Phylogenetics Flashcards
Phylogenetic tree
Graphical summary of inferred phylogeny, marks on limbs mark new traits
Phylogenetics
The study of evolutionary relationships among taxa
Sister taxa
Closest relatives
How to determine similarities/differences in phylogenetic trees
Look at sister taxa, swing branches around in head if necessary
Characters for phylogenetic analysis
Morphology (historically), behavior, physiology, biochemistry, DNA or protein sequences (today)
Characters for phylogenetic analysis require
Being independent of each other (characters not closely related), variable among taxa due to genetic differences (not environmental), reflect homology
Homology
Similarity due to common ancestry, useful in phylogenetic analysis
Analogy
Similarity not due to common ancestry, confuses phylogenetic analysis
Convergence
Type of analogy, independent evolution of a similar trait (ability to fly in birds and bats)
Reversal
Type of analogy, loss of diverged trait or loss of new trait (loss if wings in flightless birds)
Synapomorphy
Shared, derived character state, reflect homology, useful in phylogenetic analysis (trait along the main branch that distinguishes one set of species from another - tetrapods, amniotes, reptilia)
Symplesiomorphy
Shared, primitive character state, old homology or trait shared beyond the group, not useful (something further back when referring to just one group - amniotic egg for crocs and birds since reptilia still in that classification too)
Autapomorphy
Unique, derived character state, not shared by multiple groups, not useful (trait that is present just in that one species - feathers for birds)
Cladistics
A way to infer relationships among taxa using principle of parsimony
Parsimony
Simpler hypotheses are preferred over more complex hypotheses
Parsimony informative
Must have at least two states, each represented at least two times - TTTCC is because T and C are both present twice at least
Parsimony uninformative
Not having at least two states two times each at least - GGGGG is not because it only has one state, AAGCT is not since there are not two each
Preferred phylogeny identification
Compare all possible trees, sum the # of character states across all characters for each tree, the preferred tree is the one that implies the lowest overall character state changes
Bootstrapping
Randomly sampling characters from the data set to estimate support for each branch of the tree (%age means how sure this branch goes there and >70% is a good thing)
Monophyletic group
Includes all descendants of common ancestor
Paraphyletic group
Includes only some descendants of a common ancestor
Polyphyletic group
Usually a mistake, includes distantly related species not sharing a recent common ancestor
Taxonomic classification should include
Monophyletic groups because they are more based on genetics and show similar relations in genes not just appearance
Coevolution
Evolving together with changes in the environment and mutations
Cospeciation
Separate species evolve along similar lineages due to their relationships (aphids and bacteria)
Phylogenetic trees to detect cospeciation
Look and see if divergence of two species looks similar in terms of time and how it branched (% support)
Phylogenetic trees to study adaptation
Comparative method, look at the order of changes based on tree, if this adaptation evolved before another then the second one isn’t an adaptation but rather a pre-adaptation
Phylogenetics and disease transmission
Look at which species has which virus species when based on genetic information and look and number of changes
