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The following topics were covered in lecture in the Spring 2026 version of EEB 5349 (Phylogenetics). Please refer to the schedule to find links to the slides for the dates indicated.

additivity of distances, Jan-29

among-site rate heterogeneity (ASRV), Feb-10 apomorphy, Jan-29

among-site state frequency heterogeneity, Mar-24

archery priors example, Feb-19

ascertainment bias, Mar-24

autoapomorphy trail, Mar-24

bat monophyly test, Feb-12

Bayes’ rule, Feb-17

bootstrapping (non-parametric), Feb-17

bootstrapping (IQ-TREE ultrafast), Feb-17

clade, Jan-29

coalescence, Mar-9

conditioning on variability, Mar-24

consensus trees, Jan-22, Jan-29

density example (gold-to-aluminum brick), Feb-19

discrete Gamma model, Feb-12

distribution, Beta, Mar-3

distribution, Dirichlet, Mar-3

distribution, discrete Uniform, Mar-3

distribution, Gamma, Feb-12

distribution, Gamma-Dirichlet, Mar-3

distribution, Lognormal, Mar-3

distribution, proposal (for MCMC), Feb-19

distribution, support, Mar-3

distribution, target (for MCMC), Feb-19

effective population size (Ne), Mar-9

evolutionary distance, Jan-22

exhaustive search, Jan-22

expected time to coalescence, Mar-9

Farris’ paraphyly/polyphyly algorithm, Jan-29

Felsenstein (1981) model (F81), Feb-5

Felsenstein (1984) model (F84), Feb-5

fence analogy (truncated priors), Mar-3

Fitch’s parsimony algorithm, Jan-29

four-point condition, Jan-29

free rates model (+R), Feb-12

frequencies, equilibrium state, Mar-24

gene trees, Mar-9

general time-reversible model (GTR), Feb-5

Hasegawa, Kishino, and Yano (1985) model (HKY85), Feb-5

Hastings ratio, Feb-26

heated chains (MCMC), Feb-19

heterotachy, Feb-10

hyperparameter, Mar-3

hyperprior, Mar-3

independence of events, Feb-10

integrals, Feb-19

invariable sites model (+I), Feb-10

Jukes-Cantor (1969) model (JC69), Feb-3

kappa (transition-transversion rate ratio), Feb-5

kernel density estimation, Feb-26

Kimura (1980) 2-parameter model (K2P, K80), Feb-3

induced prior, Mar-3

likelihood (criterion), Jan-20

likelihood (single sequence), Feb-5

likelihood (evolutionary distance), Feb-10

likelihood (tree), Feb-10

likelihood, vs. probability, Feb-5

marginal likelihood, Feb-17

maximum agreement subtree, Jan-22

maximum likelihood estimate (MLE), Feb-10

MCMC, local move proposal, Feb-26

MCMC, Markov-chain Monte Carlo, Feb-19

MCMC, sliding window proposal, Feb-26

MCMC, robot metaphor, Feb-19

Metropolis algorithm, Feb-19

Metropolis-Hastings algorithm, Feb-26

mixing (MCMC), Feb-19

models, asymmetric, Mar-24

models, discrete Gamma, Feb-8=10

models, discrete morphology, Mar-24

models, empirical Bayesian, Mar-3

models, hierarchical, Mar-3

models, mixture (+I, +G, Q matrix, edge length), Feb-10

models, Mk, Mar-24

models, partition, Feb-10

models, symmetric, Mar-24

monophyly, Jan-29

nearest-neighbor interchange (NNI) branch swapping, Jan-22

neighbor-joining (NJ), Jan-29

newick trees, Jan-20

paraphyly, Jan-29

parsimony criterion, Jan-20, Jan-29

partitioned models, Feb-10

paternity example, Feb-17

plesiomorphy, Jan-29

polyphyly, Jan-29

prior, distribution, Mar-3

prior, Gamma-Dirichlet, Mar-3

prior, induced split, Mar-3

probability, “and” rule, Feb-5

probability, conditional, Feb-10

probability, density, Feb-19

probability, joint, Feb-10

probability, marginal, Feb-17

probability, mass vs. density, Feb-19

probability, no coalescence, Mar-9

probability, “or” rule, Feb-5

probability, posterior, Feb-17

probability, prior, Feb-17

probability, total, Feb-17

probability, vs. likelihood, Feb-5

pruning algorithm, Feb-10

rare disease example, Feb-17

rate heterogeneity, Feb-10

rate matrix (instantaneous), Feb-3

reconnection limit, Jan-22

running on empty (MCMC without data), Mar-3

simulation, Feb-12

site-specific rates, Feb-10

software, PAUP*, Jan-22

splits, Jan-20

split decomposition, Jan-29

splitstree, Jan-29

star decomposition, Jan-22

stepwise addition, Jan-22

subtree-pruning-regrafting (SPR) branch swapping, Jan-22

symplesiomorphy, Jan-29

synapomorphy, Jan-29

theta (population genetics parameter), Mar-9

trace plots, Feb-19

traffic accidents Poisson example, Mar-24

transition (probability), Feb-3

transition (substitution type), Feb-3

transition-transversion rate ratio, Feb-5

transition-transversion ratio, Feb-5

transversion (substitution type), Feb-3

tree islands, Jan-22

tree-bisection-reconnection (TBR) branch swapping, Jan-22

ultrametric, Jan-20