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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.

adaptive radiations, Apr-21

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

Bayesian analysis of macroevolutionary mixtures (BAMM), Apr-21

binary-state speciation and extinction (BiSSE) model, Apr-21

birth-death tree model, Apr-9

Blomberg’s K, Apr-2

bootstrapping (non-parametric), Feb-17

bootstrapping (parametric), Mar-26

bootstrapping (IQ-TREE ultrafast), Feb-17

Brownian motion model, Mar-31

calibration prior, Apr-9

clade, Jan-29

coalescence, Mar-9

codon models, Apr-16

columbine example, Apr-21

comparative method, Mar-31

concordance factor (CF), Apr-14

conditioning on variability, Mar-24

confidence intervals, Apr-9

consensus trees, Jan-22, Jan-29

confidence intervals, Apr-9

correlated relaxed clock model, Apr-9

covarion, Apr-14

credible intervals, Apr-9

deep coalescence, Mar-12

delta, Pagel’s, Apr-2

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

dependence model, Mar-26

Dirichlet process prior, Apr-9, Apr-14

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

diversification rate, Apr-21

effective population size (Ne), Mar-9

estrus advertisement example, Mar-26

evolutionary correlation, Mar-26

evolutionary distance, Jan-22

exhaustive search, Jan-22

expected time to coalescence, Mar-9

extinction rate, Apr-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

exchangeabilities, amino acid, Apr-16

extinction rate, Apr-9

fossilized birth-death process, Apr-9

four-point condition, Jan-29

free rates model (+R), Feb-12

frequencies, equilibrium amino acid, Apr-16

frequencies, equilibrium nucleotide, Mar-24

gamma, Pybus and Harvey, Apr-21

gene trees, Mar-9

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

genetic code, Apr-16

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

K, Blomberg’s, Apr-2

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

lambda, Pagel’s, Apr-2

likelihood (criterion), Jan-20

likelihood (single sequence), Feb-5

likelihood (evolutionary distance), Feb-10

likelihood (tree), Feb-10

likelihood, vs. probability, Feb-5

lineage-through-time (LTT) plots, Apr-21

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, reversible jump, Mar-26

MCMC, robot metaphor, Feb-19

Metropolis algorithm, Feb-19

Metropolis-Hastings algorithm, Feb-26

mixing (MCMC), Feb-19

models, amino acid, Apr-16

models, asymmetric, Mar-24

models, Brownian motion, Mar-31

models, codon, Apr-16

models, covarion, Apr-14

models, dependence, Mar-26

models, Dirichlet process prior, Apr-9, Apr-14

models, discrete Gamma, Feb-8=10

models, discrete morphology, Mar-24

models, empirical Bayesian, Mar-3

models, hierarchical, Mar-3

models, independence, Mar-26

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

models, Mk, Mar-24

models, partition, Feb-10

models, protein, Apr-16

models, relaxed clock Apr-9

models, state-dependent diversification (BiSSE, MuSSE, GeoSSE, QuaSSE, HiSSE), Apr-21

models, symmetric, Mar-24

monophyly, Jan-29

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

neighbor-joining (NJ), Jan-29

newick trees, Jan-20

nonsynonymous/synonymous rate ratio (omega), Apr-16

paraphyly, Jan-29

parsimony criterion, Jan-20, Jan-29

partitioned models, Feb-10

paternity example, Feb-17

phylogenetically generalized least squares (PGLS), Mar-31

phylogenetically independent contrasts (PIC), mar-31

plesiomorphy, Jan-29

point accepted mutation (PAM) unit, Apr-16

polyphyly, Jan-29

prior, calibration, Apr-9

prior, distribution, Mar-3

prior, Gamma-Dirichlet, Mar-3

prior, induced split, Mar-3

prior, polytomy, Mar-26

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

pull of the present, Apr-21

random local clocks model, Apr-9

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, BayesTraits, Apr-2

software, BUCKy, Apr-14

software, PAUP*, Jan-22

software, PhyloBayes, Apr-14

software, RevBayes, Mar-5, Mar-12

speciation rate, Apr-9

splits, Jan-20

split decomposition, Jan-29

splitstree, Jan-29

star decomposition, Jan-22

state-dependent diversification models, Apr-21

stepwise addition, Jan-22

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

symplesiomorphy, Jan-29

synapomorphy, Jan-29

theta (population genetics parameter), Mar-9

tip dating, Apr-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

turnover, Apr-21

ultrametric, Jan-20

uncorrelated lognormal relaxed clock model, Apr-9

variance-covariance matrix, Apr-2

Yule pure-birth tree model, Apr-9