Sex, drugs, · Phylogenetics = the study of evolutionary relationships within and between groups of organisms . ... 1789 is the starting point for the creation of legitimate family

Sex, drugs, &

York - Monday, June 17th 2013 [email protected]

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A FEW DEFINITIONS: Taxonomy = the science of describing, naming & classifying living organisms Binomial nomenclature = formal scientific Latin names in two parts; Genus & species (or specific epithet) Angiosperms = the flowering plants Phylogenetics = the study of evolutionary relationships within and between groups of organisms

Fact No.1:

Taxonomy is the oldest profession in the World

GENESIS chapter 2: 19 And out of the ground the LORD God formed every beast of the field, and every fowl of the air; and brought them unto Adam to see what he would call them: and whatsoever Adam called every living creature, that was the name thereof. 20 And Adam gave names to all cattle, and to the fowl of the air, and to every beast of the field; but for Adam there was not found an help meet for him. 21 And the LORD God caused a deep sleep to fall upon Adam, and he slept: and He took one of his ribs, and closed up the flesh instead thereof; 22 And the rib, which the LORD God had taken from man, made He a woman, and brought her unto the man.

Fact No.2: Biology is a process

Biology is not a static and un-altering

product.

This means that species cannot always be clearly & easily forced into neat boxes.

NAMING & CLASSIFYING

these are not necessarily the same thing (but they can be)

Why do we NAME plants?

Moon daisy, dog daisy, ox-eye daisy or marguerite?

Always Leucanthemum vulgare everywhere

The purpose of NAMING plants is for communication & gaining access to

knowledge

WHICH IS BETTER; vernacular or scientific

names?

NAMES of plants can be vernacular or scientific

The advantage of vernacular names is that they are in the local language & so easier to remember. Also they

can often be descriptive.

The advantage of scientific names is that they are universal & unique to that species

The accepted system of naming & classifying plants uses Latin names for each rank in a hierarchy. Latin is used because no one can claim that one nationality of botanists has an unfair advantage. ◄ Mahonia fortunei

Why do we CLASSIFY plants?

A purpose of CLASSIFYING is to create groups in order to organise information & knowledge. Without classification there would be chaos.

HOW DO YOU CLASSIFY YOURS?



GROUPS & CLASSIFICATIONS of plants can

be vernacular or scientific

WHICH IS BETTER; vernacular or scientific

classification?

The advantage of vernacular groups is that they are for a specific,

local, practical purposes

The advantage of scientific groups is that they are

hierarchical predictive (practical)

universal and each plant has one exclusive place

Moss, fern, conifer, flowering plant

The advantage of using scientific names AND groups is that they can be combined and related to each other. There are rules for the scientific naming of plants – the International Code for Botanical Nomenclature – and there are now some rules for scientific classification - it is not just intuition

A BRIEF HISTORY of pre-Darwin

NAMING & CLASSIFYING plants

Chinese herbals

Theophrastus 3rd century BC

Theophrastus on umbels

Umbellifers

DIOSCORIDES

1st century AD De Materia Medica

Robert Morison 17th century Oxford

John Ray 1634-1703 - the 2nd greatest English natural historian ever 1) Defined “species”

What is a species?

A species is a group of individual plants that share a unique combination of

characters (or features) which can be replicated

John Ray 1634-1703 2) If you want to conserve a species then you need seeds not just cuttings etc.

John Ray 1634-1703 3) He saw that when classifying plants, you must use every character that you can measure and that you cannot ignore anything without good reason

John Ray 1634-1703 4) He put all flowering plants into either the monocots or the dicots

Seeds with a single cotyledon

Flowers with perianth and androecium segments in multiple of three

Leaves with parallel veins

Roots that function for one year only

John Ray 1634-1703 5) He recognised many families that we still use

Borage family

Linnaeus 1707-1778

“The value of an aggregate of characters is very evident in natural history.

Hence also, it has been found that a classification founded on any single

character, however important that may be, has always failed.”

Charles Darwin – Origin of Species

Ray was right & Linnaeus was wrong

1753 is the starting point for legitimate species names

Medicinal plants

De Jussieu late 18th century French botanist

1789 is the starting point for the creation of legitimate family names.

A family is a group of similar genera. All of the species in these genera share a unique combination of characters. One genus is considered to be typical of the family and the family name is derived from that genus by adding –aceae.

19th century Kew

Mr George Bentham & Sir Joseph Hooker

19th century plant hunting expedition

Making herbarium sheet for pasteurii

Herbarium sheets

Bentham & Hooker Genera Plantarum (1862-1883) 1) retained Ray’s Monocot/Dicot split 2) divided Dicots into three sub-classes i) petals free (not joined to each other) ii) petals fused (at least two petals joined) iii) petals absent (no obvious petals) 3) within these three sub-classes of dicots & the monocots, families were grouped on visible characters into orders

Bentham & Hooker Genera Plantarum (1862-1883) No attempt was made to reflect evolution, perhaps because much of their work was carried out before the publication of The Origin of Species in 1859. Joseph Hooker was a regular correspondent of Charles Darwin

Charles Darwin chapter 13 of the Origin of Species

The birth of truly

natural classifications

From the first dawn of life, all organic being are found to resemble each other in

descending degrees, so that they can be classified in groups under groups.

This classification is evidently not arbitrary

like the grouping of the stars in the constellations.


In the hierarchy, each rank is just a group of the rank below. The accepted hierarchy is

KINGDOM - kinky

PHYLUM - prostitutes CLASS - can ORDER - offer

FAMILY - fairly GENUS - good SPECIES - sex

But once we know it is a flowering plant we generally only use

FAMILY GENUS

SPECIES

The Natural System is founded on descent with modification;

the characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited

from a common parent.


