecules, pigments, and structural materials

Amino Acid Sequencing

The sequence of amino acids in a given protein can be used as taxonomic characters

Proteins that have been used in determining phylogenetic relationships among organisms include cytochrome c, plastocyanin, ferredoxin, and ribulose-1,5-bisphosphate carboxylase (small subunit).

Systematic Serology

Proteins (commonly from seeds) are used as antigens to elicit the production of antibodies in a mammal (commonly rabbits or horses)

Serum containing the antigens is then mixed with protein extracts of the plant species to be compared

The amount of precipitate formed (antigen-antibody reaction) is taken as an index of relationship between the species that was used to generate the antibodies and the one or more being compared.

Electrophoresis

Seed or pollen proteins or specific enzymes are extracted and spotted on a stationary gel through which electric current is passed

Proteins will migrate through the gel according to their net charge, shape, and size

Proteins migrating to the same position in the gel are considered homologous

Presence or absence of bands in extracts being compared can be used as taxonomic characters

Most useful when applied at and below the species level.

Nucleic Acids – The current rage in systematics is the use of DNA and RNA to infer relationships among organisms. This approach is commonly referred to as Molecular Systematics. Advantages include virtually unlimited characters and generally straightforward interpretation compared to morphological characters.

Genomes examined

Chloroplast genome (Judd, p. 94, Fig. 5.1) – inheritance usually maternal in angiosperms, smallest with 135-165 kilobase pairs (kbp), circular, relatively stable, characterized by two inverted repeat segments delimited one small and one large single copy region, useful to infer relationships of major groups and sometimes at lower levels in the hierarchy

Mitochondrial genome – inheritance usually maternal in angiosperms, intermediate in size with 200-2500 kbp, circular, frequent rearrangement, order of genes variable, not very useful to establish relationships

Nuclear genome – inheritance biparental, very large, measured in megabases, packaged in 2-many linear segments (chromosomes) order of genes apparently stable, at least among closely related species and sometimes across larger groupings as well

Types of Molecular Data

Gene Mapping (Mapping the location of genes in the genome)

Restriction site analysis – In this procedure DNA is extracted from a plant is cut with a restriction enzyme that cleaves the DNA at a specific nucleotide sequence and creates an array of fragments of various sizes. The same procedure is done for a second restriction enzyme that recognizes a different gene sequence, and finally both enzymes are used together. This creates a sort of puzzle from which the order of the restriction sites in the original segment of DNA can be inferred.

Southern Blot Technique – This method involves cutting the DNA in question and transferring it to a nylon membrane – this DNA is then allowed to bind with a cloned, radioactively labeled, single-stranded “probe” that will attach only to matching sites on the chloroplast DNA fragments – when the membrane is placed next to a piece of X-ray film, the bands that include the bound radioactive probe will appear as dark lines on the film.

Systematic utility of the data – changes in the order of genes or gain or loss of genes may distinguish taxonomic groups or clarify relationships – Most members of the Asteraceae have a unique order of genes in a segment of the large single-copy region of the chloroplast genome that can be explained on the basis of a single inversion of that region of DNA. This inversion distinguishes most Asteraceae from all other angiosperms. Only members of the small subtribe Barnedesiinae from South Africa have the ancestral, non-inverted segment in common with other angiosperms. Thus it appears that the Barnedesiinae comprise the sister group to the rest of the enormous, monophyletic sunflower family.

Gene Sequencing (Determining the sequence of nucleotides in a gene)

DNA Amplification

Originally relied on cloning the desired gene into bacteria – the gene is then replicated along with the rest of the bacterial genome

Now usually done by way of the polymerase chain reaction (PCR), a largely automated procedure that relies on enzyme moderated DNA replication (Judd, p. 96, Fig 5.2)

Sequencing Gel – allows visualization of the sequence of nucleotides in the unknown DNA

Alignment of Sequences – matching comparable regions – this is easy if not much genomic evolution has occurred but becomes more difficult as genomes diverge

Once aligned, sequences of different species can be compared and analyzed with computer programs and phylogenies based on these comparison can be generated

A good example of the application of gene sequencing in plants is the chloroplast gene rbcL which encodes the large subunit of the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the major carbon acceptor in all photosynthetic eukaryotes and cyanobacteria. The analysis of rbcL sequences have been used very widely to evaluate relationships of angiosperm families and are cited throughout the text.

