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Jul 22, 2014, 2:26:52 PM7/22/14

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Julien asks an important question about what the parameter "j" means. The answer gets somewhat complicated, so I recommend people put in some serious study, read things a few times, and look at the Excel file I link to, in order to "get it".

Once you "get it", it's actually not that hard to conceptualize. However, I think it was fairly common for researchers to not get the math on cladogenesis processes that went into the DEC likelihood calculation, so first you have to get DEC first (described below), in order to get DEC+J.

On Tue, Jul 22, 2014 at 3:07 AM, VIEU Julien <julie...@unine.ch<mailto:julie...@unine.ch>> wrote:

Hi Nick,

Congrats for your papers being accepted!

I was wandering, if I infer a per event weight of 0.03 for j, does that mean that every 100 cladogenesis event, 3 are founder speciation?

SHORT ANSWER:

no.

MEDIUM ANSWER:

j is a "per-event weight", not a straight probability. The probability of any particular cladogenetic range inheritance event is a CONDITIONAL probability, calculated as follows:

Prob(event, CONDITIONAL on a particular ancestor range) =

= P(event | range)

= (weight of event | range) / sum(all weights of all possible events | range)

I.e., probability of an individual event is the per-event weight divided by the total of all the per-event weights for all events possible given a particular ancestor range just before cladogenesis.

LONG ANSWER:

The reason for the weight/sum of weights calculation goes back to the DEC model of Ree et al. (2005) and Ree & Smith (2008), as coded in LAGRANGE.

To model the "C" (cladogenesis) part, they noted that there were a number of possible events:

single-area sympatry/range-copying, e.g. A->A,A

subset sympatry, e.g. AB -> AB, A

vicariance, e.g. AB -> B, A

They decided to give each possible event, conditional on a particular ancestor, equal weight. This translates to probabilities as follows:

(for a 3-area system...it will be different for 2, 3, 4, 5 areas, etc.)

Assuming:

DEC model, 3 area system

Weights: y=1, s=1, v=1 (and j=0)

Conditional on ancestor: A, 3 areas total

======================================

Total possible events: 1

Total weight of events: 1

Probability of EACH CLASS of events, under DEC

Prob(sympatry) = P(y) = 1 / 1 = 1

Probability of EACH INDIVIDUAL EVENT, under DEC

P(y event) = y/1 = 1

======================================

Conditional on ancestor: AB, 3 areas total

======================================

Total possible events: 6 (0 sympatry, 2 vicariance, 4 subset)

Total weight of events: 6

Probability of EACH CLASS of events, under DEC

Prob(sympatry) = P(y) = 0*y / 6.0 = 0

Prob(vicariance) = P(v) = 2*v / 6.0 = 1/3

Prob(subset-sympatry) = P(s) = 4*s / 6.0 = 2/3

Probability of EACH INDIVIDUAL EVENT, under DEC

P(y event) = y/6 = 0

P(v event) = v/6 = 1/6

P(s event) = s/6 = 1/6

======================================

Conditional on ancestor: ABC, 3 areas total

======================================

Total possible events: 12 (0 sympatry, 6 vicariance, 6 subset)

Total weight of events: 12

Probability of EACH CLASS of events, under DEC

Prob(sympatry) = P(y) = 0*y / 12 = 0

Prob(vicariance) = P(v) = 6*v / 12 = 0.5

Prob(subset-sympatry) = P(s) = 6*s / 12 = 0.5

Probability of EACH INDIVIDUAL EVENT, under DEC

P(y event) = y/12 = 0

P(v event) = v/12 = 1/12

P(s event) = s/12 = 1/12

======================================

Note the difference between the probabilities of each CLASS of events, and each individual event. The numbers of different types of cladogenesis events change depending on whether an ancestor is A, AB, ABC, etc.

There is not an obvious way to keep the probability of each CLASS of events the same between different-sized ancestors. If it were done, it would be a different model from DEC, and, I suspect, not a better one. It could be that, in real life, classes of biogeographical events that have more possible events, actually do have more probability as a class.

Yes, this weights vs probabilities issue is at the heart of why DEC is probably not understood very well even by many people who have used it.

Now, for completeness, I will repeat these calculations for the DEC+J model, where y=s=v=(3-j)/3.

