Chapter 5 Flashcards
Wrote The Principles of Numerical Taxonomy,
obert Sokal and Peter Sneath
Essentially assessed overall similarity and Often referred to as Phenetics
Numerical Taximony
- Intellectual successor to NT
* Count pairwise differences between species
Genetic Distance Based Method
Slowed American acceptance and set up a battle between pheneticists and cladists that continued until the 1980’s
• Goal: develop an objective taxonomy and a method for phylogenetic reconstruction
Willi Hennig
find the tree with the minimum amount of homoplasy (convergences, reversals, parallelisms)
fewest evolutionary changes
maximum parsimony
Phylogenetic Analysis Using Parsimony
PAUP* (Swofford)
very fast tree-searching algorithms
TNT (Goloboff)
Rarely do you get just one most parsimonious tree
• What do you do when each of these is equally likely?
Consensus Trees
only those nodes found in all most parsimonious trees represented
Strict consensus
nodes found in greater than 50% of trees represented
Majority Rule consensus
Sampling with replacement
Bootstrap analysis - about 75% is good
in tree support what is the ultimate test?
congruence
Congruence - does the tree in one analysis match the tree of another?
Transitions
purines (AG) or
pyrimidines (CT) - easier
Transversions
urines and pyrimidines (AT, AC, GT, GC) =harder
• Simplest based on transmission codes
= Neighbor Joining - doesn’t assume equal rates of DNA sequence evolution
• Third position based on transmission codes
easiest - least likely to alter amino acid •
First - based on transmission codes
middle, second - hardest
calculates the tree that best fits the data and model
Maximum Likelihood
Runs numerous simulations of the data to maximize probability for the tree (Markov Chain Monte Carlo)
Bayesian Analysis
Maximum likihood uses
bootstrap
Bayesian Analysis
posterior probabilities, close to a statistic, but tend to overestimate support
based originally on a fixed rate of change
Molecular clocks
alter rates along branches
• BEAST: Relaxed clock – requires fossil
Show us that basing a taxonomy means difficult changes
• 2 examples – horses and tetrapods
Fossils and Phylogeny
Vertebrates to Land
Without fossils, this would be confusing
• Major changes to shoulder, pelvis, ear, skull, etc.
• Well known and studied
• A group of lobe-finned fishes lost dorsal fins, lost connection of pectoral to skull, gained digits, gained connection of pelvic girdle to vertebrae, etc.
Very common fossil, long known- fish
Eusthenopteron
Recent fossil, no dorsal fin-fish
Panderichthys
Gills as adult, no dorsal fin, but with wrists and a cervical vertebra Verdict: ? Fishapod?
Tiktaalik
use phylogeography to understand what
continental drift
Who proposed Continental Drift
Alfred Wegener
movement
dispersal
sepration due to geological processes
Vicariance
Phylogenetic Independent Contrasts
( A-B ) divided by branch length