Gene Trees versus Species Trees – (Judd, p. 99, Fig. 5.3)

Data from a single gene such as rbcL may be used to generate gene trees. Ideally, trees based on the phylogeny of different genes would be the same and would correspond to species trees but this is not always the case. Some of the reasons for incongruence of this sort include the random nature of mutations, hybridization or introgression, and the random loss of ancestral polymorphisms in descendant species. This underscores the importance of generating and comparing phylogenies based on different kinds of data

NATURAL SELECTION AND EVOLUTION

Basic tenets of Darwinian evolution

1. Species are variable

2. More offspring are produced than survive to reproductive maturity

3. Therefore, there is competition (for survival)

4. Therefore, the fittest survive

This results in what is commonly referred to as natural selection, i.e., the nonrandom differential survival of genotypes in nature

"Fitness" describes the ability of an individual or higher taxonomic unit to produce fertile offspring that survive to reproductive age

Fitness is affected by

1. Reproductive capacity

2. Adaptation of offspring

In the Darwinian context, evolution may be defined as descent with modification

Blending of Darwinian and Mendelian concepts and later Population Genetics has produced a synthesis often referred to as Neo-Darwinism

In Neo-Darwinian terms, evolution is more generally defined as a change in the frequency of genes in a population

Source of new genes in a population

1. Mutation

Ultimate source of variation in a population - most mutations are deleterious - some are more or less unique - many are recurrent and have a somewhat stable forward and backward rate

where u & v may be on the order of 10^-4 - 10^-8

2. Immigration

Flow of seed or pollen from neighboring populations

New genes from mutation and immigration are constantly shuffled by recombination

Cause of change in gene frequency

1. Natural selection

Some genotypes (certain gene combinations) may be more fit than others

2. Genetic drift

A chance (stochastic) phenomenon that may occur in small populations - (example using 2 gravid female lizards) - Founder Principle as extension of concept - significance in Hawaii

Three main kinds of natural selection

1. Stabilizing

Environment remains constant - extreme phenotypes selected against - e.g., flowering period of spring flowering plants in summer dry areas - (too early - lack of pollinators, too late - lack of water)

2. Disruptive

Original environment of a population of plants differentiating into 2 or more different microhabitats - extreme phenotypes may be selected for if they allow exploitation of the newly available habitats - selection against original norm - two or more new norms are established

3. Directional

Environment changing in a constant direction with respect to one or a few parameters, e.g., temperature, moisture, etc. - one extreme phenotype selected for

Artificial selection is often directional

e.g., height of ears of corn on stem - in one experiment the initial population had ears ranging from 43-56 inches above ground - after selecting seed from the plants having the ears closest to the ground for 24 generations, the final population had ears only 8 inches above ground level

Other examples involve oil and protein content in corn kernals after 50 generation of high and low selection (see handout)

15% 19.4%

corn oil 5% corn protein 10.9%

1% 4.9%

BREEDING SYSTEMS

Series of variables that collectively determine the extent to which a plant interbreeds with other plants of the same or of different taxa

Inbreeders

Tend to be comparatively uniform within a population - however, populations tend to differ from one another by one or a few characteristics

Outbreeders

Tend to be quite variable within a population but relatively undifferentiated between populations

Apomictic taxa exhibit little or no variation

In nature there is a continuum of variation of kinds of breeding systems from one extreme to the other

The breeding system determines the amount of recombination that occurs through time - what is recombination? - what individual factors affect it? - is it effected by asexual reproduction?

*Sexual reproduction promotes recombination - How?

Random mating

Independent assortment of homologous chromosomes during meiosis

Chromatid exchange between homologues resulting from crossing over during meiosis

How much recombination is possible?

