I am looking for a phylogeny of old world vultures that would be downloaded into R for a project. I am not an expert on this kind of data, and my research has not been successful so far. Does someone know if this kind of dataset exists somewhere? A larger tree would also do the job (e.g. a tree of all raptors) as long as the level of precision is species.

Thanks in advance for the help.


A good start when you want a phylogeny that includes specific species is to use the NCBI Taxonomy Common Tree tool: https://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi

It allows you to specify 2 or more species. You specify the species by searching their binomials or TAXIDs one by one to add them, or upload a text file with one species binomial per line. It then produces the shared phylogeny that connects the entire set of species.

In your case you want the 16 species of Old World vultures. Wikipedia has them in a list here. I right clicked to inspect element, then extracted the species with this code:

Array.from(document.querySelector('#mw-content-text > div.mw-parser-output > ul:nth-child(15)').children).map(c => c.innerText.split(', ')[1]).join('\n')

Producing this list:

Aegypius monachus
Gyps fulvus
Gyps bengalensis
Gyps rueppelli
Gyps indicus
Gyps tenuirostris
Gyps himalayensis
Gyps africanus
Gyps coprotheres
Necrosyrtes monachus
Sarcogyps calvus
Torgos tracheliotos
Trigonoceps occipitalis
Gypaetus barbatus
Neophron percnopterus
Gypohierax angolensis

I uploaded that list to CommonTree, and here's your tree:

enter image description here

In Phylip format (which you can load in most phylogenetic tools, or convert easily:

'Gypohierax angolensis':4)
'Sarcogyps calvus':4)
'Gypaetus barbatus':4)
'Neophron percnopterus':4)
'Torgos tracheliotos':4)
'Necrosyrtes monachus':4)
'Trigonoceps occipitalis':4)
'Gyps tenuirostris':4,
'Gyps indicus':4,
'Gyps bengalensis':4,
'Gyps africanus':4,
'Gyps himalayensis':4,
'Gyps fulvus':4,
'Gyps rueppelli':4,
'Gyps coprotheres':4
'Aegypius monachus':4)

There are lots of other ways to achieve this but the NCBI tools are extremely useful to know about. The TAXIDs from NCBI can be used to pull data using many of the R packages for phylogenetics.

  • 1
    This is a great tool indeed, many thanks for the help! In the meawhile, I also found a quick and dirty solution as I reconstructed a "hand-made phylogeny" using the onezoom website (onezoom.org/life.html) - maybe it can be useful to know. – Recology May 10 at 19:51
  • 1
    Hey that's pretty cool, I haven't seen that one before! After I replied I remembered a couple of phylogenetic repositories you can check to see if someone has deposited a published phylogeny. It's not so important when you're looking at a small group of large animals that are very well studied like vutlures, but for anyone wanting a tree for, say, acacias or orchids, which are vast and complex groups, people spend their whole career tweaking them: phylomedb.org tolweb.org/tree treebase.org more at ucmp.berkeley.edu/subway/phylo/phylodat.html – Rik Smith-Unna May 11 at 1:19

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