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
AAAAGTCATC
AAAACTCATC
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