There is much diversity among fishes in their shape, behavior, colors, reproductive activities etc.
Interactions between the genotype and development in the context of the environment in which genetic material is expressed translates into phenotypic variation in observable characters. When a population sub-group becomes isolated, differential selection may result in divergence and eventually speciation. Thus all forms are derived from others and all organisms are related.
Therefore expect a hierarchy, expect a pattern. Classification seeks the pattern implicit in such a hierarchy.
There are relatively few morphological traits to discriminate among groups compared to gene products and genes. Morphological traits are usually the only ones available for studying genealogies including extinct species, but genetic information can be used for extant groups.
As with other organisms, fish DNA is found in the mitochondria and in the nucleus. Of the total DNA complement, mtDNA includes 16,000 to 20,000 nucleotides in a circular double strand molecule compared with >3 billion repeated nucleotide sub-units linear chromosomes of double-stranded of nDNA. The majority of mtDNA encodes for protein product and their are high levels of sequence diversity despite great conservation of gene function and arrangement. The majority of nDNA is non-coding.
Maternally inherited mtDNA is haploid, often homoplasmic, although heteroplasmy occurs among fishes. In contrast, nDNA is diploid and alleles are often heteozygous.
Both mtDNA and nDNA show variation as single nucleotide substitutions and additions/deletions of single or multiple nucleotides. Certain regions are "hot-spots". The non-coding regions of nDNA display at least an order of magnitude higher level of variation that coding regions. In contrast, mtDNA shows more rapid rates of divergence than coding sequences of nDNA. Non-coding regions of nDNA often diverge at faster rates than mtDNA.
DNA samples can be obtained from many easily obtained tissues such as blood, fin clips, barbels, scales and muscle plugs. Modern techniques can use fresh tissues, and frozen, alcohol, and formalin/alcohol preserved material.
Genomic variation is characterized using two contrasting approaches: Restriction Fragment Length Polymorphism (RFLP) and DNA sequencing.
Variation in fish DNA typically occurs among species, and within a species among individuals, populations, and geographic regions.
Observed similarities may result from a variety of causes;
Only homologous characters have equivalency among organisms and are "good" characters for elucidating phylogeny.
Errors can occur when characters appear similar but are not because of intervening diverging genetic steps. For practical purposes, homologies are often inferred by:
Classification seeks organization among organisms. In phyletics (evolutionists), classification is based on an inferred evolutionary history using features shared among organisms, new features and lost features. Phylogenetic systematics (cladistics) bases classification on delimitable monophyletic units, with pattern expressed as a dichotomous branching diagram, a cladogram. Each branch in a cladogram is of equal status, defined as sister groups.
Cladistics is based on seeking shared derived characters among organisms to delimit clades. Derived characters (apomorphy, plural synapomorphies) are new states arising through a speciation event leading to a dichotomous split between organisms that lack the new feature and those expressing the new feature. These two sets of organisms are sister groups, sharing all characters before the speciation event, but not afterward. The new characters arising from a speciation event are built onto or modify characters already present. Hence the new characters are derived characters.
Character states shared by all species in a group undoubtedly were inherited from an earlier species from which the new group was derived. These "primitive" or ancestral characteristics are plesiomorphies (plural symplesiomorphies).
Note - the synapomorphies at an early node become plesiomorphies for successively more recent nodes.
The order in which groups arose is made using out-group comparison. The outgroup is the sister group to the clade of interest, and hence not one of the taxa of interest.