DEC model, 3 area system

Weights:

j=0.03

y=s=v=(3-j)/3 = (3-0.03)/3 = 1-0.01 = 0.99

So:

y=0.99, s=0.99, v=0.99, j=0.03

Conditional on ancestor: A, 3 areas total

======================================

Total possible events: 5 (1 sympatry, 4 founder)

Total weight of events: 1*y + 4*j = 0.99 + 0.12 = 1.11

Probability of EACH CLASS of events, under DEC+J

Prob(sympatry) = P(y) = 0.99 / 1.11 = 0.8919

Prob(founder) = P(j) = 0.04 / 1.03 = 0.1081

Probability of EACH INDIVIDUAL EVENT, under DEC+J

P(y event) = y/1.11 = 0.99 / 1.11 = 0.8919

P(j event) = j/11.11 = 0.03 / 1.11 = 0.0270

======================================

Conditional on ancestor: AB, 3 areas total

======================================

Total possible events: 8 (0 sympatry, 2 vicariance, 4 subset, 2 founder)

Total weight of events: 0*y + 2*v + 4*s + 2*j = 6.0

Probability of EACH CLASS of events, under DEC+J

Prob(sympatry) = P(y) = 0*y / 6.0 = 0

Prob(vicariance) = P(v) = 2*v / 6.0 = 0.3300

Prob(subset-sympatry) = P(s) = 4*s / 6.0 = 0.6600

Prob(founder) = P(h) = 2*j / 6.0 = 0.01

Probability of EACH INDIVIDUAL EVENT, under DEC+J

P(y event) = 0

P(v event) = v/6 = 0.99/6 = 0.165

P(s event) = s/6 = 0.99/6 = 0.165

P(j event) = j/6 = 0.03/6 = 0.005

======================================

Conditional on ancestor: ABC, 3 areas total

======================================

Total possible events: 12 (0 sympatry, 6 vicariance, 6 subset, 0 founder)

Total weight of events: 0*y + 6*v + 6*s + 0*j = 11.88

Probability of EACH CLASS of events, under DEC

Prob(sympatry) = P(y) = 0*y / 11.88 = 0

Prob(vicariance) = P(v) = 6*v / 11.88 = 0.5

Prob(subset-sympatry) = P(s) = 6*s / 11.88 = 0.5

Prob(founder) = P(s) = 0*j / 11.88 = 0

Probability of EACH INDIVIDUAL EVENT, under DEC

P(y event) = 0

P(v event) = v/12 = 1/12

P(s event) = s/12 = 1/12

P(j event) = 0

======================================

FURTHER INFORMATION AND EXCEL FILE

I discuss this in more detail in my SysBio manuscript, which I have put online here:

The Supplemental Data has an Excel file which does the weight calculations for DEC and DEC+J for 2-, 3-, and 4-area systems (after that the cladogenesis matrix gets too huge).

I have put the Excel file here. Start with the "custom_wts_DECJ_1area" worksheet:

FURTHER INFORMATION

Now, BioGeoBEARS has functions that do all of the above calculations quickly (which becomes extremely non-trivial for large state spaces -- e.g., 9 areas = 2^9 ranges/states = 512 states = 511 non-null ranges = 511x511x511 combinations of (ancestor range, left descendant range, right descendant range) = 133,432,831 combinations which have to be assigned conditional probabilities from the weights).

The weights strategy makes this fast and tractable, but it does cause a problem for the interpretation of j (and y, s, and v). Higher j means more founder events, but the probability of founder events as a class will be different conditional on each possible ancestor range size (and the specific range, if there are any other modifiers due to constraints).

Furthermore, even if you calculate the per-event probabilities and the per-event-class probabilities under some specific combination of ranges and parameters, this just gives you the probabilities per cladogenesis event, conditional on each possible ancestor range.

It still doesn't get you a real estimate of the overall probability of founder events on your phylogeny. This is because that probability will depend on the ancestral state estimates and their probabilities. If you estimate that the ancestor nodes had widespread ranges, this will mean there were fewer opportunities for founder-events, compared to other sorts of events, than if the ancestor nodes had narrow ranges.

Your only real options to get the overall probability of founder-events, conditional on the data, tree, and model, are:

1. Stare at your ancestral range estimation graphic, and attempt to count obvious founder-events by hand. In other words, guestimate.

2. Do Biogeographical Stochastic Mapping (BSM) conditional on the tree, data, and model, repeat 100 times, and get the mean and variance of the counts of each event type.

As it happens, I've basically got #2 working, although testing/tutorials etc. will take awhile. Email me if you are someone who is interested in collaborating on doing this.

