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I do think you wrote what I think it should be. A DNA effort is being done, and experts draw conclusions from them.

The barcoding effort has two facets: identification of species, and DEFINITION of species. The first is completely unproblematic, the second a monstrous can of worms, and unfortunately some of the barcoders don't appear to at all see a difference.

It always worries me when I hear barcoding people give serious thought to issues such as how many percent dissimilarity in this 384 bp fragment of the COI gene is the magical line which separates species from populations - it should be screamingly obvious to them why that entire line of reasoning is flawed.

racoll wrote:Not exactly. They (Ready et al 2006) only analysed two genes. The phylogeny of a gene is not always the phylogeny of a species. If the whole genome of these two species were studied, I'll bet they are distinct.

He studied some of the fastest evolving coding genes in the entire genome; nearly all other genes will show less variation. That pattern is pretty common, e.g. most malawi cichlids and victoria cichlids have nearly indentical genomes, differing only in minute details.

The thing is that raw percentage dissimilarity is a nearly useless measure, as a very minor change can have cascading effects.
Somewhat like, for instance, changing "is" to "is not" after the word "dissimilarity" in the previous sentence would invert the meaning of the sentence even though only three letters change.

There's nothing magical about DNA. It's just another source of infomation, neither better nor worse than morphological analyses, quality wise - but certainly a lot easier to perform.

Mike_Noren wrote:neither better nor worse than morphological analyses, quality wise - but certainly a lot easier to perform.

would that not be 'easier to reproduce?'

the tools are monstrous, but available. Still, it is not easy (I'm a chemist)

Bas Pels wrote: would that not be 'easier to reproduce?'

the tools are monstrous, but available. Still, it is not easy (I'm a chemist)

You need a lab, yes, but obtaining DNA data is very easy once you have a functioning protocol. As for barcoding, the fragment is very short and a big, state-of-the-art lab will go from a set of tissues to finished DNA sequences in less than a day, whereas a small un-automated lab like the one I worked in would do so in less than a week. It's a very short snippet of a mitochondrial gene with good primer positions, meaning there's no need for cloning or other fancy & time consuming techniques.
With barcoding the ease of obtaining the fragment is of central importance to the whole concept, as the plan is to gather millions of sequences in a short time.

The barcoding effort has two facets: identification of species, and DEFINITION of species

All well and good, and DNA is a great tool, and its uses are clear when you take the example of the Ready et al (2006) discus paper, where genes were used to inform the morphological delimitation and nomenclature, but what worries me is the increasing divorce between molecular systematists and taxonomic classification.

People like Felsenstein (2004) are saying classification is now "irrelevant", and there are many papers where phylogenies are presented reporting nomenclatural incongruence, but no re-examination of material and subsequent reclassification is taking place.

Its all very well working out the tree of life, but there has to be a practical use to it. It has to relate to the organisms.

racoll wrote:

... there are many papers where phylogenies are presented reporting nomenclatural incongruence, but no re-examination of material and subsequent reclassification is taking place.

If you are saying that there are phylogenies based on DNA data being presented that highlight issues of classification for certain species without re-examination of the holotypes, that isn't surprising. An effort of that type could take a year for even one species and call for expertise that the author doesn't have. That work will likely fall to some grad student at a point in the future. Even in 'traditional' taxonomy, organisms get reassigned without all of the data being re-examined. Often these revisions are presented and the authors then wait to see how it is received by thier peres. Just part of the process of working out the tree.

Wow all this from a simple question of how do I tell the difference between L066 and L333 or whatever it was.
I think this thread should be moved again to the taxonomy bit because it most certainly not "Speak easy",someone may be just discovering Planet Catfish, see this in the speak easy section and run a mile, I don't understand what the fK some of you are On about.
Could someone please explain:
Phylogeny (is this to do with "Phylum")
Morphological delimitation
384 bp
What the universe is expanding into..
The difference between Fluff and Dust.......

Its all very well working out the tree of life, but there has to be a practical use to it

This is my original question.
Please remember I am an Engineer not a chemist, biologist, taxonomist......... Charles Darwin

Matt

I do think Matt is right: If this is easy talk, I would not want to read the rest of the forum - although I did participate in the discussion myself.

As stated, I'm not a biologist, and besides English is not even my native tongue

Phylogeny (is this to do with "Phylum") - I think it is the history of a species: it diverted from ... and than from etc

Morphological delimitation - not all fish of a species look alike. If I go into a shop, I may see fish offered as Platydoras costatus, but I can decide the nose is too long, and consider it as an Orinocodoras. Apparently the fish does not fit into the specs for Platydoras, and might be an Orinocodoras. This spec (- delimination) is morfological (based on the shape) in nature, thus a morfological delimination - an engeneer would say 'the fish does not fulfill its specs'

384 bp - bp stand for base pairs. DNA, the genetic stuff, is made of bases A, C, T and G. A gene consists of a string of DNA, and can be long, very long (100.000 characters or more). DMA consists of 2 such strings, a sense string (translated into proteins) and an antisense string (used to produce another sense string when the cell divides). The A base mates to a T and the C to G. Normally one talks of base pairs referring to DNA, or bases referring to 1 of the 2 strings.

What the universe is expanding into.. off topic

The difference between Fluff and Dust....... no idea

Phylogeny (is this to do with "Phylum")

A phylogeny is a hypothesis of relationship between organisms based on unique shared similarities (morphological or DNA) from living or fossil evidence. It indicates which species shared a common ancestor and evolutionary lineage, e.g.



There is also the "true" phylogeny, which is how this evolution actually happened, but we can never know that (without a time machine).

An effort of that type could take a year for even one species and call for expertise that the author doesn't have.

Indeed you are right, and I would not want to criticise individual researchers/labs (who do excellent work), but just comment on a trend. It seems as more and more sequences are submitted to genbank, there is a real risk of molecular research outstripping the rate that morphological taxonomists can keep up with the potential changes, especially given the gulf in funding between the two disciplines.

The difference between Fluff and Dust.......

This is easy, fluff is loosely matted fibres (often clothing), while dust is a much finer free particulate

Thank you for clearing that up guys.
Bas I am always astounded at you guys for which English is not your first language it is amazing, it just doesn't occur to me sometimes.

A time machine, well why didn't you say earlier , I have one of those tucked away behind my Doomsday devices, I'll see if I can dig it out.
Has anyone heard from Sid?

Matt

As suggested, I'm moving this to the Taxonomy and Science section, to avoid scaring the newbies.

--
Mats

Matt didn't say it directly but it bears saying that we need to keep a degree of perspective about this subject. It makes an interesting thread and causes me at least to want to do additional reading. A light intellectual discussion. There is no right or wrong answer as there is no right or wrong way classify organisms, just more accepted methods. And the accepted methods of yesterday are not those of today, nor are they apt to be the one used in the future.

Interesting discussion guys.

grokefish wrote:A time machine, well why didn't you say earlier , I have one of those tucked away behind my Doomsday devices, I'll see if I can dig it out.

please do, 'somthing went wrong with mine

Wow guys reading some of theses posts is like being in College w/o the tuition! This is awesome the other thing is I have actually been able to follow some of it.

Just reading this old thread and realizing of course that this issue comes up again and again... which means that sometimes more recent threads will shine light on old ones.

Case in point: Home > Forum index > Identification > Taxonomy & Science News > L066=L333

Cheers, Eric

P.S., Before finding this thread, by coincidence I chose the exact same phrase (as the title of this thread) when I recently gave a fish club talk on the subject of C #, L #, and species IDs. I guess our minds all go to the same place when faced with the challenge of defining species.