Reptile & Amphibian Forums

Welcome to kingsnake.com's message board system. Here you may share and discuss information with others about your favorite reptile and amphibian related topics such as care and feeding, caging requirements, permits and licenses, and more. Launched in 1997, the kingsnake.com message board system is one of the oldest and largest systems on the internet.

Click here to visit Classifieds
Southwestern Center for Herpetological Research
Click here for Dragon Serpents

Is DNA necesarry?

Tormato May 17, 2005 02:04 PM

In terms of classifying animals (specifically pythons), I wonder. There were the old days, when people couldn't go and perform a DNA sequence test, yet they still managed to classify animals. People like to jump down Hoser's throat (albiet his stance seems bloated), but I fail to see the synonyms in currently accepted taxa. I have never seen a scientific paper or publication that outlines and addresses the various genuses (morelia, python, liasis, etc). Where do these various genuses start to take some accountability? I believe I have a small python book that does a mediocre job at breaking down the various genuses. For liasis, for example, it states that "members of the liasis family do not have prehensile tales" yet my White Lip's tail is damn prehensile. Might sound like a broken record here, but same goes for water pythons I have been affiliated with. I guess my question is; people want validity out of Hoser. If he cannot provide it, then I want validity from the accepted classifications. Just what *does* liasis mean? As far as I'm concerned, my white lip is just that... a white lipped python. Where do we take the critics hats off? Id like to know how classification was dealt with before DNA testing was available.

john
1.0 D'albertis python (Liasis JohnBertisi)
-----
Many feel that I need to be balanced with equal time. Wrong. I AM equal time.

-Rush Limbaugh, 1992

Replies (4)

emoneill May 17, 2005 03:56 PM

In response to your question about DNA, the answer is: sometimes it is neccessary.
Before this technology existed, people relied on morphology and to a lesser extent other traits like behavior to classify different species. The problem is there are sometimes few if any characters that allow robust classification among closely related species. But DNA provides an almost endless number of characters, even at the level of individuals. It boils down to whether there is enough variation in non-DNA data.

E

__

Rush Limbaugh IS A BIG FAT IDIOT
-Al Franken

And I agree!

WW May 18, 2005 03:42 AM

After all, Lewis & Clarke got across the US without motor vehicles. However, by and large, most people find that transport over longer distances works considerably better if you do happen to have a car, train or plane handy. Before internal combustion engine technology became available, we lived with the limitations imposed by the technology available then, now we exploit the opportunities afforded by newer technology.

The same applies to taxonomy: before DNA sequence information became available, people worked with what they had: morphology. Now DNA information is easily available, and systematists are using it. It is not necessarily the magic bullet many people assume it to be, but it certainly does provide a huge amount of additional informationa nd a totally different perspective on the evolution of groups of organisms.

As far as pythons, specifically, are concerned, I might add that there has not so far been a comprehensive, published DNA-based study of the different genera. The most recent revision, on which the currently most widely accepted genera are based, was by Kluge (1993), and was based entirely on morphology.

Finally, as far as your charcaters are concerned, the various pythong genera have been defined based on a wide suite of often skeletal characters. The type of characters that you say are inconsistent are the ort of *identifying* charcaters that you will find in herpetoculture books or field guides - they are not necessarily the main characters used in reconstructing phylogenies, which led to the definition of the genera in the firstplace.

Cheers,

WW
-----
WW Home

CKing Apr 11, 2006 01:07 PM

>>After all, Lewis & Clarke got across the US without motor vehicles.

Yes, but that is nothing compared to what the polynesians did when they reached the remote islands in the Pacific Ocean without the benefit of motorized power. Even Homo erectus may have built boats or at least simple rafts.

>However, by and large, most people find that transport over longer distances works considerably better if you do happen to have a car, train or plane handy. Before internal combustion engine technology became available, we lived with the limitations imposed by the technology available then, now we exploit the opportunities afforded by newer technology.

Agreed. Nevertheless, DNA deteoriates rapidly once the organism died. Therefore paleontologists have been unable to use DNA to ascertain relationships except in some rare cases where DNA has been preserved in fossils. It is now known from mtDNA evidence that Neanderthals last shared a common ancestor with modern humans some 500,000 years ago, whereas all living humans shared a common ancestor around 100,000 to 150,000 years ago.