I believe that propinquity of descent is the descent, is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our

classifications


1876 – Haekel’s phylogeny of land plants

Published by AAAS

Fig. 1. Phylogenetic support across the NCBI taxonomy tree of eukaryotes

The less any part of the organisation is concerned with special habitats, the more

important it becomes for classification.

The mere physiological importance of an organ does not determine the classificatory value.


For example, we do not automatically put all

carnivorous plants in the same family

Modern Kew 21st century Kew

We have no written pedigrees; we have to make out continuity of descent by

resemblances of any kind


John Ray 1634-1703 You must use every character that you can measure and that you cannot ignore anything without good reason

By 1998 we had some EXTRA CHARACTERS In addition to the morphological data that has been around since Theophrastus was a lad, the APG botanists looked at plants using electron microscopes and DNA sequencers.

Molecular characters

• 1953: Discovery of molecular structure of DNA

• late 1980’s, DNA sequencing possible for relatively large numbers of taxa

• 1998 - the first publication from the Angiosperm Phylogeny Group (APG I) but no one would publish it

Because the major journals would not publish the new ideas it was left to The Independent,

23-11-1998 though they got some of the story wrong (the red bits)

“The science of botany has been turned upside down by a new classification of the world’s flowering plants and trees based on their DNA rather than their appearance”

The Independent, 23-11-1998

When it is published next month in the Annals of Missouri Botanic Garden the classification, which for the first time establishes the relationships of all plant families through their genetic material will do away with 200 years of previous plant taxonomy dating back to Linnaeus. This has hitherto been based on flowers and other morphological characters

CONCLUSIONS

• The 1998 classification of flowering plants did not turn 200 years of botany on its head but rather added accurate resolution at the level of family

• Some of these results were completely unexpected on the basis of morphology and highlighted the limitations of morphological data at some parts of the angiosperm tree.

• But these results mostly corroborated much of what had been discovered or observed on the basis of morphology

Changes prompted by the new classification 1) 73% of Bentham & Hooker’s families did not change 2) 13% had to change 3) 14% are still uncertain

Plane trees & the Sacred Lotus, closest relatives?

THE NEW BIT - MONOPHYLY formal adoption of Darwin’s philosophy

All groups at every rank in the hierarchy must be

monophyletic.

A monophyletic group contains all of the descendants

of an ancestral plant

A BIG change that confirmed our worries: The dicots are NOT monophyletic meaning that there are some oddballs but the monocots defined by John Ray 300 years ago are still intact

The independent, problem,basal dicots plants do not have pollen with three apertures (and other things) and so they

are not true dicots

Phylogeny Evolution

other problem plants

The Eudicots (the true dicots)

The Monocots

basal angiosperms

Naturalists try to arrange species, genera, families in each class, in what is called THE NATURAL SYSTEM. … The ingenuity and

utility of this system are indisputable


Utility No.1

Identification

Identifying plants quickly with just a x10 hand lens

Within the flowering plants there are

431 FAMILIES 13,479 GENERA

350,000 SPECIES

350,000 individuals is far too many to remember but if you identify a plant to family, & then

genus, the number of options falls

So when identifying the white water-lily we start with 350,000 species but when we

have put it in a family the number of possible species falls to just 60.

Then there are just 6 possible genera to

choose from.

Genera in the Nymphaeaceae

When we have decided that this is in the genus Nymphaea there are just 35 possible

species.

Utility No.2

Revealing history

Current distribution of the Proteaceae

(the protea family)

Utility No.3

Objectively measuring & comparing different areas of vegetation

Utility No.4

Understanding biogeography

From where did the plants of Tenerife come originally?

Utility No.5

crop breeding

Rice yellow stunt virus

C4 rice - how difficult can it be if C4 photosynthesis has evolved more than 40 times?

C4 rice - would grow better in drought, at high temperatures and when nitrogen is in short

supply e.g. at 30oC C3 grass losses 3 times the volume of water that C4 loses at the same

temperature

Utility No.6

proving that evolution happens: do ring-species exist?

Do hypothetical ring species exist?

Do ring species exist? - yes Euphorbia tithymaloides in the Carribean

Utility No.7

Predictions

Fabaceae (the bean family or the

legumes) Potential invasive species

Nitrogen fixers

Orchidaceae (orchid family) need a fungus to germinate & an insect pollinator

Araceae (the arum family)

all toxic

Ranunculaceae (buttercup family) toxic & fresh seed needed for good germination

Rosaceae (the rose family) need a cold spell for seeds to germinate

Solanaceae (the potato family) toxic but good pharmaceutical chemists

Utility No.8

Searching for drugs

Paclitaxel and docetaxel from yew trees

& harringtonine from Cephalotaxus

Galantamine to treat Alzheimer's

Fact No.3: Taxonomy is not finished

We do not have all the answers and we do not have a perfect

classification yet

What next? 1) Clearing up the problem groups 2) dating the emergence of families 3) building super trees that include every family, every genus and eventually every species 4) solving Darwin’s Abominable Mystery

Frohlich & Chase (2007) Nature 450 20/27 December 2007 p1184-1189

We shall never, probably, disentangle, the inextricable web of affinities between the members of any one class; but when we have a distant object in view, and do not look to some unknown plan or

creation, we may hope to make sure but slow progress.


Documents

Sex, drugs, · Phylogenetics = the study of evolutionary relationships within and between groups of organisms . ... 1789 is the starting point for the creation of legitimate family