[Taxacom] Fwd: Are you aware of the ballot on the proposal to modify the ICNP to allow a sequence as type?

[James Beach]

This from the GGBN mailing list a few minutes ago.

---------- Forwarded message ---------
From: Barker, Katharine B. <
0000013bbdada19e-dmarc-request at si-listserv.si.edu>
Date: Fri, Feb 7, 2020 at 8:18 AM
Subject: Are you aware of the ballot on the proposal to modify the ICNP to
allow a sequence as type?
To: <GGBN-INFO at si-listserv.si.edu>


Dear staff members of a culture collection,

I am contacting you to notify you about possible changes to the rules of
microbial nomenclature that might affect the operations of culture
collections worldwide. In case some of your colleagues may better be suited
to deal with this issue please accept my apologies for bothering you and
feel free to forward this message to them.

Valid publication of names of species and subspecies of Archaea and
Bacteria currently requires the deposit of the type strain in at least two
culture collections in two distinct countries. The proposal to modify the
International Code of Nomenclature of Prokaryotes (ICNP) to permit genome
sequences as types instead may dramatically reduce the incentive for
researchers to deposit material in collections.

Evidence indicates that most microbiologists, even those dealing with
taxonomy and nomenclature, are unaware of the forthcoming ballot by the
International Committee on Systematics of Prokaryotes (ICSP) about this
proposal. I think whatever your opinion regarding this issue, we all should
agree that it must be avoided to let a decision of far-reaching
consequences be made by a handful of people without a proper representation
of the affected scientific communities.

As you see in the attached file, two kinds of action can be taken:

1. Participate in the discussion until March 1, 2020.

2. Determine a delegate of one of the member organizations of the
International Union of Microbiological Societies (IUMS) which participates
in the forthcoming ICSP vote during March 2020.

Please feel free to spread the core content of this message as far as
possible.

Sincerely yours
Markus Göker, DSMZ



*Text of original attachment to this message on GGBN-INFO:*

5th January 2020

To the members of the International Committee on Systematics of Prokaryotes

In keeping with Article 4 of the ICSP Statutes, the Editorial Board of the
International Code of Nomenclature of Prokaryotes (ICNP) is conducting an
open electronic meeting concerning proposals for changes in the ICNP.

The first phase of the meeting will take place from January 5, 2020, until
March 1, 2020. It is intended to allow open discussion of the proposals as
an email chain among the members of the ICSP and other interested parties.
Comments may be made by the ‘reply-all’ option on your email server. Comments
should be less than 500 words in length and should identify the author’s
name(s) and affiliation(s). Comments should be respectful, and ad hominem
comments will be deleted from the record. As comments accumulate, the
Editorial Board will transfer them to the ICSP website, and the edited
comments will serve as the minutes of the meeting. Please feel free to add
interested parties to the email recipient list and solicit comments from
interested parties outside the ICSP.

The second phase of the meeting will consist of voting and will take place
from March 1 to March 31, 2020. Only members of the ICSP may vote.

The issues for the current discussion are the “Modest proposals to expand
the type material for naming of prokaryotes” made by Whitman (2016; IJSEM
66: 2018-2112; https://doi.org/10.1099/ijsem.0.000980) and a related
proposal by Whitman et al. (2019; IJSEM 69: 2174-2175;
https://doi.org/10.1099/ijsem.0.003419) concerning granting priority
to Candidatus
names. To simplify the discussion, the ICSP and contributing colleagues are
asked to give particular consideration to the following statements, which
represent the central concepts. Should they be passed at the voting stage,
other rules will be changed as described in Whitman (2016) and Whitman et
al. (2019) to make the remainder of the Code consistent with these changes.

Proposal 1 (Whitman 2016). Extend the nature of the type acceptable for
valid publication of a species or subspecies name to allow the use of
complete or partial genome sequences as type (Whitman 2016). The new rules
would be worded [new text is underlined]:

Rule 18a. The type of a species or subspecies must unambiguously identify
the taxonomic group and is a designated strain or other material. Whenever
possible, the type of a species or subspecies is a designated strain.

(3) [first section] As from 1 April 2020*, sequences of genomic DNA may
also serve as the type when it unambiguously identifies the species. When
possible, it should be a high quality draft or better genome sequence.

Rule 30.3.c. [new rule] When a sequence is the type, the accession number
in a publically available database or the sequence must be given. It is
recommended that, when possible, a sample of the DNA be deposited in at
least two publically accessible service collections in different countries
and the catalog numbers be indicated.

*The original date of January 2016 proposed in Whitman (2016) is changed to
reflect the time necessary to bring this matter to a vote. All of the other
proposals in Whitman (2016) will be taken as originally worded.

Proposal 2 (Whitman 2016). Articulates a general concept for what can serve
as type for a species.

Rule 18a (3). [second section] As new methods are developed, they may serve
as the type material so long as they unambiguously identify the species or
subspecies and can be readily archived and compared.

Proposal 3 (Whitman 2016). Allows valid publication of the name of a genus
in the absence of a type species if the type is too ambiguous to
circumscribe a species.

The rule would be: "Rule 20a. The nomenclatural type (see Rule 15) of a
genus or subgenus is the type species or the sequence of one or more genes
that unambiguously identifies the genus or subgenus. The type species is
the single species or one of the species included when the name was
originally validly published. Only species whose names are legitimate may
serve as types."

Proposal 4 (Whitman et al. 2019). Upon acceptance of Proposal 1, the
priority of the names of Candidatus taxa published before 1 April 2020*
which are otherwise in accordance with the rules of the Code will have
priority based upon their date of publication in the IJSEM unless a
synonymous name already exists based upon deposition of type cultures.

Whitman et al. (2019) also provides a simple nomenclature for identifying
the nature of the type material:

‘When the type is a culture, the superscript “T” will be used immediately
following the name or strain identifier. If the type is a sequence, the
superscript “Ts” will be used. If the type is a description, preserved
specimen or illustration, the superscript “Td” will be used. If a
representative of a taxon is brought into culture, the type strain is then
designated as described in Rule 18f. The name may be emended by the new
authors, and the superscript “Ts” or “Td” is replaced by the superscript
“T”.’

*The original date of 1 January 2020 is changed to reflect the time
necessary to bring this matter to a vote.

For further guidance, major publications that discuss these proposals
include:

(in favour)

Whitman 2015. Syst. Appl. Microbiol. 38: 217-222 (
https://doi.org/10.1016/j.syapm.2015.02.003)

Konstantinidis et al. 2017. ISME J 11: 2399-2406 (
https://www.nature.com/articles/ismej2017113)

Rossello-Mora and Whitman 2019. Syst. Appl. Microbiol. 42: 5-14 (
https://doi.org/10.1016/j.syapm.2018.07.002)

(against)

Overmann et al. 2019. Syst. Appl. Microbiol. 42: 22-29. (
https://doi.org/10.1016/j.syapm.2018.08.009)

Bisgaard et al. 2019. Diagn. Microbiol. Infect. Dis. 95: 102-103. (
https://doi.org/10.1016/j.diagmicrobio.2019.03.007)