Plant Systematics Reading Notes Spring 2005, Issue 1

Plant Systematics May 5th, 2005 :

Overview of Malvaceae(From Tuesday)

Do folks know how to do a t-test?

Keying update and advice - read the species descriptions

Heterostyly (primulaceae from last week)

Pop quiz

Hope to outline chapters very briefly in advance (prior tues or prior thurs)

************ Lecture start*********

Overview of the systematics and the book (where we are going, how it all ties together)

Keying - read species description

Family familiarity

Evolutionary relationships (uncovering them) Phylogenetics

Plant classification - taxonomy Evolutionary processes

Green plant evolution

Classification goals and characteristics vs phylogenetic analysis

Why do we need to classify things?

1 Common vocabulary to aid communication

2 Stable

3 Informative or predictive

4 Anything else we've forgotten?

Brief history of classification goals -

How would you classify plants and animals before Darwin?

God's creatures catalogued (Macroscopic morphology primary)

Similar things grouped for ease of study

Evolution is implied by similarity (microscopic, development, chemistry, proteins) Classification MUST adhere to evolutionary relationships - strict monophyly

Let's get explicit about evolutionary hypotheses - not characters but DNA,

genetic environment

Umm. Perhaps classification could be decoupled somewhat from evolutionary

relationships -

usefulness of classification is primary to classification;

phylogeny is primary for evolutionary relationships

Da Book

Ch 2 Methods and philosophy of uncovering evolutionary relationships (phylogenetics) and creating a classification system - the heart of the matter, the multiple ways.

Ch 3 The history of thinking about classification- how things got to be such a mess now Ch 4 Morphological traits and methods used to classify (sans pollination)

Ch 5 Genetic methods used to model evolutionary relationships

Ch 6 Evolution + pollination - speciation, change and how diversity is created - the good stuff. Ch 7 Green plant evolution- how did plants evolve into angiosperms and what makes them so special. - More good stuff Ch 2 brief outline

That which has transpired

What is phylogeny (13-- 15) basic concepts and terms

lineages

characters

character states

derived characters or character states (apomorphies) - NEW!

ancestral character states (pleisomorphies) - OLD!

shared derived character states (synapomorphies) Creating trees of evolutionary relationships (16 -30)

characters and states

determining similarity of state among taxa

good characters (non-overlapping states, heritable, more than one

distinguishable state, consistent within taxa)

*evolutionary relationship networks ( path from one species to the next via

character state changes) - topology

*creating evolutionary relationship Trees (rooting networks)

Outgroups (assumed! )

*Mono/para/polyphyly homology (common ancestor)

determined by creating phylogeny

e.g. limb -> arm-fin homoplaisy (not common ancestor)

parallelism, reversal

e.g. bees wing xxx bird wing Onward!

Choosing the best tree -

three ways although book focuses on parsimony

1 *Parsimony (Fig 2-10, p 22)

fewest character state changes

parallelism- number of times it evolved

reversal- number of times it got lost 2 Distance

p distance, Jukes-Cantor, Kimura 2-parameter

P-distance - proportional difference

n= total number of nucleotides compared

d= number that are different

p = d/n

A A A A G T C A T C

A A A A C T C A T C 3 Maximum likelihood (probability of events)

takes into account the complex nature of life and assigns probabilities to

different evolutionary events.

creates the tree with the highest probability of happening

complex characters are less likely to occur twice than simple characters

may be easier to lose complex characters than gain them Compromising among several "best" trees. (Fig 2.11 p24)

Strict consensus -

Branch present on tree A AND B

Semi strict -

Branch present on tree A OR B but no incompatibilities

Majority rule -

Branch present on 50% or more trees - who says politics doesn't affect

science?

WE Stopped HERE ON THE 5th

Dealing with the real world - models Model assumptions

*Different character states evolve differently (ordering) (2.13 p26)

Fitch parsimony - unordered

Wagner parsimony - ordered

increases required steps in some cases

*Different characters evolve differently

complex characters are less likely to evolve (all else equal)

Parsimony - weighting

ML - different probabilities

*Reversals and parallelism

it can be harder to evolve (parallelism) than to lose (reversal) a

character state. - Dollo parsimony - forget this name weighting and probability should be based on biology or underlying knowledge "unweighted" is still an assumption Belief in the tree

The best tree (fewest steps, min dist, max likelihood)

The following for parsimony only (but some ideas may apply more broadly)

How good are the others - assessing homoplasy

autapomorphy

unique derived character - un shared and uninformative

adding these doesn't help but makes it look like you are

assessing more characters (fig 2.25 p38)

*consistency index (length = number of steps) (fig 2.10 matrix)

Min Length = number of character states in the group- need at

least 1 change to obtain the character

Actual length - reversals and parallelisms add to number of steps

Maximum length = every change to new state is unique. This

equals the number of new character states for each

taxon. CI = min/actual - 1.0 is the best 0 the worst

RI = (max-actual)/(max-min)= (9-5)/(9-4)=0.8 (fig 2.10)

Parts of trees may be good even if the tree has problems

for a branch,

# changes compared to the *CI of these changes

decay rate and number of boot straps (fig 2.17 p 30)

*decay(d) -

in a tree with more steps, a branch may be gone, how many

steps are needed. A d value of 6 means that even with a

tree that has 6 more steps, the branch is still there

Bootstrap (%) (fig 2.16, 1.10)

random sample of characters to be used in analysis

character state stays the same for each taxon use different character sets *Belief in trees in general

Branched tree or net (hybridization and introgression)

species can re-merge after differentiation

OK so what do we do with these trees ? Classification of taxa (31-39)

*Placing the character traits on trees

*Ambiguities (2.18, 2.19

equally parsimonious reconstructions - placement random (2.19a)

outgroup can determine placement (2.19b)

placement depends on the outgroup used (2.20a,b)

unknown character states don't help -

*Constructing a classification

Goals (repeat from above)

Rant about cladistics

Named groups are monophyletic

Not all monophyletic groups are named

Ranks are arbitrary (not much to say unless you don't intuitively see this) Abandon Linean system (incl genera)

*Reality check - other ways of thinking about classification

*Cladistics

*Phenetics (2.24)

*Evolutionary Taxonomy (2.25)

*Practical implications of not adhering strictly to monophyly (for our studies)

Use malvaceae and Sapindales/maple as examples - put up the cladograms