[r(r+1)/2]ⁿ defines the number of possible recombinants where n=the number of loci/genome, and r=the number of alleles/locus -- if we assume n=10000 and r=3 then the number of possible recombinants is 6¹⁰⁰⁰⁰

However, genes are fixed on chromosomes and therefore cannot recombine this freely -- the number of chromosomes is thus of paramount importance, notwithstanding the effects of chiasmatal exchange

Other factors affecting recombination

Length of generation

Chromosome number

Crossover frequency

Breeding system (in the strict sense)

Pollination system

Dispersal potential

Population size

Isolating mechanisms and incompatibility barriers

The amount of recombination within and between populations of plants (which is in turn related to the breeding system of plants) is of concern to taxonomists because of its effect on the pattern of phenotypic variation. Remember, the taxonomist seeks discontinuities in the pattern of variation to delimit taxa worthy of formal recognition. An understanding of the causal factors involved in complicated cases may reduce the temptation to erect a formal taxonomy that is meaningless or impractical

AVOIDANCE OF SELF FERTILIZATION

Spatial or temporal isolation of the sexes

Monoecy, Dioecy

Protandry, Protogyny

Self-incompatibility

Monomorphic

Gametophytic – (Judd, p. 62, Fig. 4.25) widespread

Sporophytic – Asteraceae, Brassicaceae, and a few other families

Heteromorphic – Heterostyly – (Sporophytic) – (Judd, p. 62-63, Fig. 4.26) occurs in 24 families, especially common in Rubiaceae

HYBRIDIZATION

Definitions

Hybrid -- zygote produced by union of dissimilar gametes

Taxonomic hybrid -- product of breeding between formally recognized taxa

Extent of hybridization

Interspecific

Natural -- estimated 70,000 different combinations

Artificial -- many more possible - 45,000 have been synthesized in the Orchidaceae alone

Intergeneric

Natural -- estimated 250 different generic combinations

Artificial - many more possible - hybrids involving 3-5 genera have been synthesized in Orchidaceae and Poaceae

Interfamilial -- exceedingly rare or none - one that has been reported (Verbena - Verbenaceae X Veronica - Scrophulariaceae) needs substantiation

Recognition of hybrids

1. Phenetic intermediacy between the parents

May be assessed by using techniques such as the hybrid index or the pictorialized scatter diagram (Stace, p. 134. Other, more sophisticated methods such as Principal Component Analysis (PCA) are available for use on the computer (Judd, p. 121, Fig. 616-617).

Phenetic intermediacy also extends to chromosome numbers

Hybrids are not always intermediate and when they aren't, most frequently they bear a closer than anticipated resemblance to the maternal parent.

Also, chromosome numbers may not be intermediate due to the possible participation of an unreduced gamete in the production of the hybrid zygote -- this could also affect the phenotype

2. Reduced viability

Hybrids may die at any stage from the zygote to subadult stage

3. Reduced fertility

Hybrids may range from 0-100% fertile -- this may be assessed by comparing seed set of hybrid with parental types or by comparing pollen stainability of hybrid with parental types (caution)

In some cases hybridity may be detected by studying meiotic chromosome behavior

4. F₂ segregation

Progeny testing F₁ hybrids

A large number of progeny from an F₁ hybrid will ordinarily exhibit a wide continuous spectrum of types including and bridging the gap between the parental morphologies

5. Distributional evidence

6. Artificial resynthesis

Consequences of Hybridization – (Judd, p. 119) Stace, p. 142

If the number of hybrids produced are few and highly localized the taxonomic implications may be minimal, i.e. the integrity of the taxa may remain more or less intact

In other instances the extent of hybridization may be so great that every conceivable intermediate morphological type between the parental types becomes established -- this is called a hybrid swarm. In such cases the discontinuities that may have originally existed are transcended and the result can be a difficult taxonomic problem.

