Hunting New Species: Competitive Sport of the 21st century?

[Jason Bobe]

I hope "species hunting", where the goal is to identify all species on
earth becomes a something of a competitive sport during the next
decade. With bacteria alone, there are likely enough unidentified
bacterial species on Earth for every single human to discover one new
one (# bacterial OTUs in greengenes database at LBNL is ~50k,
estimated # of bacterial OTUs on earth is likely equivalent to # of
stars in sky).

A few questions:

(1) Who currently holds the record for most species ever identified?

(2) Besides Nabakov and his "blues", any other famous non-professional
scientists who are associated with the discovery of a species?
Reference: "Nabokov's Blues: The Scientific Odyssey of a Literary
Genius". (Or funny stories about discoveries of new species: http://bit.ly/q6BYZ)

(3) Perhaps there is a better term than "species hunting" since goal
is to identify/conserve rather than kill. But I like the relationship
with microbe hunting, bone hunting, etc.

Thanks,
Jason Bobe

[Bryan Bishop]

On Tue, Jul 28, 2009 at 8:45 PM, Jason Bobe wrote:
> I hope "species hunting", where the goal is to identify all species on
> earth becomes a something of a competitive sport during the next

Let's hold off on calling things new species until we can get a better
idea of what a species actually is. Are you talking about mating
incompatibilities? And what does that even mean? How about ligers?
These are really man made definitions, so there's a lot of opportunity
to cheat your game, Jason.

- Bryan
http://heybryan.org/
1 512 203 0507

[Jason Bobe]

On Jul 28, 9:49 pm, Bryan Bishop <kanz...@gmail.com> wrote:
> there's a lot of opportunity
> to cheat your game, Jason.

Fair enough. There are a lot opportunities to inspire and educate
people too. And get them involved in biological research. Perhaps
the discovery of a potential new species will motivate people to up
your challenge and understand various interpretations of what it means
to be a species.

Thanks,
Jason

[Bryan Bishop]

On Tue, Jul 28, 2009 at 9:02 PM, Jason Bobe wrote:
> On Jul 28, 9:49 pm, Bryan Bishop wrote:
>> there's a lot of opportunity
>> to cheat your game, Jason.
>
> Fair enough.  There are a lot opportunities to inspire and educate
> people too.  And get them involved in biological research.  Perhaps
> the discovery of a potential new species will motivate people to up
> your challenge and understand various interpretations of what it means
> to be a species.

What? All I was asking was for some rules to the game. As the game
maker, I think it's your job to provide the definitions of the game.
The players then play by the rules, and maybe explore some new rules,
but you need to at least propose some rules for them to start with I
think.

[Aaron Hicks]

On Tue, Jul 28, 2009 at 6:45 PM, Jason Bobe <jaso...@gmail.com> wrote:

I hope "species hunting", where the goal is to identify all species on
earth becomes a something of a competitive sport during the next
decade.  With bacteria alone, there are likely enough unidentified
bacterial species on Earth for every single human to discover one new
one (# bacterial OTUs in greengenes database at LBNL is ~50k,
estimated # of bacterial OTUs on earth is likely equivalent to # of
stars in sky).

A few questions:

(1) Who currently holds the record for most species ever identified?

I'd guess Carl Linnaeus. As authority for a huge number of plant species, it's simply "L." to acknowledge his contribution.

(2) Besides Nabakov and his "blues", any other famous non-professional
scientists who are associated with the discovery of a species?
Reference: "Nabokov's Blues: The Scientific Odyssey of a Literary
Genius". (Or funny stories about discoveries of new species: http://bit.ly/q6BYZ)

Associated? I know a number of folks involved in the invertebrate trade that are responsible for new species being identified- whether they were the collector, the importer, or simply the guy who said, "Well, this tarantula has a tiny morphological difference than the others in this disjunct population over there. Looks new to me, so lemme send some off to Professor X, who happens to be an authority I know." Happens all the time.
 

(3) Perhaps there is a better term than "species hunting" since goal
is to identify/conserve rather than kill.  But I like the relationship
with microbe hunting, bone hunting, etc.

 

There's also the matter of splitters versus lumpers. Taxonomy is messy in that anyone can publish a reassessment of a species- or a higher taxonomic level, for what that's worth. The question is whether one must believe their reassignment- whether the grounds are reasonable, based on morphology, molecular phylogeny, or (increasingly) a combination of factors including molecular phylogeny. It's not uncommon in the realm of plant taxonomy for someone to reassign a species, but everyone keeps calling it by its old name for years; one can "date" horticulturists based on what they call a given plant. Indeed, some species are given new names several times; I can think of a couple given at least three names, and there are undoubtedly more with additional names.

But is it a new species? Does two warts on a dorsal sepal qualify it as a different species that typically has three? Splitters versus lumpers. It's simply not that easy- and if you want to drag interbreeding into the equation, it gets very sticky very quickly, particularly with plants.