>>The same applies to taxonomy: before DNA sequence information became available, people worked with what they had: morphology.

That is not all taxonomists used though. Many relied on developmental biology. It is amazing how similar the early embryos of various vertebrate groups are. These similarities provide important clues to their common ancestry. Unfortunately, many practicing cladists simply ignore embryological evidence.

>Now DNA information is easily available, and systematists are using it. It is not necessarily the magic bullet many people assume it to be, but it certainly does provide a huge amount of additional informationa nd a totally different perspective on the evolution of groups of organisms.

Indeed. DNA evidence can be very informative. mtDNA evidence has also provided additional information about past migrations. Morphology alone would not have been as informative. Since the past cannot be directly observed, all sorts of evidence that provide clues about what actually happened in the past are welcome.

>>As far as pythons, specifically, are concerned, I might add that there has not so far been a comprehensive, published DNA-based study of the different genera. The most recent revision, on which the currently most widely accepted genera are based, was by Kluge (1993), and was based entirely on morphology.

And of course, we all know that the so-called "monophyletic" groups that are delineated using morphology often turn out to be paraphyletic or even polyphyletic when DNA evidence becomes available. Kluge's morphological analyses are no exception.

>>Finally, as far as your charcaters are concerned, the various pythong genera have been defined based on a wide suite of often skeletal characters. The type of characters that you say are inconsistent are the ort of *identifying* charcaters that you will find in herpetoculture books or field guides - they are not necessarily the main characters used in reconstructing phylogenies, which led to the definition of the genera in the firstplace.
>>
>>Cheers,
>>
>>WW
>>-----
>> WW Home

Unfortunately, the morphological characters used to reconstruct phylogenies are often convergent similarities instead of Hennigian synapomorphies. This is especially true of cladistic analyses using morphological characters. The cladists favor using as large a set of characters as possible, while spending little or no time anlyzing the goodness of the characters they use. Some even claim that their ignorance of character goodness somehow made their analyses "objective." Ignorance is definitely not objectivity.

Below is a critique of current cladistic methodology from Feduccia et al. (2005):

It should give one pause that while paleontologists employing cladistic methodology use a list of a hundred or more characters that link birds and theropods, most are simple binary designations, one step removed from the organisms. The vast majority are plesiomorphic, not qualifying as Hennigian synapomorphies, and in this view there is no accounting for acceptance of large groupings of the characters that are co-correlated. Thus, 15 or more characters may simply represent one character complex, diluting their phylogenetic resolving power. These facts have rendered modern cladistic methodology a form of ¡§Sokalian¡¨ phenetics, which can be termed ¡§cladophenetics.¡¨ Homology is usually ascertained in an a posteriori fashion to conform to the established cladogram, and embryonic connectivity and position are largely ignored. It should also be a matter of concern that bipedal reptiles first appeared in prearchosaurian lineages as the Permian Eudibamus (Berman et al., 2000). Of further concern should be the fact that among basal archosaurs, most ornithosuchids (without the ankle) would easily reach the ceratosaur level in any cladogram. The inability of cladistic methodology to deal with convergence has been pointed out time and again (Carroll and Dong, 1991; Feduccia, 1999a). This methodology always groups as clades convergent avian pairs such as loons and grebes, which form the bones of their swimming feet by disparate means embryologically, and most recently the pelecaniform wing-propelled divers, the plotopterids, form a cladistic clade with penguins (Mayr, 2005), another convergent pair. Dodson (2000, p. 504) correctly notes that: Cladistics systematically excludes data from stratigraphy, embryology, ecology, and biogeography that could otherwise be employed to bring maximum evolutionary coherence to biological data. Darwin would have convinced no one if he had been so restrictive in his theory of evolution. What was once ¡§Hennigian cladistics¡¨ has now turned into a distinctive methodology, nicely summarized by Fisher and Owens (2004, p. 39): ¡§The phylogenetic approach is a statistical method for analyzing correlations between traits across species.¡¨ And, like the earlier statistical approaches of the 1970s, this approach frequently groups ecological morphologies instead of clades: the methodology is incapable of discerning massive convergence.

