I note that Treefam includes S.cerevisiae (Sc), S.pombe (Sp), Arabidopsis and rice as an "Outgroup" set of species. I find this a really good idea, to give a sense of how genes have been conserved (or not) during evolution, on a wider scale than 'just' animals. And also, these are key model organisms of interest to a great many researchers worldwide.

However in several cases where I know a (human) gene has S.pombe or S.cerevisiae orthologues, these are often not found in Treefam.

Just one example: Chk1 / CHEK1
Here are links to these genes in their "home" (species-specific) databases:
Human: http://www.genenames.org/data/hgnc_data.php?hgnc_id=1925
Sp: http://www.pombase.org/spombe/result/SPCC1259.13
Sc: http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=chk1

Searching Treefam for CHEK1, and opening the tree TF351441 does not include these Sp and Sc orthologs:
http://www.treefam.org/family/TF351441#tabview=tab1

Oddly enough, Ensembl reports the Sc, but not the Sp orthologue:
http://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?g=CHEK1
As the chk1 gene was in fact first discovered in S.pombe (www.pubmed.org/8497322), to me it seems rather strange not to include Sp in the list of organisms that shares that gene!

In this case, the NCBI's HomoloGene correctly identifies the Sc and Sp orthologues:
http://www.ncbi.nlm.nih.gov/homologene?term=CHEK1

Clearly these different sites (Treefam / Ensembl / HomoloGene) use different methods and stringencies to define what is included as being an orthologue.

Happily, Treefam does find Sc, Sp and At orthologues for the well-conserved gene DNA Polymerase alpha (POLA1):
http://www.treefam.org/family/TF103001#tabview=tab1
- so at the "highly conserved" end of the conservation spectrum, this aspect of Treefam works just fine.

My questions related to this are:
- do you think it's possible that Treefam could be missing out on some genuine and important orthologues, by being a bit too stringent?
- what do you think of the idea of (automatically) 'cross-checking' between Treefam and Ensembl orthologues/paralogues, to ensure some consistency between these?