To date, most of our understanding of light responses in any given model plant species has been derived from experiments performed on a limited number of varieties or accessions. For example, much of the genetic analysis of Arabidopsis has been performed using the Columbia or Landsberg erecta ecotypes, and genome sequencing efforts in rice and maize have focused on two accessions for each species. As a result, plant research programs throughout the world have tended to focus on a small number of accessions.

When considering the role of phytochromes in an ecological context, however, it is essential to examine a much broader germplasm collection. Surveys of the light responses in Arabidopsis and maize have revealed tremendous ecotypic variation, both in the physiology of their light responses and in their phytochrome gene families. For instance, the Wassilewskija (Ws) accession of Arabidopsis contains a naturally occurring deletion of the phyD gene, whereas an accession from Le Mans, France (Lm-2) carries a light-stable form of PHYA that fails to mediate responses to continuous far-red light. These studies indicate that variations in phytochrome responses may have some adaptive value. Determining how such variations contribute to fitness in diverse habitats is a challenge for the future.