[Taxacom] Two million molecular synonyms on the way

Mon Feb 15 03:49:01 CST 2021

Why not broaden this discussion and look not just at the question sequence or not, but how Sharkey et al, published and how this data is accessible, then it is clear that it is part of a taxonomic publishing change which delivers what we always wanted: Make our extremely valuable data immediately accessible.

The article has been published open access by the authors in 
Zookeys: https://doi.org/10.3897/zookeys.130.1569
Within a day, the species have been added to GBIF: https://www.gbif.org/dataset/a967c90e-ea10-4a10-b43b-cd5328a1d6e6 where each species has its own page: https://www.gbif.org/species/177205678 and with a bit more even each holotype has its own record: https://www.gbif.org/occurrence/3036825301 all with extensive metadata, accessible for you as a reader as well as the machine.

On TreatmentBank, which does the transfer from Pensoft to GBIF, there is an alternative version of the publication: http://treatment.plazi.org/GgServer/summary/E4329863A39E5EEBA395938413BDD579 and the above treatment: http://treatment.plazi.org/id/0E45721B-53E5-4DD9-8547-8A3C88EEFA0E that also includes the links to the cited resources, such as the BarCode or the specimens.

These links are provided in the article itself, which has two versions, a human and machine readable, of which the latter can be used.

This set up is in a sense an automated registration of the new species, which has persistent identifier provided by Plazi via TreatmentBank http://treatment.plazi.org/id/0E45721B-53E5-4DD9-8547-8A3C88EEFA0E or alternatively using a persistent identifier using the DataCite DOI, shown here: https://zenodo.org/communities/biosyslit/search?page=1&size=20&subtype=taxonomictreatment using one of the most reliable repositories for science, Zenodo.

This does not include the tools that are out there to find species based on barcode sequences.

Reducing this article to a barcode is missing out the huge stack of data that is provided around the Barcode itself. Here is an one example, Aerophilus paulmarshi
http://boldsystems.org/index.php/Public_BarcodeCluster?clusteruri=BOLD:ADC6602
http://www.boldsystems.org/index.php/Public_RecordView?processid=JICCP291-16
https://zookeys.pensoft.net/article/55600/element/7/0/aerophilus%20paulmarshi/
http://zoobank.org/0E45721B-53E5-4DD9-8547-8A3C88EEFA0E
and then reused
http://treatment.plazi.org/id/0E45721B-53E5-4DD9-8547-8A3C88EEFA0E (persistent identifier)
https://www.gbif.org/occurrence/3036825301 materials citation in GBIF
https://www.gbif.org/species/177205678 species in GBIF

There are still some improvements possible, such as bidirectional linking, etc. But this is what we should see the challenge to beat in taxonomic publishing.

Together with the omics world we have a bright future.

Donat / Plazi

Hi Carlos,

I’ve been trying to follow (most of) your posts – largely out of courtesy.  But this comment from you:

> given that in the opinion of the Commission such comparison is not necessary.

clearly shows that you have not extended the same courtesy in paying attention to the posts from Commissioners.

You are objectively wrong about this.

Aloha,
Rich

Richard L. Pyle, PhD
Senior Curator of Ichthyology | Director of XCoRE Bernice Pauahi Bishop Museum
1525 Bernice Street, Honolulu, HI 96817-2704
Office: (808) 848-4115;  Fax: (808) 847-8252
eMail: deepreef at bishopmuseum.org
BishopMuseum.org
Our Mission: Bishop Museum inspires our community and visitors through the exploration and celebration of the extraordinary history, culture, and environment of Hawaiʻi and the Pacific.

> -----Original Message-----
> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> On Behalf Of Carlos 
> Alberto Martínez Muñoz via Taxacom
> Sent: Sunday, February 14, 2021 11:16 AM
> To: Taxa com <taxacom at mailman.nhm.ku.edu>
> Subject: [Taxacom] Two million molecular synonyms on the way
>
> Dear Taxacomers,
> After many, many emails, here are some final messages which I will 
> have to transmit to the myriapodological community tomorrow. I will 
> let my colleagues know that our Myriapoda community should:
> 1) Be prepared to take the hit of at least 20 000 new molecular 
> synonyms over the next ten years.
> 2) Additionally expect the vast majority of the truly new species to 
> be named at an industrial scale from molecular data only, by barcoders 
> and not by our experts.
> 3) Stop worrying about comparing our new species to known species, 
> given that in the opinion of the Commission such comparison is not necessary.
> 4) Forget about complying with the Code, given that we are a 
> scientific community and that in the opinion of the Commission the 
> Code is not a scientific standard.
>
> You may use this email as a template to announce the same to your 
> communities. You just need to change the expected number of new 
> synonyms to match the number of valid species your communities deal 
> with. The combination of global barcoding projects such as BIOSCAN, 
> and the understanding that there is no need to compare "new" molecular 
> species with current morphological species, will certainly generate 
> one new molecular synonym per each valid morphological species. Two million valid species?
> Two million molecular synonyms!
>
> Cheers!
>
>
> Carlos A. Martínez Muñoz
> Zoological Museum, Biodiversity Unit
> FI-20014 University of Turku
> Finland
> Myriatrix 
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