sex, drugs, - university of oxford sciences...sex, drugs, & york - monday, june 17th 2013 ......
TRANSCRIPT
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?
A purpose of CLASSIFYING is to create groups in order to organise information & knowledge. Without classification there would be chaos.
A purpose of CLASSIFYING is to create groups in order to organise information & knowledge. Without classification there would be chaos.
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.
Charles Darwin – Origin of Species
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.
Charles Darwin – Origin of Species
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
Charles Darwin – Origin of Species
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.
Charles Darwin – Origin of Species
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
Charles Darwin – Origin of Species
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
Charles Darwin – Origin of Species
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.
Charles Darwin – Origin of Species