Even stickier are natural hybrids. Agave arizonica was afforded protection under the Endangered Species Act due to its rarity. Discovered in 1959, it was listed in 1984, and de-listed (I think) quite recently after being discovered that it was, in fact, a natural hybrid between A. chrysantha and A. toumeyana v. bella. Instead of being critically imperiled, it is apparently found in areas where the two parent species occur naturally and interbreed. Given the "plasticity" of genes in the genus agave, it is not unreasonable to assume it could eventually spawn its own species.

-AJ

[Splicer]

On 29 Juli, 03:45, Jason Bobe <jasonb...@gmail.com> wrote:
> (1) Who currently holds the record for most species ever identified?

That would have to be Craig Venter with his ocean sampling
expeditions.


-Splicer

[Tom Knight]

I disagree. Venter has isolated DNA from a large number of organisms,
many unknown, but has identified zero new species. The rules for
species identification are rigid and include culturing and deposition
of the cultures in a culture collection in two or more countries.
Furthermore, you must characterize the species such that others can
identify it, and "validly publish" the result. Venter's approach
sequences a huge amount of DNA, but in short snippets which are not
assembled into entire genomes, so we have zero new complete genomes
from his work. It is still valuable work, since it provides a lot of
information about the diversity of life, many new proteins, relative
amounts of proteins present, indications of common known and unknown
species, and crude identification of the groups of bacteria present
through analysis of their 16S and other conserved gene sequences.

[fhapgood]

When I saw this thread title I thought it was about using genetic
engineering to
spice up recreational hunting.

Will happen someday, I guess.

[Jason Bobe]

On Jul 29, 8:36 am, Tom Knight <t...@csail.mit.edu> wrote:
> The rules for  
> species identification are rigid and include culturing and deposition  
> of the cultures in a culture collection in two or more countries.  
> Furthermore, you must characterize the species such that others can  
> identify it, and "validly publish" the result.  

Thanks Tom. Here is one reference where a model process is proposed
for new bacterial species identification.

"...we propose to create an Internet-based repository for orphan
isolates alongside sequence databases and international collections of
bacteria. Such an electronic repository would incorporate an identity
card with specific mentions of the collection number of the isolate in
at least two international bacterial inventories, the source of
isolation, phenotypic characters, antibiotic susceptibility pattern,
complete 16S rRNA sequence with GenBank accession number and
percentage of sequence similarity with the five closest relatives, any
other significant gene sequence with GenBank accession number, any
relevant criterion for the accurate identification, and the names and
addresses of at least two corresponding authors.

Also, such an electronic repository would automatically offer the
first depositor of a new bacterial species the opportunity to propose
a name under a “Candidatus” status pending publication of the results
in a peer-reviewed journal. Entries into such a database would be
filed by microbiologists interested in the field of bacterial taxonomy
up to the report of three to five isolates of potential new species.
At that point, the automatic regulation system of the orphan isolate
repository would electronically question the successive discoverers in
the order of deposition with respect to their intention to describe
the new species on the basis of collected data in the database in any
relevant peer-reviewed journal, subject to contractual delay. The
advantages of such an electronic repository would include
normalization of criteria for the description of new bacterial
species, reasonable enforcement of a three- to five-isolate rule, a
shortened delay for precise description of new bacterial species, and
a competitive system for such description among leading international
groups. We propose that such an electronic repository should be held
under the auspices of the American Society for Microbiology, alongside
the relevant databases and bacterial collections, and named the
Electronic Orphan Bacterium Repository, or EOBR, as its abbreviated
form."

Drancourt M et al. Sequence-based identification of new bacteria: a
proposition for creation of an orphan bacterium repository. [PMID:
16145070]

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1234117

[Jason Bobe]

On Jul 28, 9:45 pm, Jason Bobe <jasonb...@gmail.com> wrote:
> (1) Who currently holds the record for most species ever identified?

I still don't have a good answer for this. But here is one piece of
data on # new bacterial species from human samples:

"With the use of 16S rDNA sequencing, 215 novel bacterial species, 29
of which belong to novel genera, have been discovered from human
specimens in the past 7 years of the 21st century (2001-2007)." Woo
PC et al. Then and now: use of 16S rDNA...[PMID: 18828852]

Thanks,
Jason Bobe

[Jason Bobe]

On Jul 29, 3:37 pm, Jason Bobe <jasonb...@gmail.com> wrote:
> On Jul 29, 8:36 am, Tom Knight <t...@csail.mit.edu> wrote:
>
> > The rules for  
> > species identification are rigid and include culturing and deposition  
> > of the cultures in a culture collection in two or more countries.  
> > Furthermore, you must characterize the species such that others can  
> > identify it, and "validly publish" the result.

Here is a short history of the "Bacteriological Code" which has
defined and re-defined the rules for naming bacteria:

http://www.the-icsp.org/misc/Code_history.htm