There has been a fascinating discussion of phylogenetics in the on-line discussion group of the Pacific Bulb Society the past several days. I've not been able to resist getting involved, even though my professional expertise does not include taxonomy or phylogenetics, and not even DNA sequencing. I'll try to reproduce the ideas raised by several participants here, but in a very general way.
Geography's Relation to Species
Every botanist and zoologist knows that the single most important piece of data that must accompany every specimen collected is its precise geographical location when collected. Date when collected is also important and very helpful. The name of the collector is usually included in the collection data. But the "where" is the sine qua non for biological specimens collected in the wild.
In our discussion of the possible identity of a bulb specimen one of the members had received, we felt that the missing collection locality would have been of critical importance in providing an identification. While this seems self-evident to me, it was apparently not seen that way by all the participants in the discussion. What is the importance of geography, and why is it questionable?
Locality is important, of course, because it confirms and potentially extends the known habitat range of the species. It is of uncertain value in determining what species one has collected, since species may grow wild outside their known range, or other species ranges may overlap a given species' range.
Where locality data is helpful in determining species identities is where the known species resemble each other closely in physical appearance but are known to have discrete and separate geographical ranges. Since this is not all that rare a circumstance in biology, knowing the collection locality for an ambiguous specimen can tell you its identity.
Still, I see geography as two levels removed from the actual identity of a specimen.
Morphology's Relation to Species
Traditionally, morphology, the physical structure of the organism, was the sole basis for classification. We identified species by the physical characteristics of the plant or animal, and inferred relationships strictly on the basis of these. Used this way, morphology will give you answers that are determined by the limitations of the kinds of data you utilize. Morphology is actually one level removed from phylogenetic relationship. It does not actually address genetic relatedness, as far as I can tell, although it was the traditional basis for all phylogenetics.
Since morphology is comprised of the results of genotype interacting with environment, a given species may have a variable morphology depending on climate, geography, and human alterations to its environment. Then too, different species may converge in physical appearance in response to living in a similar or the identical environment and habitat. Questions of structural convergence in response of similar evolutionary pressures seem to me to require molecular genetic analyses for clarification. I am reminded of the phenomenon of "cryptic sibling species" in butterflies, but those were first uncovered by detailed morphological studies (of the male genitalia, as I recall), prompted by observed behavioral differences. They nonetheless still pose an epistemological question.
Morphology was our first and original tool for studying phylogenetics and, if I'm not mistaken, the sole basis until DNA sequencing was invented; but it can also mislead.
When DNA sequencing came along, it opened a new and entirely different window on what constituted a species.
Species Definitions and DNA
We have reached the point in modern biology where one can say that the DNA sequence IS the organism. The genome defines the organism. It would follow from this then that the species is definable from DNA sequence data as well. Since we know that sexually-reproducing organisms almost never have two individuals who are precisely identical in the DNA sequences, we will have to learn to define the sequence variation that a given species concept can include.
How one defines "species" is dependent on what one intends to use the definition for. Look in many books on phylogenetics and you will see several formal definitions of species. Biologists use different ones of those several definitions depending on what direction their research is taking and what methodologies are available to them to use.
The one I think is most popular, the concept of the Biological Species as the interbreeding population, is fraught with problems. Operationally, the weakness in the biological species concept is that we can rarely if ever actually define the "breeding population." It is not really definable (in terms of "do this then this and you define the breeding population") using any doable steps so it is not really a scientific concept.
This leads me to feel that there is probably no such thing as a "species" but rather many ways of viewing the biological world. That is, it seems clear that there is not at present a single unambiguous working definition for the concept. I infer from this that the concept we are trying to define may in fact not exist as a single logical entity. Our discomfort with this, if any, is probably because our subconscious minds are still trying to fit everything into a pre-Darwinian frame of reference, which contained fixed, rigid species. Taxonomy needs to be viewed not as the Platonic Ideal of biology but rather as a heuristic tool for use in real life.
I think that a future definition(s) of "species" will attempt to circumscribe the "envelope" of DNA sequences that are encompassed by a given species. This answer will probably be different for different species. I think it will be very different for plants than for animals; and microbiologists seem to have already gone off on their own very separate track for defining populations rather than species. Binomial nomenclature seems to be giving way to serial numbers that computers can more easily handle. You don't draw pictures of phylogenetic trees, you calculate new ones using the latest data as you need them. Today's tree won't look like yesterday's unless the databases were locked down overnight.
An excellent reference for the nature of species is "Speciation" by Jerry A. Coyne and H. Allen Orr, available from amazon.com, as of this writing. Pub. 2004 by Sinauer Associates, Sunderland, MA.
These comments contain direct quotes from my personal posts to the on-line discussion group of the Pacific Bulb Society on October 31, 2012, with minor changes in wording.
We will be traveling to Tanzania for a tour of Tarangire, Ngorongoro, Serengeti, and Olduvai. I don't know how to post new entries to this blog using the iPad we are carrying with us, so I will post some pictures during the trip to my facebook page, ShieldsGardens on Facebook.com. After we return home, I'll try to post more pictures and a summary of the trip to this blog. I think this is the dry season in Tanzania, so I don't really expect to see many plants. We're going in order to see the animals!
Good gardening, from here in central Indiana
Look up technical terms in the Glossary of Plant Biology