Evolutionary rate per module per genus

[Stine Keibel Blom]

Hi all, 

I hope you can help me with this. I have a landmark dataset containing 12 genera where I have assigned subsets of the landmarks to modules. I am looking for a way to estimate the evolutionary rate per module per genus for pairwise comparisons, and for that I have considered using the compare.evol.rates() function, but the problem is that some of the genera only contain one species, which seems not optimal for this function. 

Using geomorph, or not, how would you estimate the evolutionary rate per module per genus? 

Sincerely, 

Stine 

[Adams, Dean [EEOB]]

Stine,

Evolutiononary rates may be estimated in different ways depending on the data and the question. Phylogenenetic evolutionary rates, such as those calculated in 'compare.evol.rates' use a set of species and a phylogeny. These are equivalent to a phylogeny-standardized variance and thus require multiple species for estimation.

If one has a single species (or genus), one can use 'darwins'. These are simply the change in the trait from ancestor - descendant, standardized by the branch length in MYA. These are commonly used in fossil datasets, where the ancestor trait value may be measured.

Incidentally, evolutionary rates across generations and shorter time spans may be estimated using 'haldanes': the change of the trait across generations divided by time, and standardized by within-sample variances. 

Dean

-- 
Dr. Dean C. Adams
Distinguished Professor
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
www.public.iastate.edu/~dcadams/
phone: 515-294-3834

---

From: geomorph-...@googlegroups.com <geomorph-...@googlegroups.com> on behalf of Stine Keibel Blom <stine...@gmail.com>
Sent: Monday, March 24, 2025 7:47 AM
To: geomorph R package <geomorph-...@googlegroups.com>
Subject: [geomorph-r-package] Evolutionary rate per module per genus

 

--
You received this message because you are subscribed to the Google Groups "geomorph R package" group.
To unsubscribe from this group and stop receiving emails from it, send an email to geomorph-r-pack...@googlegroups.com.
To view this discussion, visit https://groups.google.com/d/msgid/geomorph-r-package/0e099d8c-451b-4986-aa56-5e919598c38an%40googlegroups.com.

[Stine Keibel Blom]

Dear Dean, 

Thank you for your rapid response! 

I am wondering (and confused) because I have used the compare.evol.rates with my landmark datasets, 

   fullscap_evolrate <- compare.evol.rates(A = mean_LM_array2,
                                        phy = phylotree2,
                                        gp = group_membership,
                                        iter = 999, method = "simulation")

which provided me rates for every group: 

  > summary(fullscap_evolrate)

Call: Observed Rate Ratio: 15.7248 P-value: 0.002 Effect Size: 3.4922 Based on 1000 random permutations The rate for group Gorilla is 1.86577843326962e-07 The rate for group Homo is 1.78471729684361e-06 The rate for group Hoolock is 1.72174050168419e-07 The rate for group Hylobates is 7.7402866480952e-07 The rate for group Pan is 3.44122727119845e-07 The rate for group Pongo is 1.13497259516306e-07 The rate for group Symphalangus is 5.86273920101665e-07

which is what I originally expected, however how is the function able to calculate an evolutionary rate for a group that only has one LM consensus (e.g., Homo, which only contains one Homo sapiens LM set)?

Thanks a lot, 

Stine

[Adams, Dean [EEOB]]

Re how with 1 species: Technically the math will work, but biologically I would not place much in that. What would such a rate mean? 

I would argue that this is a misuse of the rate method, and that if one has as single species in a group, then a branch-based approach (darwins, haldanes) is more appropriate.

Dean

-- 
Dr. Dean C. Adams
Distinguished Professor
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
www.public.iastate.edu/~dcadams/
phone: 515-294-3834

---

From: geomorph-...@googlegroups.com <geomorph-...@googlegroups.com> on behalf of Stine Keibel Blom <stine...@gmail.com>

Sent: Monday, March 24, 2025 11:31 AM

To: geomorph R package <geomorph-...@googlegroups.com>

Subject: Re: [geomorph-r-package] Evolutionary rate per module per genus

 

To view this discussion, visit https://groups.google.com/d/msgid/geomorph-r-package/422429b9-e9ac-479d-9a17-95febcd73947n%40googlegroups.com.

[Stine Keibel Blom]

Great, thank you very much for the help! I am also looking into estimating the evol. rates of modules of this LM set per genus. Would you use these approaches as well for this purpose? 

[Adams, Dean [EEOB]]

Generally yes, though the same precautions regarding the number of species per genus (in this case) apply.

D

-- 
Dr. Dean C. Adams
Distinguished Professor
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
www.public.iastate.edu/~dcadams/
phone: 515-294-3834

---

From: geomorph-...@googlegroups.com <geomorph-...@googlegroups.com> on behalf of Stine Keibel Blom <stine...@gmail.com>

Sent: Tuesday, March 25, 2025 4:33 AM

To view this discussion, visit https://groups.google.com/d/msgid/geomorph-r-package/3f85e47e-8ca1-49de-b88e-addad2d149bfn%40googlegroups.com.