Youngest Person To Name A New Species

[RichW9090]

It is worth noting here that some current, mostly young, researchers have the attitude that "OK, we'll check the DNA, and that will tell us unequivocally if it is a new species".

No, it will not. There is no magic number of single base-pair changes that defines a species boundary. DNA evidence in defining species is every bit as subjective as is morphology, perhaps more so, since you cannot "see" the difference in the whole organism by looking at a single base-pair, or all the base-pairs in the entire genome. The evidence of DNA is objective - base-pairs are what they are, after all - but the interpretation of what those differences mean in terms of biological (or any other type ) species is entirely subjective.

There is no Molecular Species Definition. There is a Biological Species Definition, and a Phylogenetic Species Definition (which is the same, although many cladists would deny it, as the Evolutionary Species Definition.

Rich

[Auspex]

...There is no Molecular Species Definition. There is a Biological Species Definition, and a Phylogenetic Species Definition (which is the same, although many cladists would deny it, as the Evolutionary Species Definition...

And throughout it all, every critter goes on being exactly what it is...

[RichW9090]

George Gaylord Simpson, one of my three or four idols, had a saying when in came to the incessant arguments about the names of animals, and the species definition.

He said "Ask not what is a mouse; instead, ask what is mouse-ness".

He was the first Zen-Paleontologist!

Edited September 3, 2013 by RichW9090

[painshill]

Form the Wiki entry on "DNA barcoding":

DNA barcoding is a taxonomic method that uses a short genetic marker in an organism's DNA to identify it as belonging to a particular species. It differs from molecular phylogeny in that the main goal is not to determine patterns of relationship but to identify an unknown sample in terms of a preexisting classification. Although barcodes are sometimes used in an effort to identify unknown species or assess whether species should be combined or separated, the utility of DNA barcoding for these purposes is subject to debate.The most commonly used barcode region, for animals, at least, is a segment of approximately 600 base pairs of the mitochondrial gene cytochrome oxidase I (COI).

In an effort to find a correspondence between traditional species boundaries established by taxonomy and those inferred by DNA barcoding, Hebert and co-workers sequenced DNA barcodes of 260 of the 667 bird species that breed in North America (Hebert et al. 2004). They found that every single one of the 260 species had a different COI sequence. 130 species were represented by two or more specimens; in all of these species, COI sequences were either identical or were most similar to sequences of the same species. COI variations between species averaged 7.93%, whereas variation within species averaged 0.43%. In four cases there were deep intraspecific divergences, indicating possible new species. Three out of these four polytypic species are already split into two by some taxonomists. Hebert et al.'s (2004) results reinforce these views and strengthen the case for DNA barcoding. Hebert et al. also proposed a standard sequence threshold to define new species, this threshold, the so-called "barcoding gap", was defined as 10 times the mean intraspecific variation for the group under study.

[RichW9090]

Yes, that fits with what I said - how were the OTUs defined for the analysis? By traditional morphological approaches - then they were analyzed.

Simply defining the necessary difference as 10 X the mean intraspecific variability is every bit as subjective. Suppose the difference is only 9X - you'd not define it as a "new species"? What if it were 9.5 X? or 9.95 X? If it was 12X, you'd be comfortable with calling it a new species, regardless of its morphological or behavioral correlates, and regardless of its geographical cohesiveness? What about 10.5 X, or 10.05 X?

This approach is also subject to the same problem as species definition in fossil populations. If you had every individual in a lineage from Species A to Species C, and did the "barcoding" (an odius term, because it implies an absolute precision entirely lacking) of all of them, you'd not be able to draw the boundaries in any other than a completely arbitrary fashion, as successive generations would always lie within 10X of the population mean of the previous generation.

Molecular phylogeny is particulalry sensitive to the small sample problems from which early cladistic analyses suffered from, and from which modern analyses still suffer when fossils aren't included. They all boil down to three-taxon statements. A and B are more closely related than either is to C. Pick A, B, and C far enough apart (ie, the common ancestor remote enough) and the comparision becomes meaningless at the species level, and useless at higher levels because of underrepresentation of branching events.

Understand that I am not arguing aginst the use of molecules in phylogeny*. But they are not inherently better than morphology, and have their own limitations. Some limitations will be minimized or removed as taxon samplings and sequence samplings increase and accumulate, some will not because they are intrinsic to the nature of evolution itself.

As Auspex noted, regardless of our understanding of the morphology and the molecules, living organisms keep on doing what they do, which is evolve.

* In fact, a comparison of total evidence phylogenies, to the subsets of morphology and molecules, are often helpful in identifying homoplasies which otherwise might elude us.

Edited September 4, 2013 by RichW9090

[AgrilusHunter]

As a 'mostly young' researcher I am a huge supporter of the use of molecular data in taxonomic research and I am very confident and comfortable using DNA barcoding within the scope of its boundaries. Several times, when giving presentations, I've been confronted by 'old guard' taxonomists who are concerned and a bit frustrated by the rapid adoption of molecular techniques into taxonomy. I don't blame them. As Rich states above there is no red line that when crossed immediately indicates a new species. In presentations I've given in the past I liken molecular barcoding to a very powerful microscope that lets taxonomists view new, different, characteristics about their species of interest. It is particularly helpful when examining essentially unidentifiable life stages in insects such as eggs or early larval instars. What's clear though is that third base wobble (changes that result in amino acid substitutions occur as well but they are rare when comparing similar species) in one 658bp (708bp with primers) region of the COI gene is not equivalent to morphological or behavioral differences and should not be given equal weight. Far more extensive molecular analyses are needed for proper phylogenetic studies.

Here are just a couple of the challenges associated with DNA barcoding. First, it tends to break down over large distances. What does this mean? Well, individuals from the same species from widely seperated populations will often display divergent COI sequences. This can be caused by landscape barriers or simply by clinal variation. Second, determing the accuracy of a COI sequence is not trivial. In many species the COI gene has been translocated into the organism's nuclear genome. Once there it is no longer conserved and can begin to mutate randomly. Hebert's primers (actually from Folmer et al. 1994 ) do not discriminate between nuclear and mitochondrial DNA and will amplify both sequences. Having two sequences in the resulting PCR product complicates downstream analysis and intepretation. The take home is that this technology is still in its infancy and more research is needed. Making broad claims or, worse yet, policy decisions based on it would be a mistake. Molecular barcoding shines in specific situations and fails in others; it has certainly become a powerful and important tool but it cannot replace classical taxonomy in defining a species.

side note: DNA barcoding with Agrilus here.

Edited September 5, 2013 by AgrilusHunter

[piranha]

...Molecular barcoding shines in specific situations and fails in others; it has certainly become a powerful and important tool but it cannot replace classical taxonomy in defining a species.

A sigh of relief for all the amateur specialists!

[RichW9090]

There is hope for the "young researchers" yet! And yes, I am firmly in the ranks of the old guard, where I have remained in spite of having developed some skill with cladistics, and using cladistics as a tool in my work. And I'd be happy to use DNA as well, except for the fact that there is only one living species in the family I work the most with (Antilocapridae).

Nice poster.

Edited September 4, 2013 by RichW9090