Hi Russell:
Glad to hear you’re using the VertLife mammal trees — they are built on a
taxonomy of 5,911 species of which only 4,098 are sampled for DNA, so there is
already a ~30% chunk that is placed using taxonomic constraints and birth-death
branch lengths as sampled during the estimation of 28 Bayesian patch clades.
Adding additional species described since the 2015 cutoff of that VertLife
taxonomy makes sense (e.g., up to ~6,500 species on mammaldiversity.org).
However, keep in mind that they will not have birth-death estimated branch
lengths, but rather more likely be added as a polygamy to given clade and then
randomly resolved.
Given the sample code you provided, the key thing you’ll want to do is run a
*loop* rather than using lapply, so that you can specify a given tree each
time, e.g.:
newtrees<-vector(“list”,length(trees))
for(j in 1:length(trees)){
newtrees[[j]] <- bind.tip(tree=trees[[j]],
tip.label="Cercopithecus_albogularis”, position=0.59,edge.length = 0.59,
where=mrca(tree[[j]])["Cercopithecus_mitis","Cercopithecus_mitis"])
}
I also wrote some code to prune mammal trees and add extinct Caribbean species,
which uses a similar approach of making polytomies and randomly resolving them
— here is the repo:
https://github.com/n8upham/CaribbeanExtinctions-WTWTW/tree/master/mamPhy_pruningCode
And here is the code file:
https://github.com/n8upham/CaribbeanExtinctions-WTWTW/blob/master/mamPhy_pruningCode/pruningCode_MamPhy-to-CaribbeanTaxa.R
Hope that helps,
—nate
========================================================================
Nathan S. Upham, Ph.D. (he/him)
Assistant Research Professor & Associate Curator of Mammals
Arizona State University, School of Life Sciences
~> Check out the new Mammal Tree of Life
<http://vertlife.org/data/mammals/> and the Mammal Diversity Database
<https://mammaldiversity.org/>
Research Associate, Yale University (Ecology and Evolutionary Biology)
Research Associate, Field Museum of Natural History (Negaunee Integrative
Research Center)
Chair, Biodiversity Committee, American Society of Mammalogists
Taxonomy Advisor, IUCN/SSC Small Mammal Specialist Group
personal web: n8u.org | Google Scholar
<https://scholar.google.com/citations?hl=en&user=zIn4NoUAAAAJ&view_op=list_works&gmla=AJsN-F6ybkfthmTdjTpow6sgMhWKn1EKcfNtmIF_wzZcev7yeHuEu5_aolFS85rWiVRHpiQgbwg43i6eS6kArrabLdFL4bntzUSRmlRP2CW4lbZqeEcColw>
| ASU profile <https://isearch.asu.edu/profile/3682356>
e: nathan.up...@asu.edu | Skype: nate_upham | Twitter: @n8_upham
<https://twitter.com/n8_upham>
========================================================================
> On Jun 2, 2021, at 4:19 PM, Eliot Miller <eliot.is...@gmail.com> wrote:
>
> Hi Russell,
>
> A package I wrote a while back should be able to do that fairly easily.
> https://urldefense.com/v3/__https://github.com/eliotmiller/addTaxa__;!!IKRxdwAv5BmarQ!OZj7-dFRbxvUothKjSj6hr9B0eXscAO6LVWi1-a0w3J_PxlDqvsFDNb0lQrzxl2aIw$
> The only paper it's described in
> remains
> https://urldefense.com/v3/__https://bsapubs.onlinelibrary.wiley.com/doi/full/10.3732/ajb.1500195__;!!IKRxdwAv5BmarQ!OZj7-dFRbxvUothKjSj6hr9B0eXscAO6LVWi1-a0w3J_PxlDqvsFDNb0lQp7PnRRHg$
>
> It's a wrapper for bind.tip, with some additional stuff. You basically
> would give it a taxonomic file where you identify the clades you're
> interested in (e.g. both of those Cercopithecus species could be named some
> unique clade name and off you go, it'd add the missing one to the other),
> then lapply that whole addTaxa command over the list of trees in
> multiPhylo. At some point I made laser a dependency, and it's possible I
> left it in that state. If that's the case, you can still get laser from old
> CRAN mirrors I believe. Let me know if you want more help.
>
> Best,
> Eliot
>
> On Wed, Jun 2, 2021 at 7:05 PM Russell Engelman <neovenatori...@gmail.com>
> wrote:
>
>> Dear R-sig-phylo,
>>
>> I have been working with a mammalian phylogeny I recently downloaded from
>> VertLife
>> (https://urldefense.com/v3/__http://vertlife.org/phylosubsets/__;!!IKRxdwAv5BmarQ!OZj7-dFRbxvUothKjSj6hr9B0eXscAO6LVWi1-a0w3J_PxlDqvsFDNb0lQoEdEnMAg$
>> ). Unfortunately, the phylogeny
>> is missing a large number of species, so I am trying to manually add these
>> taxa to the phylogeny. I have a series of 100 trees that I am using to do
>> things such as test for phylogenetic signal. I know how to use bind.tip to
>> add new taxa to a single tree, but I am having more trouble with a
>> multiPhylo object. I am primarily adding these taxa by placing them as
>> sister to their nearest included relative (since most of them are elevated
>> former subspecies), but the issue here is that in the 100 trees in the
>> multiPhylo object the node representing the taxon to bind these taxa to is
>> not the same across all trees due to shifting topologies.
>>
>> This is an example of the code I have been using, in which "tree" is the
>> tree object. This works for a single 'phylo' tree but not 'multiphylo'.
>>
>> ```
>> newtree<-lapply(tree,bind.tip,tip.label="Cercopithecus_albogularis",
>> position=0.59,edge.length = 0.59,
>>
>> where=mrca(tree)["Cercopithecus_mitis","Cercopithecus_mitis"])
>> ```
>>
>> Now, this code will not work, but I know exactly why: 'tree' is a
>> multiPhylo object and so the 'where' argument cannot find the node for the
>> terminal taxon. However, the issue is how can I tell R to repeat this
>> 'where' argument for each of the 100 trees, since the node in question is
>> not identical across these trees? Is there an easier way to do this than
>> using the 'mrca' call for each terminal taxon? I've noticed adding a 'mrca'
>> argument also increases computation time and if I am reinventing the wheel
>> it would be nice to know if I am overthinking things.
>>
>> Sincerely,
>> Russell
>>
>> [[alternative HTML version deleted]]
>>
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>>
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