Though accused of not getting it I do. I simply agree with the general conclusion of most scientists. Read on (again not my words...the words of researchers who use the tool)
Cladistics reliability
What is cladistics? How reliable is it?
“However, like any computerized method, cladistics suffers from the problem
that the quality of the output it produces is entirely dependent on the quality of the input it is given - or, to put it another way, ``garbage in, garbage out''.
There are several choices that the worker must make before the computer, in all its objectivity, can be put to work,
and some further issues may also cast doubt over the results of a cladistic analysis.
Example: “
Poorly chosen characters can yield incorrect results.”
Another way in which
a worker's preconceived ideas can affect the result of a cladistic analysis is in the assumptions about the primitive states of the characters. Since we can't know what taxon is actually the most recent common ancestor of those being analyzed, we use a well-understood
outgroup as a proxy for that ancestor - that is, a taxon outside of, but as close as possible to, the clade containing the taxa to be analysed. For example, in the analysis above, if we think that the phylogeny looks like this:
A, B and C (in some combination)
\ | /
\|/
V Haplocanthosaurus
\/
\ Jobaria
\/
Then
we might perform the analysis on the assumption that A, B and C's common
ancestor had the same character states as
Haplocanthosaurus; or,
if we decided that its remains are too fragmentary to be used in this way,
we might use the less closely related but better represented
Jobaria. In practice, several different outgroups are typically analyzed to help determine the most likely ancestral state of characters...
the choice of taxa to use as outgroups is clearly a subjective one: it is chosen on the basis of how the phylogeny is likely to look...
In choosing the most likely candidate tree,
cladistics programs rely on the principle of parsimony; but nature is not always parsimonious!
Finally, there is an implicit assumption that similarity of form - which is what cladistic analysis discovers and measures
- implies commonality of descent."
Problems with the use of cladistic analysis in palaeoanthropology
D. Curnoe
Problems with the use of cladistic analysis in palaeoanthropology. - PubMed - NCBI
"Cladistic analysis is a popular method for reconstructing evolutionary relationships on the human lineage.
However, it has limitations and hidden assumptions that are often not considered by palaeoanthropologists. Some researchers who are opposed to its use regard cladistics as the preferred method for taxonomic "splitters" and claim it has lead to a revitalization of typology. Typology remains a part of human evolutionary studies, regardless of the acceptance or use of cladistics.
The assumption/preference for "splitting" over "lumping" in cladistics (alpha) taxonomy and the general failure to evaluate (post-hoc) such taxonomies have served to reinforce this assertion.
Researchers have also adopted a number of practices that are logically untenable or introduce considerable error.
The method suffers a logical weakness, or circularity, leading to bias when characters with multiple states are used. Coding of such characters can only be done using prior criteria, and this is usually done using an existing phylogenetic scheme.
...variation within species...While this form of variation is usually ignored by palaeoanthropologists,
when characters are recognized as varying, their treatment as a separate state adds considerable error to cladograms.
All published human cladograms fail to meet standard quality criteria indicating that none of them may be considered reliable. The continuing uncertainty over the number and composition of fossil human species is the largest single source of error for cladistics and human phylogenetic reconstruction."
The UCLA Phylogeny Student handout says...
“
Cladistic analysis makes the assumption that species share derived characters because they share a common ancestor that had that derived character.
However, sometimes convergences occur and
there are independent origins of a feature in unrelated lineages. For example, the fins of sharks, the flippers of dolphins, and the wings of penguins look alike but arose independently in the cartilaginous fishes, the mammals, and the birds. These structures are analogous, not homlogous.
Second,
cladistic analysis assumes that if a species does not have a derived character, it is because its ancestor diverged from the lineage that developed the derived character before the derive character originated. However, sometimes lineages have reversals—they have a derived character and it reverts to an ancestral type. For example, having hair is a derived character of mammals as compared with reptiles. Dolphins have no hair because of a reversal—the mammalian ancestors of dolphins had hair and then the dolphin ancestor lost it. Hairlessness in dolphins and alligators (for example) is analogous, not homologous”
Now does this mean cladograms are not useful tools? No! Cladograms are very useful tools for categorization (on many levels). In fact they are one of our more reliable tools (though still being inherently unreliable for all these reasons these scientists have described).
Via clades assimilating molecular data used to formulate phylogenetic trees we have now classified 26,000 species and sub-species of ray fish out of 448 families going all the way back to the Jurasic period. These constitute, in Evolutionary terms, around 40 orders of fish. Though still all fish.
Besides the movable jaw almost all hold in common, and the fan quality of their fins, there are three of four regions on the genome that are almost identical. In this method of classification we can group about 90% of all extant fish into distinct sub-groups for further identification. The tool function of Clades allows us to do all this for organizational purposes making the focus much clearer for researchers. But as these scientists point out they have a number of factors making them unreliable.