In my stochastic mapping test run on the Psychotria data (19 taxa, 4 areas, M0 unconstrained model), I get:

DEC model ML parameters: d=0.034, e=0.028, j=0

==========================================

Biogeographical stochastic mapping event counts, 100 realizations on Psychotria (19 taxa, 4 area, M0 unconstrained)

Mean of event counts:

d e a y s v j

5.527778 1.629630 0.000000 9.842593 3.444444 4.712963 0.000000

Standard deviation of event counts:

d e a y s v j

0.8367531 1.0987894 0.0000000 1.5234125 1.4997404 0.8652257 0.0000000

==========================================

DEC+J model ML parameters: d=0.0, e=0.0, j=0.11

==========================================

Biogeographical stochastic mapping event counts, 100 realizations on Psychotria (19 taxa, 4 area, M0 unconstrained)

Mean of event counts:

d e a y s v j

0.0000000 0.0000000 0.0000000 9.9629630 0.4537037 0.4259259 7.1574074

Standard deviation of event counts:

d e a y s v j

0.0000000 0.0000000 0.0000000 1.1991112 0.8579944 0.4967879 0.8877361

==========================================

So, you can see that, for the Hawaiian Psychotria M0 DEC+J model, when the j parameter ~0.11, about 40% of the cladogenesis events are founder-events, about 55% are within-island sympatry, and only about 5% are vicariance or subset sympatry, even though y=s=v=(3-j)/3 = 0.96.

The Psychotria tree has only 19 tips and thus 18 internal nodes, so 5% vicariance/subset means that, on average across the stochastic maps, perhaps only one of the nodes has an event that is vicariance or subset.

Note that all of these statements are UNDER THE SPECIFIED MODEL, PARAMETERS, DATA, AND TREE (which we assume, incorrectly, to be the true tree without extinction, which may or may not be important, depending). Change any of these, and you may get different answers about what the estimated weight parameters imply.

The nice thing about stochastic mapping is that the counts of events are comparable, or at least one can compare e.g. events per million years of branchlength, events per (observed) cladogenesis event, etc.

OTHER MODELS

Because of this weighting strategy, it is VERY IMPORTANT to think carefully about what you are doing with y,s, v, and j in other models. In my example models DIVALIKE+J and BAYAREALIKE+J, you can see via...

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table

...that I have set:

DIVALIKE+J:

y = (2-j)/2

v = (2-j)/2

s = 0

j = j, 0<j<2

BAYAREALIKE+J:

y = (1-j)/1

v = 0

s = 0

j = j, 0<j<1

This was done to imitate the DEC idea, that each event that is possible gets a weight of 1. Note that this means that j in DEC+J is not strictly comparable to J in DIVALIKE+J or BAYAREALIKE+J. There actually is not a way to make them strictly equivalent, because the weights are all relative to the other weights, and e.g. DIVALIKE has different numbers of possible vicariance events than DEC, has 0 subset sympatry events, etc.

Note: As I mention in the SysBio ms, because everything is divided by the sum of the per-event weights, a number of parameterizations could be imagined which would all be equivalent. If you modify the default models, you have to ensure identifiability. If you set y,s,v, and j to all be free, then y=s=v=j=1 would be the same model as y=s=v=j=0.1, and would get the same likelihood, and your ML search will never converge.

Note also: The correct way to do the hypothetical 4-free-parameter cladogenesis model would be with a simplex (and actually this would just be 3 free parameters), but it would take some somewhat serious experimentation first, to ensure that your specification of the BioGeoBEARS model is doing a simplex (it may take some new code, I haven't thought about it), and second, that your ML optimization routine is searching the simplex parameter space properly, and third, that your data actually supports that many free parameters.

Final note: The whole BioGeoBEARS strategy for doing cladogenesis models was just an attempt to extend and test DEC, and is just a first attempt. There could be better ways, although they might be more complex and require new programming. There is no particular reason, for instance, that we have to link weight parameters across different ancestral range sizes. This linkage causes some interesting effects, e.g. in DEC+J if you have a lot of single-area sympatry (e.g. within-island speciation), this will force y to be high, which also forces s and v to be high, even if they are completely unnecessary.

Cheers,

Nick

PS: The above is sufficiently thorough that I will turn it into a PhyloWiki page.

cid:3368612452<tel:3368612452>_342129

Cheers!

Julien

Julien Vieu, doctorant

Laboratoire de botanique évolutive

Institut de biologie, Faculté des Sciences

Université de Neuchâtel, Rue Emile-Argand 11

CH - 2000 Neuchâtel SWITZERLAND

On Tue, Jul 22, 2014 at 12:05 PM, VIEU Julien <julie...@unine.ch> wrote:

yep, sure!________________________________

Julien Vieu, doctorant

Laboratoire de botanique évolutive

Institut de biologie, Faculté des Sciences

Université de Neuchâtel, Rue Emile-Argand 11

CH - 2000 Neuchâtel SWITZERLAND

cid:3368612452_342129

De : nickmat...@gmail.com [nickmat...@gmail.com] de la part de Nick Matzke [mat...@nimbios.org]

Envoyé : mardi 22 juillet 2014 17:51

À : VIEU Julien

Objet : Re: per event weight?

