Till the rank of species, it is better we follow morphological observation rather than molecular studies. It is easy to identify the species rank of almost all plants except some monocots.
Andrew Paul McKenzie Pegman I believe classical taxonomy is better till the specific rank. For identification of sub-species and varieties molecular taxonomy and neumerical taxonomy can be used.
The first thing to agree on is the concept of species. In Biology this concept seems to be clear. But it is not always possible to attempt fertilization between individuals from different populations to find out if they are of the same species. Then we resort to phenetics and molecular characters (DNA, proteins), and other methodologies, although it is when the controversy arises about the extent to which these methods can identify species. I do not think it is a problem that has a solution or that there is a universal consensus among taxonomists.
Taoheed Kolawole In my opinion only in intraspecific taxa we can use molecular taxonomy in case of doubt. Till species level its better to use classical taxonomy.
In my own opinion, some mutations might be in heterozygous recessive form till they are able to present themselves in dominant homozygous forms. Therefore if the facility is available constant check of characters will help understand the possible point of speciation
Taoheed Kolawole Mutations of specific gene will result in a sub species or variety. Not another species. In the case of sub species or varieties we can use molecular taxonomy. But till the Specific rank classical is better option. Even keys are available for the identification of all the species till the specific rank.
A lot of subspecific classifications (varietal or subspecies rank) were lumped or created years ago without a real basis for converting from their own species level. So many modern taxonomists are actually employing genetic means to validate or (disprove) these taxonomic lumps. Many splits can be verified through genetic/phylogenetic methods. So actually, at the sub species or variety level, these methods are needed more than ever to validate taxonomic viewpoints. What's actually interesting is a lot of species that were recognized at the species level years ago from basic morphological means are actually being validated with modern methods (genetic analyses, etc...) today.