# Index to topics covered in 2024 (EEB 5349)

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The following topics were covered in lecture in the Spring 2024 version of EEB 5349 (Phylogenetics). Please refer to the schedule to find links to the slides for the dates indicated.

adaptive radiations, Apr-23

Akaike Information Criterion (AIC), Feb-29

among-site state frequency heterogeneity, Mar-21

among-site rate heterogeneity (ASRV), Feb-8

archery priors example, Feb-20

ascertainment bias, Mar-21

autoapomorphy trail, Mar-21

Bayesian analysis of macroevolutionary mixtures (BAMM), Apr-23

bat monophyly test, Feb-15

Bayes’ rule, Feb-20

Bayesian Information Criterion (BIC), Feb-29

binary-state speciation and extinction (BiSSE) model, Apr-23

birth-death tree model, Apr-16

bootstrapping (non-parametric), Feb-15

bootstrapping (parametric), Mar-26

bootstrapping (IQ-TREE ultrafast), Feb-15

branch-and-bound, Jan-18

Brownian motion model, Apr-2

calibration prior, Apr-16

coalescence, Mar-7

codon models, Apr-11

columbine example, Apr-23

comparative method, Apr-2

concordance factor (CF), Apr-9

conditioning on variability, Mar-21

confidence intervals, Apr-16

consensus trees, Jan-18

correlated relaxed clock model, Apr-16

covarion, Apr-18

credible intervals, Apr-16

deep coalescence, Mar-7

delta, Pagel’s, Apr-4

density example (gold-to-aluminum brick), Feb-20

dependence model, Mar-26

Dirichlet process prior, Apr-9

discrete Gamma model, Feb-8

dissonance, Apr-25

distribution, Beta, Mar-5, Mar-21

distribution, Dirichlet, Mar-5

distribution, discrete Uniform, Mar-5

distribution, Gamma, Feb-8, Mar-5

distribution, Gamma-Dirichlet, Mar-5

distribution, Lognormal, Mar-5

distribution, marginal posterior, Feb-27

distribution, proposal (for MCMC), Feb-22

distribution, support, Mar-5

distribution, target (for MCMC), Feb-22

diversification rate, Apr-23

dwell time, Mar-28

edge length, Jan-30

effective population size (Ne), Mar-19

estrus advertisement example, Mar-26

evolutionary distance, Feb-6

exchangeabilities, nucleotide, Jan-30

exchangeabilities, amino acid, Apr-11

exhaustive search, Jan-18

expected time to coalescence, Mar-7

extinction rate, Apr-23

evolutionary correlation, Mar-26

Felsenstein (1981) model (F81), Feb-1

Felsenstein (1984) model (F84), Feb-1

fence analogy (truncated priors), Mar-5

fossilized birth-death process, Apr-16

free rates model (+R), Feb-15

frequencies, equilibrium nucleotide, Jan-30

frequencies, equilibrium amino acid, Apr-11

frequencies, equilibrium state, Mar-21

gamma, Pybus and Harvey, Apr-23

gene trees, Mar-7

general time-reversible model (GTR), Feb-1

genetic code, Apr-11

Hasegawa, Kishino, and Yano (1985) model (HKY85), Feb-1

heated chains (MCMC), Feb-22

heterotachy, Feb-8, Apr-18

hyperparameter, Mar-5

hyperprior, Mar-5

independence of events, Feb-6

induced prior, Mar-5

information content, Apr-25

integrals, Feb-20

invariable sites model (+I), Feb-8

Jukes-Cantor (1969) model (JC69), Jan-30

K, Blomberg’s, Apr-4

kernel density estimation, Feb-27

Kimura (1980) 2-parameter model (K2P, K80), Feb-1

lambda, Pagel’s, Apr-4

likelihood criterion, Jan-18

likelihood (single sequence), Feb-6

likelihood (evolutionary distance), Feb-6

likelihood ratio test, Feb-6

likelihood, vs. probability, Feb-20

lineage-through-time (LTT) plots, Apr-23

marginal likelihood, Feb-20, Feb-29

marginal likelihood (steppingstone method, Feb-29

Markov model, Jan-30

maximum agreement subtree, Jan-18

maximum likelihood estimate (MLE), Feb-6

Markov-chain Monte Carlo (MCMC), Feb-22

MCMC, robot metaphor, Feb-22

