Following are the deficiencies of the traditional phenetics methodPractical difficulties :
This method is laborious, and time consuming because of their insistence on the equal weighting of all charachters. And due to assembly of large number of charachters the true chrachters become dilluted with useless charachters as well.
Their studies depends upon the availablity of large number of charachters, but some taxa do not have rich supply of charachters and morphological variability is not available, e.g Arthopods and sponges.
phenetics classification cant be improved gradually, because addition of new charachters requires a new analysis.
They do not provide any solid contributions to the classification of any mature group or to the classification of highr taxa.
Inability to meet the claims of objectivity and repeatability:
This method is unable to avoid subjectivity (personal choice) in the selection of charachters that are analyzed and in the handling of variations. They do not have any meaning full OTUs to assemble phena and thus a failure to apply biological criteria at the species level leads to the unreasonable classification.
The choice of clusterring method is also based upon personal preference, as a consequence, different clustering methods yield different fits by cophenetic correlation coefficinets to the same resemblance matrix. This imparts a great deal of subjectivity to the phenetic approach.
The choice of different algorithms yields different results, which is against their claim that if two systematics independently working on same group would achieve the same results.
They claim that if larger number of charachters is used the selection of particular charachters become irrelevant, but adding new charachters derived from different components of the phenotype or genotype, almost changeleslly affects the classification.
Other unsubstantiated assumptions :
Pheneticstis are inconsistent in application of their own non weighting principle, as giving all charachters the same weight is, of cource also a method of weighting. Sokal and Sneath devote an entire section of their work to the principles governing the proper selection of charachters.
They have the assumption that the amount of unweighted phenetic similarity reflects an equal amount of underlying similarity of genotype and can be safely used for ranking. thier this assumption proved wrong later on by evidences, e.g they forced to assign sibbling species in single OTU.
pheneticsts state that similarity is to be decent from a common ancestor. but a phenogram cannot provide a good estimate of Phylogeny. because parallel, convergent and reversed charachters are treated as equivalent similarities in purely phenetics method. Only cladistic analysis can detect homoplasy and reversals and treated them as differences. Homoplasy and homology are not the important component of phenetics methodology. Moreover sokal acknowledged this that classification based upon unweighting charachters would be affected by parallelism, convergence and by unequal evolutionary rates and hence would not yield monophyletic lineages.
The numerical values of phena cannot be compared in different taxa because they are based on very different set of charachters and thus do not permit to establish universal scale.
Weakness in the theoretical foundation of phenetics:
phenetists are strict empiricists and reject theoretical concepts. they don’t consider factors that are responsible for the causation of a group. pheneticsts fail to test their taxa for monophyly. pheneticsts do not recognize that taxa are historical groups but consider supraspecific taxa as classes and are not concerned with their reality.
Different charachters, parts of body, stages, have different evolutionary rates, As a consequence it will lead to the different similarity estimates if either one of the charachter or other is used. it is a mistake to assume that random charachter selection will reflect equivalent differences in genotype as external morphotypes reveals only very small and biased portion of genotype. e.g larvae and adult of the mosquito have hardly contain any correlation and simiarity but no one shed light on their genotypes. Hence phenetic techniques will not have any compatibility with classifications when they are based on different sets of charachters.
Pheneticsts are not be able to distinguish between ancesterol and derived groups. however the term pre groups and ex groups were used by pheneticsts
The strict inductionism( laws induced from set of data) of numerical phenetics represnt a step back from hypotheticodeductive methodology( scientific inquiry proceeds by formulating a hypothesis) allow for no meaningful testing, predictions and interpretations.They lack all properties of theory and therefore can not be tested.