Module 3 Flashcards
DNA barcoding
Identifying samples to species based on a short, standardized gene sequence
Uses co1 for animals and rcbl and mark for plants
Issues include that it doesn’t distinguish ancestral polymorphisms, male based gene flow, selection on mtdna, gene flow after hybridizations, transfer bw mtdna and nuclear, recent speciation, slowed rates of molecular evolution
Barcoding gap
Gap in variation within a species to between species
Assumes separate species will have a greater degree of variation than within species
Biological species concept
A species is group of interbreeding populations with unique genetic identities and are reproductively isolated from other populations allowing for independent evolution
Tips
End of the process, usually present day. Taxonomic level depends on research question
Nodes
Most recent common ancestor, can rotate
Monophyletic clade
Natural grouping of node and all tips and ancestors
Paraphyletic clade
Non natural groupings of selected tips and/or ancestors
Branches
Edges or internodes
Phylogram
Tree that models rate of change
Chronogram
Tree that indicates absolute time
Roots
Starting points
Informs outgroup of rooted trees
Synapomorphy
Characteristic shared bw ancestor and all evolutionary descendants
Analogies
Traits shared by unrelated species through convergent evolution
Autapomorphy
A distinctive feature/derived trait that is unique to a given taxon
Distance based phylogeny
Uses measures of overall similarity to compare taxa by creating distance (not genetic) matrices b/w samples
Quick, easy, initial approximation but not v accurate
UPGMA
Unweighted pair group methods with arithmetic means used as a distance based method to cluster OTUs
NJ (neighbor joining)
Clustering method of distance based trees that pairs neighbors connected by a single node.
Reduces overall length if tree -> shortest tree
ME (minimum evolution)
Distance based optimization method that produces the shortest branch lengths (minimum distance)
Observed distance
Genetic distance considered by distance methods (only measures difference bw input and output)
Genetic distance
The total amount of mutations that occur between two taxa
Discrete character
Tree searching method that finds best evolutionary explanation for taxonomy
Maximum parsimony
Discrete character method
Functions on concept that the fewest change possible is best
Mist common for non-molecular data
Maximum likelihood
Discrete character method
Tests the probability of the hypothesis of the data to match a given tree
Bootstrap
Resampling/ testing of the data to provide support for ML method
Rearrangement methods of ml
Nearest neighbor joining (NNI)
Sub tree pruning and regrafting (SPR)
Tree bisection and recombination (TBR)
Hill climbing approach
Optimizes trees by only using best tree to proceed
Has issues with local optimization
Bayesian phylogenetically
Finding the best option in tree space by using prior knowledge to inform tree searching
Markov chain Monte Carlo (mcmc)
Random walking through tree face that allows all uphill transitions, slight downhills but negates drastic downhills
Mc3
Uses cold chains and hot chain robots (scouts) to optimize mcmc approach
Maximum a posteriori (MAP) tree
After Bayesian methods
Topology with max posterior probability (like ml tree)
Majority rule consensus tree
After Bayesian methods
Constructed w/o that it contains all clades that occur in at least x% of trees in distribution
95% credible set
After Bayesian methods
The set of all tree topologies that account for 95% of posterior probability
Molecular clock hypothesis
Mutation rate has a rate of change and sequence divergence is proportional to time
Rate heterogeneity
Rates of evolution differ among lineages
Strict clock model
All branches have same rate of change
Local clock model
Clusters rates and branches
Relaxed branch
Rate for each branch, impossible to directly estimate
Phylogeny calibration
Uses known events to date tree
Like fossil data
Phylogenetic comparative methods (PCM)
Analytical study of species, populations, and individuals in a historical framework to elucidate the mechanisms at the origin of the diversity of life
Phylogenetic non independence
Related species may share the same traits which violates the assumption of independence for biological data
A single heritable change can be inherited by many descendants and get counted multiple times
Species richness
The number of different species in a given area
= speciation - extinction
Speciation
Splitting of ancestral lineage into 2 evolutionarily independent descendant lines
Extinction
Termination of a branch in a phylogenetic tree. A branch with no living descendants
Phylogenetic imbalance
How taxa are distributed among different clades of a phylogeny
Low may be due to competition while high may be due to heritable characters that effect diversification
Phylogenetic diversification timing
Refers to when clades split
Early may be due to adaptive radiation while late may be due to island pops
Lineage through time (LTT) plots
Counts each time it branches off until tips are reached to investigate diversification rates
3 different models: constant, abrupt, and gradual
Gamma stat
Used to measure if per-lineage speciation and extinction rates have remained constant through time
