Interpreting results of stochastic character mapping (pt2)

[joel...@gmail.com]

Hello! I'm back with another question about the results of stochastic character mapping.

So, the result of BioGeoBEARS::runBSM() is a list including RES_clado_events_tables and RES_ana_events_tables. I'm confused about RES_ana_events_tables; it includes columns for both "event_type" (either "d" for dispersal or "e" for extinction) AND "clado_event_type", which includes "" (nothing), "subset (s)", "sympatry (y)", or "vicariance (v)".

I've noticed that all of the nodes in the RES_ana_events_tables with a non-missing clado_event_type are also in the RES_clado_events_tables.

Why is this information seemingly duplicated? And why do these have both "event_type" (d or e) AND clado_event_type (vicariance, etc)? Doesn't that contradict - how can you have a node that is both a dispersal and a vicariance event?

Thanks!

Best,

Joel

[Ivan Magalhães]

Dear Joel,

Cladogenetic events happen exactly *at* the speciation event (the node), and can be either sympatry (each descendant inherits the same range as the ancestor), vicariance (each descendant inherits part of the range of the ancestor; can be narrow or wide vicariance), subset sympatry (one of the descendants inherits a single area from the ancestor's range, while the other inherits exactly the same range as the ancestor) or founder-event speciation (one of the descendants inherits the same range as the ancestor, while the other descendant "moves" to a single area that is not contained in the ancestor's range). 

Anagenetic events (any number of dispersals or extinctions) occur along the branchs. So you can easily have a cladogenetic event (at the node) followed by an anagenetic event (along the branch). When you look at a BioGeoBEARS output figure, you will notice that there are probabilities of ranges at the bottom of a branch, by the sides of the node. This is the probability of the range occupied by the descendants, immediately after the cladogenetic event. On the other hand, you have probabilities at the top of the branch. In the example below, you have a dispersal event (A >AB) followed by a vicariant event (ancestor: AB > descendant 1: A + descendent 2: B), followed by a dispersal event (B > BC in descendant 2).

                                 A  ------------------------ A                          

               (A > AB)      |      

        A ----------------- AB

                                  |           (B > BC)

                                  B  ----------------------- BC

                           (probability                     (probability at the

                            immediately                     end of the branch)

                            after cladogenetic

                             event)

So, to sum up,  it is not contradictory. Each node can have both cladogenetic events and anagenetic events associated (the former happens at the node itself, the latter happens along the branch that immediately precedes the node). I don't exactly recall the output for BSM tables, but I think that for the example above, it would show both a cladogenetic event (AB > A + B) and an anagenetic event (A > AB) for the same node.

Best,

Ivan

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[Nick Matzke]

Thanks for this Ivan!

Cheers,

Nick

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[joel...@gmail.com]

Thanks for the very clear answer! This needs to go in some sort of "BioGeoBEARS forum greatest hits" :)

Just to make sure I have this straight: for example, in the RES_ana_events_tables I have a series of events (event_txt) associated with a node like this: C->CD (event_type = d, for dispersal), CD->CDI (d), CDI->CDFI (d), CDFI->CDF (e, for extinction). They are all associated with the clado_event_txt CDF->D,CF. So that means that series of dispersals/extinctions occurred along the branch leading to the node, then there was a vicariance event at the node, right?

If so then I can make sense of these tables now, thanks!

Best,

Joel

[Nick Matzke]

On Thu, Apr 1, 2021 at 10:59 AM joel...@gmail.com <joel...@gmail.com> wrote:

Thanks for the very clear answer! This needs to go in some sort of "BioGeoBEARS forum greatest hits" :)

Just to make sure I have this straight: for example, in the RES_ana_events_tables I have a series of events (event_txt) associated with a node like this: C->CD (event_type = d, for dispersal), CD->CDI (d), CDI->CDFI (d), CDFI->CDF (e, for extinction). They are all associated with the clado_event_txt CDF->D,CF. So that means that series of dispersals/extinctions occurred along the branch leading to the node, then there was a vicariance event at the node, right?

That's right!  And the individual anagenetic events are recorded in a long text string on that node's row of the RES_clado_events_table, this text string is then processed to produce a series of rows in the RES_ana_events_table.

Thanks for being patient with it, I know it is confusing and I've never done the documentation properly!  Much of the complexity traces back to the weirdness of the phylo object in APE. -- hopefully you've seen that the prt(tr) command can at least convert a tree to a tree-table with the same rows as RES_clado_events_table.

Cheers!

nick

 

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[cge...@gmail.com]

Hello

Thanks all for the explanation! Finally I understand how correctly interpret correctly the event matrix in RASP!

Best Regards
Caio