ISPN

[tmkeesey]

The PhyloCode uses the phrase "extant (or Recent)" in several places when discussing crown clades, total clades, etc. The new "Pan-" prefix even depends on on the phrase. But the exact definition of "extant (or Recent)" is left up to individual authors, with a "backup" definition should they fail to define it:

[leowsham]

As I noted in the mailing list discussion, the essence of being extant is (only) that scientists have both anatomical and extra-anatomical character states documented for them. Having just a good stuffed specimen in the museum is perhaps none better that recovering something excellent from a Lagerstatten. For example, that Ivory-bill woodpecker may be treated as extant because its call was recorded.
Besides, I'm not sure if a museum/herberium criteria works for life other than Animalia and Plantae. Do we have databank for "protists"? ... my ignorance
The use of Recent may also be ambigious. Holocene spanned 10000 years - is that "Recent"?
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vivat scientia !!!

[tmkeesey]

It does seem like the best route is to explore why "extant" is such a useful specifier. There are several different reasons I can think of:

1. Soft tissue is available. (Lagerstätten remains are still not as good as stuffed specimens, I think.)
2. More specifically, the entire genome is available.
3. Behavior can be observed.

The problem with basing the definition on #3 is that the status can change between papers. One decade there might be an observable population, the next decade it might go missing. (And the next decade it could be discovered again!)

The problem with basing the definition on #1 is that it doesn't specify which type of soft tissue: if one type is available but another is not, is it extant?

But which types of soft tissue do all organisms have, anyway? Well, #2 is one. What about that for a definition of extant: "having the entire genome retrievable for research"?

(Well, that does kind of have the same problem as #3 ... hmmm....)
_________________
T. Michael Keesey
Director of Technology, Exopolis, Inc.

[leowsham]

Good point - I'd thought about the genome issue, too, but it may get one some potential mess:
(1) It's not a tradition for Darwin and others to collect the genome. One may well found some species beautifully stuffed or even videoed but well - lacking a collected genome.
(2) In what sense is a genome collected? Save a stem cell-line? Or demand that a genome be sequenced (quite impractical to date).
(3) If the phylocode intend to cover bacteria, lateral gene transfer may make genome-based database unstable.
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vivat scientia !!!

[tmkeesey]

I didn't say "collected", but rather "retrievable" or "available", in the sense of "collected or potentially collectible", i.e., existing in living organisms and/or in collections.

As I mentioned before, though, this can change from date to date (species goes extinct before its DNA can be collected), so perhaps it's not the best idea.
_________________
T. Michael Keesey
Director of Technology, Exopolis, Inc.

[leowsham]

Yep, Mike, I agree! The loophole I was thinking about are those species like the dodo, moas, korean gray (whale), messenger dove or even the mammoth in permafrost - no DNA available but recent enough to some who would treat them as extant...

(Oh no , are we able to extract complete genome from Mammuthus primigineus? Please advise)

P.S. Where's everybody else?
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[David Marjanović]

Complete mitochondrial genomes have been sequenced from a mammoth and a moa.

[leowsham]

Mitochondrial DNA is useful for calculating lineage divergence, but may not be totally equivalent to the nuclear genome required for the definition of the species (theorectically), I suppose? ... It was somewhat a fad to leave out biochemistry/genetics at med school and now I should hold some remorse
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vivat scientia !!!

[ottscay]

There are larger pragmatic problems with the genome definition; Whether we have thylacine specimens in museums, or can ever retrieve its entire genome (apparently unlikely), no neontologist will accept (nor should they) that the thylacine is "extant", except in the eventuality that one is cloned.

This, by the way, is the same problem with anastamosing species (or even more inclusive clades, in the case of asexual reproduction). If we are going to try and study messy systems like living organisms, we are going to have to accept that the status (e.g. extinct, or reproductively isolated) may change with time. The best we can hope to do is provide simple non-changing definitions to judge character status by. And even then we are lucky to get as succint of a definition as "at least one member alive at time of writing".

It's like criticising an author for listing how many specimens of a fossil taxa are known...since this could change and future researchers will have to verify the data.

[tmkeesey]

Hmmm. What about defining "extant" as "living and published upon as of [insert date here]"?
_________________
T. Michael Keesey
Director of Technology, Exopolis, Inc.

[leowsham]

Scientifically this is sound, but this blatantly admits that we are just going to deal with a small portion of life that is actually extant Sometimes it remains hard to determine whether a species is actually living. So my original proposal was similar to TMK's second criteria - that science can provide anatomical plus extra-anatomical data - demonstrating that the species must have been reasonably recent enough living and known to science.
_________________
vivat scientia !!!

[tmkeesey]

But extra-anatomical data can fossilize, too: footprints, burrows, etc.
_________________
T. Michael Keesey
Director of Technology, Exopolis, Inc.

[ottscay]

I guess you have to ask what makes a definition "better"? For 99% of organisms that would be classified as "extant", the definition Keesey gives above would work with little problem and would be in line with how the term is already used (it'd just be more rigorous). With an anatomy + extra anatomical definition you invoke the much, much more common problem of fossils from deep time qualifying as "extant", plus you have to re-educate the entirety of neontologists to use a counter-intuitive definition. So how would it be more useful?

Don't get me wrong, I want as rigorous and easy-to-use of a definition as anyone else, but we have to take into account how disparate a proposed definition is with traditional usage, because it won't be used at all if we can't convince the majority of scientsts to use it. It'll just fail and then clutter up the wastebin of discarded nomenclatural terms (making the problem worse). Not that we should be a slave to traditional usage, but there really will only be a few (ivory-billed woodpecker) animals for which "extant" is contentious, and even then Keesey's solution would work with little modification.

[tmkeesey]

I mentioned several options (not all of them my own)--which one are you referring to, Scott?
_________________
T. Michael Keesey
Director of Technology, Exopolis, Inc.

[ottscay]

The one most directly above my post, specifically: