Molecular population genetics of the Arabidopsis CAULIFLOWER regulatory gene: nonneutral evolution and naturally occurring variation in floral homeotic function

Abstract

The evolution of interspecies differences in morphology requires sufficient within-species variation in developmental regulatory systems on which evolutionary forces can act. Molecular analyses of naturally occurring alleles of the Arabidopsis thaliana CAULIFLOWER locus reveal considerable intraspecific diversity at this floral homeotic gene, and the McDonald-Kreitman test suggests that this gene is evolving in a nonneutral fashion, with an excess of intraspecific replacement polymorphisms. The naturally occurring molecular variation within this floral regulatory gene is associated with functionally different alleles, which can be distinguished phenotypically by their differential ability to direct floral meristem development.

Figure 1

Distribution of polymorphisms along the Arabidopsis CAL gene. The circles and squares denote the approximate location of nucleotide and insertion/deletion polymorphisms, respectively. The actual nucleotide polymorphisms are tabulated and are partitioned according to intron (I) and exon (E) positions. The differentiation between class A and class B alleles are shown. The replacement polymorphisms are indicated at the bottom, with the upper row showing the encoded amino acid for the Li-8 allele. The distribution of exon polymorphisms according to the protein domains also are indicated.

Figure 2

Gene genealogy of the Arabidopsis CAL alleles based on maximum parsimony analysis. The distinctions between class A and B alleles are based on the pattern of shared polymorphisms. The numbers next to the nodes are the bootstrap values after 500 bootstrap replicates of the data; all nodes with <50% support are collapsed in the tree. Ten equally parsimonious trees (length = 528 steps) were obtained from a heuristic analysis; these trees were all congruent with the bootstrap results. The consistency index is 0.926, with the A. lyrata CAL orthologue as the outgroup. The genealogy is based on the sequence from exon 2 to the 3′ untranslated region. If only the recombinant exon 7 and flanking intron sequences are used, the Ws and Kent-2 alleles group together in the phylogeny (see text).

Figure 3

Differences in floral phenotypes. Clockwise from upper left: (i) AP1/AP1 cal(Ws) cal(Ws), (ii) ap1–1/ap1–1 Cal(Ler)/Cal(Ler), (iii) ap1–1/ap1–1 cal(Kent-2)/cal(Kent-2), (iv) ap1–1/ap1–1 cal(Ws)/cal(Ws).

Figure 4

Sliding window analysis of nucleotide diversity (31). The analysis is based on a 100-bp window that moves across the gene in 25-bp intervals. The exon/intron structure of the gene is indicated as a reference. The position of the K182 → R replacement polymorphism in exon 7 is indicated with an arrow.