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GENE 3000Fall 2013
slides 127-159
wiki. wiki. wiki.
4 species can be related to each other in only 3 ways
4 species can be related to each other in only 3 ways
A B
C
evolution - story of gain and loss
•when and how were complex eyes evolved? in what species are they lost? are the genes required to develop eyes still there? can they be expressed in different ways?
•how frequently are genes gained and lost? how often is there lateral gene transfer between hosts and pathogens, or microbes?
•why are there more A/T bases in parts of the mitochondrion?
Nature, June 2012
all starts with this
terms• phylogeny: visual representation of the
evolutionary history of populations, genes, species
• tips: terminal ends of a phylogeny, representing the populations, genes, species
• branches: lineages evolving through time
• node: where lineages split; the common ancestor to descendants
• clade: a group all descended from one ancestor
terms• phylogeny: visual representation of the
evolutionary history of populations, genes, species
• tips: terminal ends of a phylogeny, representing the populations, genes, species
• branches: lineages evolving through time
• node: where lineages split; the common ancestor to descendants
• clade: a group all descended from one ancestordiscovermagazine.com
organisms are related through descent from
ancestors
progression of generations
more than 2 million identified and classified
species extant
taxonomy (systematics)
•groups defined on previous slides are clades
•group comprised of one organism and all its descendants (mono-phyly)
•indication of homology
Archosaurs
how do we know?
•inference, reconstruction
•characters are heritable traits that can be compared (an A in position 117; body hair)
•careful evaluation of homology
•assume that having more things in common indicates more recent common ancestor (longer shared history)
homology and homoplasy
•similarity without shared descent is homoplasy - convergent evolution (wings) or evolutionary reversal (snakes don’t have legs)
•homology may require full evidence, e.g. development of insect wings very different from development of bird wings
phylogeny inference
•morphological characters (presence, absence, quality)
•DNA-based characters work the same (idea is there may be more independence, and more of them)
our data matrix
Text? in NEXUS format
parsimony analysis
•assume each state evolved only once (not necessarily true)
•principle of parsimony: the simplest explanation is the most likely
•we can identify how often this assumption is violated
one character
•tentacular forelimbs might be able to split into 2 clades, but cannot fully resolve tree
parsimony is a CRITERION
•our assumption of parsimony does not find the tree, it is a score given to a tree
•trees are searched algorithmically for all possible topologies (or all possible better than score X)
•a parsimony phylogeny analysis returns the set of most-parsimonious trees
our tree
eyeless
“presence of 2 eyes” - obviouslynegatively correlated with “eyeless”
tail
digits
dark stripeshmmm correlated with digits!?
wings
circular tail fin“forked” tail fin
“protruding body”
2 digits - an autapomorphy
our tree
•parsimony tree(s) from class data matrix
•which characters exhibit HOMOPLASY
•remember: homoplasy may be evolutionary convergence/reversal, may also reflect our own uncertainty about the character and how it develops!
•see Box 1 (chapter 4) for another example
molecular data• we will come to this later how it is analyzed, but
we see the problems of
• highly correlated, non-independent characters
• hard to identify very many characters
• thus not a fully resolved phylogeny (but good!)
• if you sequence a single gene region, might have 100 characters that are unbiased by the person collecting the data
example of carnivores
define “carnivore” please...define “carnivore” please...
why study phylogeny of carnivores?
lets ask a simple question: did aquatic pinnipeds evolve only once, or were there multiple transitions to the sea?
12 characters, 10 carnivores
synapomorphies
1313
1313
20 characters, 3 equallyparsimonious trees
our result is robust to this uncertainty: one origin of pinnipeds (consensus at
left)
parsimony•simple assumption, simple model -
may lead to several ‘equally parsimonious’ results
•more data will not always solve the problem
•more complex models evaluate the non-independence of data, the empirical patterns of DNA substitution, and probability theory