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The following 236 topics were covered in lecture in the Spring 2022 version of EEB 5349 (Phylogenetics). Please refer to the schedule to find links to the slides for the dates indicated.

additivity of distances, Jan-27

Akaike Information Criterion (AIC), Mar-22

amino acid models, Feb-22

among-site rate heterogeneity (ASRV), Feb-10

AND probability rule, Feb-3

anomalous gene trees, Apr-14

Anthony Edwards, Jan-25

ascertainment bias, Mar-24

ASRV and LBA, Feb-17

ASTRAL species tree method, Apr-14

asymmetric morphology model, Mar-24

AU topology test, Feb-17

autapomorphy trail, Mar-24

bats and the flying DNA hypothesis, Feb-15

Bayes rule, Feb-24

Bayesian Analysis of Macroevolutionary Mixtures (BAMM), Apr-26

Bayesian concordance analysis (BUCKy), Mar-10

Bayesian Information Criterion (BIC), Mar-22

Bayesian model selection, Mar-22

Bayesian phylogenetic information, Apr-28

Bayesian species delimitation model (BPP), Apr-28

Beta distribution, Mar-3

Beta-distributed among character frequency variation, Mar-24

binary state-dependent speciation-extinction (BISSE) model, Apr-21

birth-death process, Apr-19

Blomberg’s K, Apr-12

branch-and-bound, Jan-20

brownian motion model, Apr-5

C20 protein mixture model, Feb-22

calibrated clock, Apr-19

cladistics, Jan-25

coalescent process, Apr-12

coalescent tree prior, Apr-12

codon models, Feb-22

compensatory substitutions, Feb-22

conditional probabilities, Feb-3

conditioning on variability, Mar-24

confidence interval, Mar-8

consensus trees, Jan-20

consistency index, Jan-25

correlated evolution models, Mar-29

correlated relaxed clock model, Apr-19

covarion model, Apr-26

David Sankoff, Jan-25

deep coalescence, Apr-14

diagonalization of a matrix, Feb-22

Dirichlet distribution, Mar-3

Dirichlet process prior (DPP), Mar-10

discrete gamma (+G) ASRV model, Feb-10

discrete morphological data, Mar-24

Discrete Uniform distribution, Mar-3

diversification, Apr-21

DPP covarion model, Apr-26

DPP protein mixture models (PhyloBayes), Mar-10

effective population size, Apr-14

eigenvectors/eigenvalues, Feb-22

empirical Bayes, Mar-3

equal-tail-area (ETA) credible interval, Mar-8

equilibrium frequencies, Feb-1

estrus advertisement example, Mar-29

evolutionary distances, Feb-3

exchangeabilty mixture model, Apr-26

exhaustive search, Jan-20

expected bootstrap support, Mar-29

expected value of a random variable, Mar-22

exponential population growth and the coalescent, Apr-12

F81 model, Feb-1

F84 model, Feb-1

fair coin analogy, Mar-29

Felsenstein Zone, Feb-17

fossilized birth-death process, Apr-19

Gamma distribution, Mar-3

Gamma-Dirichlet edge length prior, Mar-3

generalized parsimony, Jan-25

GeoSSE, Apr-21

goodness-of-fit, Feb-1

GTR model, Feb-1

harmonic mean method, Mar-22

Hastings ratio, Mar-1

heated chains (Metropolis-coupled MCMC), Mar-1

Herb Wagner, Jan-25

heterotachy mixture model, Apr-26

heterotachy, Feb-10

hierarchical model, Mar-3

highest-probability-density (HPD) credible interval, Mar-8

HISSE, Apr-21

HKY85 model, Feb-1

homoplasy, Jan-25

incomplete lineage sorting, Apr-14

independence, Feb-3

induced prior, Mar-3

informative prior, Mar-3

inheritance vs convergence explanations of similarity, Feb-17

integration of a probability density, Feb-24

invariable sites (+I) ASRV model, Feb-10

irreversible parsimony, Jan-25

JC69 model, Feb-1

joint posterior, Feb-24

Joseph Camin, Jan-25

K80 model, Feb-1

KH topology test, Feb-17

Larget-Simon proposal, Mar-1

least-squares criterion, Jan-27

likelihood criterion, Jan-20

likelihood of an evolutionary distance, Feb-3

likelihood of an isolated vertex, Feb-3

likelihood of an unrooted tree, Feb-3

likelihood ratio test (LRT), Feb-3

lineages through time (LTT) plots, Apr-21

local clocks relaxed clock model, Apr-19

log likelihood, Feb-3

Lognormal distribution, Mar-3

long branch attraction (LBA), Feb-15