Literature cited
Feduccia, Alan, Theagarten Lingham-Soliar, and J. Richard Hinchliffe 2005. Do Feathered Dinosaurs Exist? Testing the Hypothesis on Neontological and Paleontological Evidence. JOURNAL OF MORPHOLOGY 266:125¡V166

CKing Apr 11, 2006 11:20 AM

>>In terms of classifying animals (specifically pythons), I wonder. There were the old days, when people couldn't go and perform a DNA sequence test, yet they still managed to classify animals.

Sure thing. Even Linnaeus produced a pretty good classification, even though he had no idea how evolution worked.

> People like to jump down Hoser's throat (albiet his stance seems bloated), but I fail to see the synonyms in currently accepted taxa. I have never seen a scientific paper or publication that outlines and addresses the various genuses (morelia, python, liasis, etc). Where do these various genuses start to take some accountability? I believe I have a small python book that does a mediocre job at breaking down the various genuses. For liasis, for example, it states that "members of the liasis family do not have prehensile tales" yet my White Lip's tail is damn prehensile. Might sound like a broken record here, but same goes for water pythons I have been affiliated with. I guess my question is; people want validity out of Hoser. If he cannot provide it, then I want validity from the accepted classifications. Just what *does* liasis mean? As far as I'm concerned, my white lip is just that... a white lipped python. Where do we take the critics hats off? Id like to know how classification was dealt with before DNA testing was available.

Before DNA evidence or molecular evidence in general was available, the most powerful technique that was used (and still being used) was comparative anatomy. According to Dollo's principle, superficial similarities are common between convergent characters, but detailed examination of the minutiae of morphological characters can reveal evidence of different ancestry. For example, the forelimb of birds like Archaeopteryx look remarkably similar to the forelimb of some small theropod dinosaurs such as Deinonychus. Both have 3 fingers on their forelimbs and both have the same number of segments on their fingers. Yet, detailed comparative anatomy of available fossils shows that the theropod lineage evolved from a 5 fingered ancestor that had lost the ring and little fingers, while retaining the thumb, index finger and middle fingers. Birds, however, have lost the thumb and little finger, while retaining the index finger, middle finger and ring finger. Theropod dinosaurs therefore have fingers 1-2-3 according to fossil evidence. Bird have fingers 2-3-4 according to developmental evidence. In this case, applying Dollo's principle, birds and theropods are only convergently similar. They did not acquire their similar hands from a common ancestor with 3 fingers. The differences in finger identity is one of the biggest obstacles to the acceptance of the dinosaurian origin of birds. Most ornithologists, therefore, do not believe that birds are descended from a theropod dinosaur.

Enough digression. Python systematics is still in a state of flux because a comprehensive DNA analysis has not been performed on this group. The lesson we learned from morphology is that convergences can sometimes be so remarkable that it may mislead taxonomists into grouping animals that are not closely related. Morphological features are often adaptive. E.g. the prehensile tail can be quite useful for a snake that lives in tress. Therefore many unrelaed snakes can independently evolve this same feature, whereas a tree snake that has returned to the ground may lose all traces of a once prehensile tail. It is often necessary to separate adaptive and non-adaptive characters in one's analysis. The same is true of DNA. The advantage that DNA evidence offers is that there are so many DNA characters that finding neutral characters to analyze relationships can be much easier. Since neutral characters may mutate randomly, there is very little chance of convergence due to adaptation to similar environments. Similarities due to pure chance are much less frequent than convergent similarities as a result of adaptaton to similar enviroments. It is for this reason that Darwinian systematists have relied on neutral characters for grouping relationships since the days of Darwin.

Reference
Feduccia, Alan, Theagarten Lingham-Soliar, and J. Richard Hinchliffe 2005. Do Feathered Dinosaurs Exist? Testing the Hypothesis on Neontological and Paleontological Evidence. JOURNAL OF MORPHOLOGY 266:125¡V166

Site Tools