A primer on phylogenetic biogeography and DEC models. March 13, 2017 Michael Landis Bodega Bay Workshop Sunny California

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1 A primer on phylogenetic biogeography and DEC models March 13, 2017 Michael Landis Bodega Bay Workshop Sunny California

2 Epidemiology Air travel communities H3N2 Influenza virus samples CE Flu, H3N2 Pybus et al, 2015

3 Conservation Eastern forests relatively new habitat Cercopithecidae (Old World Monkeys) Primates Guschanski et al, 2013

4 Origin stories Out-of-Australia Radiation Wallacea rises (20 25 Ma) Songbirds Moyle et al, 201

5 Biogeographic events

6 Discrete areas (character states) Time-calibrated phylogeny Data matrix Octodon degus Ancestral state estimates Photo, José Cañas Upham & Patterson, 2012 (Mol Phylo Evol)

7 Species occurrence data (gbif.org, 2013) Discrete presence-absence (Upham & Patterson, 2012)

8 Data matrix taxon i, character j Continuous e.g. latitude-longitude Discrete e.g. single area presence-absence (range)

9 Models Continuous e.g. Brownian motion (Gaussian) Discrete e.g. continuous-time Markov chain

10 Discrete Island Model Dispersal-only model One area per taxon (endemic/individual) Learn favored dispersal routes Work by: Sanmartín et al., 2008 (J Biogeog) Lemey et al., 2009 (PLoS Comp Biol)

11 Dispersal on a graph Sanmartin et al., 2008 (J Biogeog)

12 Embedding the graph in Q General Time Reversible (a c) Stepping Stone (b f) Sanmartin et al., 2008 (J Biogeog)

13 Continuous models Brownian motion Each taxon is an individual sample Population and epidemiology models Work by: Lemmon & Lemmon, 2008 (Syst Biol) Lemey et al., 2010 (Mol Biol Evol) Bouckaert et al (Science)

14 2D Brownian motion X(T) X(0)

diffuse by Brownian motion for each branch: Branch

15 Relaxed random walk Joint inference of gene tree using relaxed molecular clock Latitude, longitude diffuse by Brownian motion for each branch: Branch rate rescaled ( relaxed ): Lemey et al., 2009 (Mol Biol Evol)

16 Earth is round Sphere Plane Diffusion distance for T=0.1, T=1 Bouckaert, 2014 (biorxiv)

17 Earth is wet Numerical integration + rasters to forbid certain areas Bouckaert et al., 2012 (Science)

18 Continuous range evolution models Diffusion of set of individual coordinates??? Diffusion of range as polygon??? Harder problem, underexplored

19 DEC Dispersal-(Local) Extinction-Cladogenesis (DEC) Many areas per taxon (range) D,E as parameterized event types Work by: Ree et al., 2005 (Evolution) Ree & Smith, 2008 (Syst Biol)

20 DEC event types

21 Rate matrix for anagenesis Ree and Smith, 2008 (Syst Biol)

22 Dispersal & Extirpation Exponentially-distributed times between events Ree et al., 2005 (Evolution)

23 DEC event types

24 Prob Sympatry (narrow) 1/1 1/1 Allopatry 1/6, 1/6 Sympatry (subset) 1/6, 1/6 1/6, 1/6 Ree et al., 2005 (Evolution)

25 DEC likelihood Anagenesis Cladogenesis

26 Generalized DEC model Anagenetic Cladogenetic Matzke, 2013 (Frontiers Biogeog)

27 Unconstrained (constant, equal rates) Stepping stone (Small adjacent ranges: K, O, M, H, KO, OM, MH) Psychotria mariniana Stratified (time-dependent probs) Ree and Smith, 2008 (Syst Biol)

28 Stratified model

29 Island origin times (Ma) Q i varies over time! Transition probability over epochs

30 Dispersal should occur before areas split Event common Event rare A!B CCGT B A CCGA CTCA A A A B A B Geological time Less probable observation given tree Biogeographic dating Landis, 2016

31 Dispersal should occur before areas split Event common A!B Event rare CCGT B A CCGA CTCA A A A B A B Geological time More probable observation given tree Biogeographic dating Landis, 2016

32 Dispersal should occur after areas merge Event rare Event common A!B CCGT B CCGA B A CTCA A TTCC A A B A B Geological time Less probable observation given tree

33 Dispersal should occur after areas merge Event rare Event common A!B CCGT B CCGA B A CTCA A TTCC A A B A B Geological time More probable observation given tree

35 Speciation hidden by extinction 2 2 x x x x x

36 Geographic State Speciation Extinction (GeoSSE) DEC model Joint birth-death process & range evolution Accounts for hidden speciation Range evolution, speciation, extinction intertwined Work by: Goldberg et al., 2011 (Syst. Biol.) Goldberg & Igić, 2012 (Evolution)

37 Parameter Areas Event Speciation A New lineage in area A B AB New lineage in area B New lineage in area A or B Dispersal A and/or B This lineage gains an area Extinction AB This lineage loses an area A or B This lineage goes extinct Golberg et al., 2011 (Syst Biol)

38 GeoSSE likelihood Likelihood of anagenic change Likelihood of extinction Likelihood at observed speciation Golberg et al., 2011 (Syst Biol)

39 explodes with many areas 3 areas 10 areas Each additional area doubles the number of ranges

40 MCMC proposal to sample histories Efficient sampling under iid model Efficient likelihood under non-iid model BayArea Landis et al. (2013)

41 MCMC proposal to sample histories Efficient sampling under iid model Efficient likelihood under non-iid model accept BayArea Landis et al. (2013)

42 MCMC proposal to sample histories Efficient sampling under iid model Efficient likelihood under non-iid model reject BayArea Landis et al. (2013)

43 Estimate using MCMC high low BayArea Landis et al. (2013)

44 Discrete biogeography in RevBayes Range size # Areas Anagenesis Cladogenesis Island One Many Area-switching No DEC Many < 10 Dispersalextirpation Yes GeoSSE Many < 4 Dispersalextirpation Linked to diversification BayArea Many 100+ Dispersalextirpation Yes Linked to diversification Some (experimental) Choose the right model for your question!

Taming the Beast Workshop

Taming the Beast Workshop Workshop and Chi Zhang June 28, 2016 1 / 19 Species tree Species tree the phylogeny representing the relationships among a group of species Figure adapted from [Rogers and Gibbs, 2014] Gene tree the phylogeny