This is relevant if you are interested in the biology of one particular gene: ontogeny, conservation across evolution, selective constraints on various regions, etc. If you are more globally interested in evolution of species, recombination rates or selective pressures, of course you need to compare more genes.

This is relevant if you are interested in the biology of one particular gene: ontogeny, conservation across evolution, selective constraints on various regions, etc. If you are more globally interested in evolution of species, recombination rates or selective pressures, of course you need to compare more genes.

In phylogeography, conservation genetics, population genetics and invasive species tracking, there are still many open questions which can be adequately answered by studies involving a single gene.

Of course, studies with many markers would be desirable, but there's a big problem with money. If you want to sequence 500 genomes to complete a phylogeography study on one species, you will need lots of money. And you could probably answer the same question in a much less expensive way, if you choose the correct marker.

In population genetics of Echinoderms, for example, studies trying to add multiple markers proved in many cases to be redundant or even, in some cases, unadressable or uninterpretable due to a too high level of polymorphism!

Ej. Calderon et al. http://digital.csic.es/handle/10261/38805

To add up, single gene studies are also relevant when dealing with induced mutants.

Several adpative mechanisms are controlled by relatively simple genetic systems that involve one or a few genes. Example: Resistance to paralytic shellfish toxins in clams is conferred by a single nucleotide substitution that codes for a mutant configuration of the binding site of saxitoxin in the sodium channel (see Bricelj et al. 2005, NATURE).