Hi Julien, can I answer this on the google group?

Nick

Jul 22, 2014, 3:20:01 PM7/22/14

to bioge...@googlegroups.com

I have edited and formatted the previous post, fixed some typos, and posted it here:

...let me know if you see mistakes, or issues that need more thorough discussion.

Cheers!

Nick

Jul 23, 2014, 3:05:16 AM7/23/14

to bioge...@googlegroups.com

Thank you Nick for this very detailed answer!

Julien Vieu, doctorant

Laboratoire de botanique évolutive

Institut de biologie, Faculté des Sciences

Université de Neuchâtel, Rue Emile-Argand 11

CH - 2000 Neuchâtel SWITZERLAND

cid:3368612452_342129

________________________________

De : bioge...@googlegroups.com [bioge...@googlegroups.com] de la part de Nick Matzke [mat...@nimbios.org]

Envoyé : mardi 22 juillet 2014 20:26

À : bioge...@googlegroups.com

Objet : [BioGeoBEARS] y,s,v, and j: per-event weights of cladogenetic range inheritance events in BioGeoBEARS

Julien asks an important question about what the parameter "j" means. The answer gets somewhat complicated, so I recommend people put in some serious study, read things a few times, and look at the Excel file I link to, in order to "get it".

Once you "get it", it's actually not that hard to conceptualize. However, I think it was fairly common for researchers to not get the math on cladogenesis processes that went into the DEC likelihood calculation, so first you have to get DEC first (described below), in order to get DEC+J.

cid:3368612452<tel:3368612452><tel:3368612452<tel:3368612452>>_342129

On Tue, Jul 22, 2014 at 12:05 PM, VIEU Julien <julie...@unine.ch<mailto:julie...@unine.ch>> wrote:

yep, sure!

Julien Vieu, doctorant

Laboratoire de botanique évolutive

Institut de biologie, Faculté des Sciences

Université de Neuchâtel, Rue Emile-Argand 11

CH - 2000 Neuchâtel SWITZERLAND

cid:3368612452<tel:3368612452>_342129

________________________________

De : nickmat...@gmail.com<mailto:nickmat...@gmail.com> [nickmat...@gmail.com<mailto:nickmat...@gmail.com>] de la part de Nick Matzke [mat...@nimbios.org<mailto:mat...@nimbios.org>]

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Julien Vieu, doctorant

Laboratoire de botanique évolutive

Institut de biologie, Faculté des Sciences

Université de Neuchâtel, Rue Emile-Argand 11

CH - 2000 Neuchâtel SWITZERLAND

cid:3368612452_342129

________________________________

Envoyé : mardi 22 juillet 2014 20:26

À : bioge...@googlegroups.com

Objet : [BioGeoBEARS] y,s,v, and j: per-event weights of cladogenetic range inheritance events in BioGeoBEARS

Julien asks an important question about what the parameter "j" means. The answer gets somewhat complicated, so I recommend people put in some serious study, read things a few times, and look at the Excel file I link to, in order to "get it".

Once you "get it", it's actually not that hard to conceptualize. However, I think it was fairly common for researchers to not get the math on cladogenesis processes that went into the DEC likelihood calculation, so first you have to get DEC first (described below), in order to get DEC+J.

On Tue, Jul 22, 2014 at 12:05 PM, VIEU Julien <julie...@unine.ch<mailto:julie...@unine.ch>> wrote:

yep, sure!

Julien Vieu, doctorant

Laboratoire de botanique évolutive

Institut de biologie, Faculté des Sciences

Université de Neuchâtel, Rue Emile-Argand 11

CH - 2000 Neuchâtel SWITZERLAND

________________________________

De : nickmat...@gmail.com<mailto:nickmat...@gmail.com> [nickmat...@gmail.com<mailto:nickmat...@gmail.com>] de la part de Nick Matzke [mat...@nimbios.org<mailto:mat...@nimbios.org>]

Envoyé : mardi 22 juillet 2014 17:51

À : VIEU Julien

Objet : Re: per event weight?

Hi Julien, can I answer this on the google group?

Nick

--
À : VIEU Julien

Objet : Re: per event weight?

Hi Julien, can I answer this on the google group?

Nick

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