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