An alternative to a morphologically symmetrical hybrid swarm is produced when successive backcrosses to only one of the two parents in the hybrid zone occur. In this instance the morphological spectrum of intermediates is skewed toward one parent cf. Stace, p. 142. This kind of situation is called introgression or introgressive hybridization (Judd, p. 119, Fig. 6.14). The pattern of hybrids established is often dictated by the diversity and quality of niches in the immediate vicinity. Through introgression one taxon may selectively assimilate one or a few characters from a second taxon. The acquisition may allow it to exploit new habitats and increase its range or may be beneficial in some other way.

Stabilization of hybrids

If hybrids can become stabilized, i.e. acquire the ability to reproduce themselves, they may become new species.

Mechanisms of Stabilization (most important)

1. Apomixis (reproduction by non-sexual means)

A. Vegetative reproduction

B. Agamospermy (embryo formed from maternal tissue)

2. Amphidiploidy (a polyploid that meiotically behaves like a diploid) (allodiploid) – This is an exceedingly important form of speciation in flowering plants. About 70% of all angiosperm species are polyploid and the great majority of them likely originated in this manner.

3. Hybrid speciation at the diploid level

A. Genetic stabilization through successive generations - usually externally isolated from parents

B. Chromosomal stabilization through successive generations - usually chromosomally isolated from parents

ISOLATING MECHANISMS (Judd, p. 115, Table 6.1)

Significance of Sympatry and Allopatry

General Categories

Prezygotic mechanisms 0-5a

Pre-mating (Pre-pollination) mechanisms 0-4

Post-mating (Post-pollination) mechanisms 5a-9

Postzygotic mechanisms 5b-9

Specific Types

0. Geographical isolation

Platanus occidentalis (E U.S.) X P. orientalis (E Mediterranean) - P. acerifolia

1a. Seasonal isolation

D. platyphylla and D. menziesii

1b. Diurnal isolation

pollen released or stigmas receptive at different times of day -- Clarkia

2. Ecological isolation, clearly related to #6

D. ciliolata -- D. scabra -- old vs. new lava flows

3a. Floral behavioral (Ethological) isolation

Aquilegia formosa -- hummingbirds

Aquilegia pubescens -- hawkmoths

3b. Floral structural (Mechanical) isolation

different floral structures in related taxa

4. Breeding behavioral isolation

selfing - fewer hybrids than outcrossing

5a. Pollen-pistil incompatibility

5a. Seed incompatibility

abortion of embryo prior to seed maturation - may be caused by failure of endosperm to provide sufficient nourishment

6. Hybrid inviability, including ecological isolation

germination may occur but F₁ dies before producing flowers

7. Hybrid floral isolation

8. F₁ hybrid sterility

F₁ viable, possibly even vigorous, but sterile - may have either genetic or chromosomal basis

9. F₂ hybrid inviability or sterility (F₂ breakdown

disability delayed until F₂ (or later) generation -- F₁ may be normal and fertile -- Hibiscadelphus

SPECIES DEFINITIONS

Given the importance of the position of species as the fundamental level in the taxonomic hierarchy, a universal definition for species would seem to be highly desirable. Unfortunately, though many have tried, no one has succeeded in providing any workable definition that addresses the problem very effectively.

The difficulty of defining species in plants appears to be primarily related to the wide range of breeding systems and modes of isolation that are inherent in plants.

One of the most popular species concepts held by zoologists, that of the biological species, fails miserably when applied to plants. The reason for this is that in plants there is often no correlation between observable divergence and reproductive isolation. Plants may appear to be identical, yet exhibit complete reproductive isolation. At the opposite extreme, plants can be extremely different in many respects and still hybridize freely in areas of contact.

Basic “kinds” of plants, “species” if you will, may fall anywhere along the continuum between these extremes, depending on the unique set of circumstances under which they have evolved. In each case natural selection has produced a finely tuned, unique blend of breeding system parameters and other reproductive traits to ensure that fitness to prevailing conditions persists from one generation to the next. On the other hand, many if not most plant species retain the ability to transcend their own comparatively limited gene pools by hybridizing with other species and even other genera. This potential confers upon such species a far greater probability of long-term survival than would be expected for selfiing or agamospermous species.