long branch attraction (LBA), Feb-17

Margaret Dayhoff, Jan-25

marginal likelihood estimation, Mar-22

marginal likelihood, Feb-24

marginal posterior distribution, Mar-3

marginal probabilities, Feb-3

Markov chain Monte Carlo (MCMC), Feb-24

Markov models, Feb-1

matrix exponentiation, Feb-22

matrix inverse, Feb-22

matrix multiplication, Feb-22

maximum agreement subtree, Jan-20

maximum likelihood estimate (MLE), Feb-3

MCMC proposal distribution, Mar-1

MCMC robot metaphor, Feb-24

measuring associations from joint dwell times, Mar-31

Metropolis algorithm, Mar-1

Metropolis-Hastings algorithm, Mar-1

minimum evolution criterion, Jan-27

mixing, Mar-1

mixture models, Feb-10

molecular clock LRT, Feb-17

molecules vs. morphology, Mar-24

monohyly, Jan-18

morphological character mapping, Mar-31

multispecies coalescent model, Apr-14

multistate morphology model, Mar-24

MUSSE, Apr-21

nearest-neighbor interchange (NNI) branch swapping, Jan-20

neighbor joining, Jan-27

newick trees, Jan-18

no common mechanism model, Mar-24

nonparametric bootstrapping, Feb-10

Ockham’s Razor, Jan-25

OR probability rule, Feb-3

ordered characters, Jan-25

Ornstein-Uhlenbeck (OU) model, Apr-7

overparameterization artifacts/symptoms, Mar-24

Pagel discrete character correlation, Mar-29

Pagel’s delta, Apr-12

Pagel’s kappa, Apr-12

Pagel’s lambda, Apr-12

PAM matrix, Feb-22

parahyly, Jan-18

parametric bootstrapping, Mar-29

parsimony criterion, Jan-20

parsimony steps, Jan-25

partitioned models, Feb-10

paternity example, Feb-24

Pelargonium example, Mar-31

perfume diffusion metaphor, Feb-1

PGLS ancestral state estimation, Apr-7

PGLS regression, Apr-5

phylogenetic generalized least squares (PGLS), Apr-5

phylogenetic signal, Apr-12

phylogenetic variance-covariance matrix, Apr-5

phylogenetically independent contrasts (PIC), Apr-5

polyphyly, Jan-18

posterior probability vs bootstrap, Mar-29

posterior probability, Feb-24

predictive variance, Feb-1

prior distribution fails, Mar-3

prior probability, Feb-24

probability density, Feb-24

pruning algorithm, Feb-3

pull of the present, Apr-21

Pybus and Harvey’s gamma, Apr-21

QuaSSE, Apr-21

rare disease example, Feb-24

reconnection limit, Jan-20

regression explained, Apr-5

RELL method, Feb-17

restaurant analogy (for DPP), Mar-10

retention index, Jan-25

reversible-jump MCMC (rjMCMC), Mar-29

rjMCMC discrete character dependence model, Mar-29

rjMCMC diversification model, Apr-26

rjMCMC heterotachy model, Apr-26

rjMCMC polytomy model, Mar-29

Robert Sokal, Jan-25

secondary structure models, Feb-22

SH topology test, Feb-17

signature of an adaptive radiation, Apr-21

simulation-based hypothesis testing, Feb-15

site likelihood, Feb-3

site-specific rates model, Feb-10

sojourn vs dwell times, Mar-31

SOWH topology test, Feb-17

split decomposition, Jan-27

split prior, Mar-3

splits, Jan-18

star decomposition, Jan-20

star tree paradox, Mar-29

StarBEAST species tree method, Apr-14

step matrix, Jan-25

steppingstone method, Mar-22

stepwise addition, Jan-20

Steven Farris, Jan-25

stick-breaking metaphor (for DPP), Mar-10

stochastic mapping, Mar-31

strict molecular clock, Apr-19

subtree-pruning-regrafting (SPR) branch swapping, Jan-20

subway map model metaphor, Feb-1

support of a probability distribution, Mar-3

SVDQuartets species tree method, Apr-14

symmetric morphology model, Mar-24

symplesiomorphy, Jan-25

synapomorphy, Jan-25

theta population-scaled mutation rate parameter, Apr-14

tip dating, Apr-19

trace plot, Mar-1

transition probability, Feb-1

transition-transversion rate ratio, Feb-1

transition-transversion ratio, Feb-1

transversion parsimony, Jan-25

tree islands, Jan-20

tree space, Mar-1

tree-bisection-reconnection (TBR) branch swapping, Jan-20

turnover, Apr-21

ultrametric, Jan-18

uncorrelated relaxed clock model, Apr-19

Willi Hennig, Jan-25

Yule pure-birth process, Apr-19