Thursday, 20 March 2014

Lampreys and Hagfishes are now reunited in a monophyletic clade (Cyclostomata) in the NCBI Taxonomy

The NCBI Taxonomy is a powerful resource and provides many tools to search for relationship between organism:
http://www.ncbi.nlm.nih.gov/taxonomy

However, according to their disclaimer, they don't pretend to be an "authoritative source for nomenclature or classification". Many nodes are unresolved, and some nodes don't reflect recent changes. For exemple, the paraphyly of Hyperotreti (Myxines) and Hyperoartia (Sea lampreys): 


In this context, Hagfishes are not considered as proper Vertebrates, but only Craniata. However, they are all Vertebrates and Hagfishes and Lampreys should be clustered in a monophyletic clade called Cyclostomata ("round mouth").

We can suggest to the NCBI team to make appropriate changes. For example, the introduction of the Dipnotetrapodomorpha clade, which group Dipnoi and Tetrapoda and let the Coelacanth clade as an outgroup:
http://people.unil.ch/marcrobinsonrechavi/2013/05/dont-complain-about-ncbi-taxonomy-improve-it/
http://bgeedb.wordpress.com/2013/05/29/new-taxon-dipnotetrapodomorpha-in-ncbi-taxonomy/



I wrote to NCBI the following email (see the following extracts), and they kindly replied and followed my suggestions:

I am writing to request a few changes in the NCBI Taxonomy, in order to reflect recent findings in the phylogeny of the basal Vertebrates.


The current NCBI taxonomy at the basis of Chordata (7711) assumes a paraphyletic relationship of Sea Lamprey (Hyperoartia, 117569) and Hagfishes (Hyperotreti, 117565):


However, recent publications strongly support the monophyly group of Hyperoartia and Hyperotreti, in a clade named “Cyclostomata”. This clade is a sister-clade of the jawed vertebrates “Gnathostomata”:

http://www.ncbi.nlm.nih.gov/pubmed/24522530
Nature. 2014 Feb 12. doi: 10.1038/nature12980.
A primitive placoderm sheds light on the origin of the jawed vertebrate face.
Dupret V1, Sanchez S2, Goujet D3, Tafforeau P4, Ahlberg PE1.

http://www.ncbi.nlm.nih.gov/pubmed/22619386
Development. 2012 Jun;139(12):2091-9. doi: 10.1242/dev.074716.
Evolutionary crossroads in developmental biology: cyclostomes (lamprey and hagfish).
Shimeld SM1, Donoghue PC.

http://www.ncbi.nlm.nih.gov/pubmed/20947532
Proc Biol Sci. 2011 Apr 22;278(1709):1150-7. doi: 10.1098/rspb.2010.1641.
Decay of vertebrate characters in hagfish and lamprey (Cyclostomata) and the implications for the vertebrate fossil record.
Sansom RS1, Gabbott SE, Purnell MA.

http://www.ncbi.nlm.nih.gov/pubmed/21041649
Proc Natl Acad Sci U S A. 2010 Nov 9;107(45):19137-8. doi: 10.1073/pnas.1014583107.
microRNAs revive old views about jawless vertebrate divergence and evolution.
Janvier P.
http://www.ncbi.nlm.nih.gov/pubmed/20959416
Proc Natl Acad Sci U S A. 2010 Nov 9;107(45):19379-83. doi: 10.1073/pnas.1010350107.
microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate.
Heimberg AM1, Cowper-Sal-lari R, Sémon M, Donoghue PC, Peterson KJ.

http://www.ncbi.nlm.nih.gov/pubmed/18842688
Mol Biol Evol. 2009 Jan;26(1):47-59. doi: 10.1093/molbev/msn222.
Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after?
Kuraku S, Meyer A, Kuratani S.

I propose the following changes in the NCBI taxonomy:

- The “Craniata” clade (89593) should be replaced by the “Vertebrata” clade (7742). Craniata could eventually be used as a synonym of Vertebrata. 
- A “Cyclostomata” clade should be created within the “Vertebrata” clade (7742). This “Cyclostomata” clade would be a sister group of the “Gnathostomata” clade (7776).

- The “Hyperotreti” clade (117565) should be moved into the new “Cyclostomata” clade.

- Similarly, the “Hyperoartia” clade (117569) should be moved into the new “Cyclostomata” clade.

The new taxonomy would look like:

- Vertebrata (vertebrates)
--- Cyclostomata (living agnathans)
------ Hyperotreti (fish)
------------ Myxiniformes
------ Hyperoartia (fish)
------------ Petromyzontiformes
--- Gnathostomata (jawed vertebrates)
------ Chondrichthyes (cartilaginous fishes)
------ Teleostomi


We are using the NCBI taxonomy to automatize the clustering of genes based on the tree of life. It would be very useful for us if the NCBI taxonomy can reflect the recent supports of the monophyly of Hyperoartia and Hyperotreti in the Cyclostomata clade.



And here is the result a few days later:
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=89593&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&srchmode=1&keep=1&unlock





Nice, isn't it ?

And the information is also transferered in the dump files:

The old one:
grep "Cyclostomata" names.dmp
97265    |    Cyclostomata                        |                |    synonym        |
97265    |    Cyclostomata Busk , 1852    |                |    authority        |
The new one:
grep "Cyclostomata" names.dmp
97265    |    Cyclostomata                       |    Cyclostomata <bryozoan>    |    synonym        |
97265    |    Cyclostomata Busk , 1852    |                |    authority    |
1476529    |    Cyclostomata              |    Cyclostomata <chordate>    |    scientific name    |



If all systematicians and other biologists around the world join their efforts and contribute to this resource, it will become a very accurate and powerful tool to assist molecular evolution analyses.









2 comments:

  1. Problem:
    Cyclostomata (or Cyclostoma) is used both for fish and bryozoans,

    ReplyDelete
    Replies
    1. Hi,

      Yes, there are some case in the taxonomy where both clades have the same name. But it is not really a probleme once you use the taxonomy ID (TaxID) to distinguish between them (97265 versus 1476529)

      https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1476529
      https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=97265

      Romain

      Delete