Ch 2 - The tree of life Flashcards
Systematics
2 branches: taxonomy - Linnaeus, Genus species; Phylogenetics: how species are related (trees)
How does tree structure aptly describe evolutionary history?
Dead branch - extinction; new branch - divergence; trunk - common ancestry; older branches - more ancient; end of branches - extant (existing) species
Taxonomic categories, and name them
Levels of classification: Kingdom, Phyla, Class, Order, Family, Genus, Species (King Phillip cried out for good soup)
Clade
aka monophyletic group, which includes all descendants of a common ancestor; a character state (ex. feathers) provides evidence - could be ancestral or derived
Cladistics
Willi Hennig: phylogenetic systematics
Divergence
New species formed and becoming more different
Character
A trait, such as shape, size, also DNA sequences
Character state
the version of a character: small/big, colour/none, etc.
Species may share similar character state because…
Share ancestral state - symplesiomorphy; share a unique derived state - synapomorphy; by independent means (ie birds and bats have wings) - homoplasy (convergence (in distantly related)/parallelism (in closely related))
Synapomorphy
Shared, derived characters - good indicator for closely related species or for a clade
Symplesiomorphy
Share an ancestral state
Autapomorphies
derived character states in only one lineage
Homoplasy
Convergent evolution of independent origin, aka - not homology; also reversals may mask synapomorphies
Convergent Evolution
independent origin of a trait in 2+ taxa
Evolutionary reversal
Trait reverts back to ancestral type; this is homoplasy
Polytomy
relationships without enough info to determine the branching order, clumped together as they stem from common ancestor
Occam’s razor
“Simplest solution tends to be the best”. We want the fewest assumption and hypothetical things - law of succinctness
Parsimony
Traits placed to minimize number of evolutionary steps, simplest explanation - shortest overall tree length - based on synapomorphies
Basic progression to mammals
Tetrapod limbs, amnion, homeothermy (in mammals and birds)
Paraphyletic
Some but not all descendants of a single common ancestor (ie reptiles did not all descends from the same common ancestor)
Retrotransposons
Genomics approach: small section of selfreplicating DNA which inserts itself into genome - really rare, little chance of homoplasy
Maximum likelihood
chooses model of evolutionary change (ie all nucleotides equally likely to change) - statistical: evaluates significance of tree shape; very time consuming, limits number of taxa you can examine
Kimura method
parameter assumes the transitions are more likely than conversions
Distance method
Don’t search all tree space; computes genetic distance among all pairs of taxa, smallest distance links pair (neighbour joining); compares how different they are (gives a value), reduces to node then recalculates matrix and repeat; fast, only makes one tree.
The Molecular Clock
Genetic distances to measure evolutionary time; Dayhoff: compares proteins sequences; mostly linear; however, some proteins can evolve lots, others don’t (ie. conserved)
Factors that affect mutation rate in different species
Lifespan (ie elephant vs bacteria), environment, accuracy of DNA polymerase
Dayhoff method
Calculates score between changes in amino acids (ie Ile and Leu not too different, but Leu and Arg would have greater score)
Calibrating molecular clock
If you have a known divergence time (fossil), then # changes/divergence time = x # substitutions/million years; also D = 2rt (D = proportion of changes, r = rate, t = time (Myr))
Why are rapidly evolving DNA sequences only good for taxa that have diverged recently?
Doesn’t work for past ones since the changes would be too fast to determine branching
Isthmus of Panama
Formed when North and South america, split the “gulf of mexico”, separated the sea urchin populations; good example of calibration
Hybridization
Inbreeding b/w closely related species forming a “middle” one; creates a net in the tree (reticulated)
Difficulties in phylogenic trees
Limited data (esp. extinct); DNA can change in several spots in concert; homoplasy; reversals hide relatedness; rapid evo. doesn’t allow enough time for lineages to develop unique character states; haplotype is fixed (lose 2nd one), ancestor on one side is polymorphic as well as the common ancestor