MCMC, local move proposal, Feb-27

MCMC, reversible jump (rjMCMC used in BAMM, heterotachy), Mar-26, Apr-18, Apr-23

MCMC, sliding window proposal, Feb-27

Metropolis algorithm, Feb-22

Metropolis-Hastings algorithm, Feb-22

mixing (MCMC), Feb-22

goodness-of-fit of a model, Jan-30

Hastings ratio, Feb-22

models, amino acid, Apr-11

models, asymmetric, Mar-21

models, Brownian motion, Apr-2

models, codon, Apr-9

models, covarion, Apr-18

models, dependence, Mar-26

models, Dirichlet process prior, Apr-9, Apr-18

models, discrete Gamma, Feb-8

models, discrete morphology, Mar-21

models, empirical Bayesian, Mar-5

models, hierarchical, Mar-5

models, independence, Mar-26

models, mixture (+I, +G, Q matrix, edge length), Feb-8, Apr-18

models, mixture (C20), Apr-11

models, Mk, Mar-21

models, partition, Feb-8

models, protein, Apr-11

models, relaxed clock Apr-11, Apr-16

models, state-dependent diversification (BiSSE, MuSSE, GeoSSE, QuaSSE, HiSSE), Apr-23

models, symmetric, Mar-21

monophyly, Jan-16

nearest-neighbor interchange (NNI) branch swapping, Jan-18

newick trees, Jan-16

nonsynonymous/synonymous rate ratio (omega), Apr-11

point accepted mutation (PAM) unit, Apr-11

paraphyly, Jan-18

parsimony criterion, Jan-18

partitioned models, Feb-8

paternity example, Feb-20

phylogenetically generalized least squares (PGLS), Apr-2

phylogenetically independent contrasts (PIC), Apr-2

polyphyly, Jan-18

predictive ability of a model, Jan-30

prior, calibration, Apr-16

prior, coalescent tree, Mar-19

prior, distribution, Mar-5

prior, Gamma-Dirichlet, Mar-5

prior, induced split, Mar-5

prior, polytomy, Mar-26

probability, “and” rule, Feb-6

probability, conditional, Feb-6

probability, density, Feb-20

probability, joint, Feb-6

probability, marginal, Feb-6

probability, mass vs. density, Feb-20

probability, no coalescence, Mar-7

probability, “or” rule, Feb-6

probability, prior, Feb-20

probability, posterior, Feb-20

probability, support, Mar-5

probability, total, Feb-6

probability, vs. likelihood, Feb-20

pruning algorithm, Feb-8

pull of the present, Apr-23

random local clocks model, Apr-16

running on empty (MCMC without data), Mar-5

site-specific rates, Feb-8

software, ape, Apr-11

software, BayesTraits, Apr-4

software, BPP, Apr-25

software, BUCKy, Apr-9

software, caper, Apr-11

software, geiger, Apr-11

software, MrBayes, Mar-7

software, PAUP*, Jan-18 (and many times after)

software, PhyloBayes, Apr-9

software, phytools, Apr-11

software, RevBayes, Mar-21, Mar-28

speciation rate, Apr-23

splits, Jan-16

state-dependent diversification models, Apr-23

steppingstone method (marginal likelihood estimation), Feb-29

stochastic character mapping, Mar-28

subway map model analogy, Jan-30

rare disease example, Feb-20

rate heterogeneity, Feb-8

rate matrix (instantaneous), Feb-1

reconnection limit, Jan-18

simulation, Feb-15

sojourn time, Mar-28

species delimitation, Apr-25

star decomposition, Jan-18

stepwise addition, Jan-18

substitution rate, Jan-30

subtree-pruning-regrafting (SPR) branch swapping, Jan-18

theta (population genetics parameter), Mar-7

tip dating, Apr-16

trace plots, Feb-22

traffic accidents Poisson example, Mar-21

transition probabilities, Jan-30

transition (substitution type), Feb-1

transition-transversion rate ratio, Feb-1

transition-transversion ratio, Feb-1

transversion (substitution type), Feb-1

tree islands, Jan-18

tree-bisection-reconnection (TBR) branch swapping, Jan-18

turnover, Apr-23

ultrametric, Jan-18

uncorrelated lognormal relaxed clock model, Apr-16

variance-covariance matrix, Apr-2

Yule pure-birth tree model, Apr-16