The obvious advantage of a phenetic species concept is that it relies on morphological discontinuities in the pattern of overall variation that can be interpreted even by people with little or no special training. It is the most practical of all of the species definitions that have been advanced. There seems to be little value to the formal designation of sibling or cryptic microspecies or agamospecies that can only be identified by a handful of experts on the basis of obscure characters, the detection of which may require special procedures or instrumentation.

ANGIOSPERM CLASSIFICATION

Evaluation of vegetative and reproductive characters

Extension of Besseyan dicta (see handout)

Consideration of all available evidence

Analysis of correlations of character states

Ancestral Fossil Record >Derived

Ancestral Vegetative Characters >Derived

Ancestral Floral Characters >Derived

Ancestral Pollination System >Derived

Ancestral Vascular Tissue >Derived

CURRENT SYSTEMS

Armen Takhtajan 1910-

Division Magnoliophyta (Angiospermae)

Class: Magnoliopsida (Dicots)

Subclass: A: Magnoliidae

B: *Ranunculidae

C: Hamamelidae

D: Caryophyllidae

E: Dilleniidae

F: Rosidae

G: Asteridae

Class: Liliopsida (Monocots)

Subclass: A: Alismatidae

B: Liliidae

C: Arecidae

Summary

10 subclasses

92 orders

28 superorders to emphasize relationships of groups above ordinal rank

Also uses suborders

410 families

Arthur Cronquist 1917 - 1992

Division Magnoliophyta

Class: Magnoliopsida

Subclass: A: Magnoliidae

B: Hamamelidae

C: Caryophyllidae

D: Dilleniidae

E: Rosidae

F: Asteridae

Class: Liliopsida

Subclass: A: Alismatidae

B: Arecidae

C: Commelinidae

D: *Zingiberidae

E: Liliidae

Summary

11 subclasses

83 orders

383 families, 215,000 species

G. L. Stebbins (1906-2000) 1974 - 77 orders, 349 families, 231000 species

R. F. Thorne (1920-) 1983 - 53 orders, monocots and dicots as classes further divided into superorders (doesn't use subclass)

R. Dahlgren (1932-1987) et al. 1985 - 108 orders, monocot and dicots as subclasses further divided into superorders

Systems of latter three workers achieve essentially the same groupings as Cronquist & Takhtajan

ANGIOSPERM PHYLOGENY GROUP

Major Angiosperm Groupings

“Non-Monocot Paleoherbs” (4 orders, 6 Families, 27 genera, 2553 species)

Nymphaeales

Ceratophyllales

Piperales

Aristolochiales

Monocots (15 orders, 59 families, 2426 genera, 51274 species)

Acorales

Alismatales

Pandanales

Lilianae (3 orders, 16 families, 1033 genera, 25,896 species

Commelinanae (8 orders, 21 families, 1232 genera, 22,165 species

“Magnoliid Complex” (3 orders, 10 families, 247 genera, 6141 species)

Magnoliales

Laurales

Iliciales

Tricolpates (30 orders, 151 families, 9328 genera, 167,673 species)

“Basal Tricolpates” (2 orders, 9 families, 264 genera, 5063 species)

Core Tricolpates (28 orders, 142 families, 9064 genera, 162,700 species)

Unresolved (3 orders, 17 families, 315 genera, 5336 species)

Caryophyllanae (2 orders, 12 families, 584 genera, 9751 species)

Rosids (13 orders, 58 families, 3317 genera, 65,763 species)

Eurosids I (7 orders, 33 families, 1744 genera, 43,621 species)

Eurosids II (4 orders, 22 families, 1538 genera, 21,127 species)

Asterids (10 orders, 55 families, 4865 genera, 81,850 species)

Cornales (3 families, 45 genera, 640 species)

Ericales (15 families, 317 genera, 7738 species)

Core Asterids (8 orders, 37 families, 4503 genera, 73,472 species)

Euasterids I (4 orders, 23 families, 2354 genera, 41,624 species)

Euasterids II (4 orders, 14 families, 2149 genera, 31,848 species)

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