Working with Sheryl White, Juan Nunez and Jesus Vargas, we sequenced a portion of one of the silk genes, that coding for the flagellaform silk that constitutes the spiral thread.  Our initial hope was to use these sequences to determine relationships among different populations of Nephila clavipes in Mexico.
	Spider silk proteins and their genes are very attractive to researchers in a wide range of disciplines because they permit linking many levels of organization.  However, hypotheses of silk gene evolution have been built primarily upon single sequences of each gene each species, and little is known about allelic variation within a species.
Silk genes are known for their repeat structure with high levels of homogenization of nucleotide and amino acid sequence among repeated units (see research by Cheryl Hayashi, UC Riverside).  One common explanation for this homogeneity is gene convergence.  To test this model, we sequenced multiple alleles of one intron-exon segment from the Flag gene from four populations of the spider Nephila clavipes and compared the new sequences to a published sequence.  Our analysis revealed very high levels of heterozygosity in this gene, with no pattern of  population differentiation.  There was no evidence of gene convergence within any of these alleles, with high levels of  nucleotide and amino acid substitution among the repeating motifs.  Our data suggest that minimally, there is relaxed selection on mutations in this gene and that there may actually be positive selection for heterozygosity
Supported by a grant from the National Science Foundation Publication:  L. Higgins, S. White, J. Nunez Farfan and J. Vargas.  2006.  Patterns of variation among distinct alleles of the Flag silk gene from Nephila clavipes.  International Journal of Biological Macromolecules 40: 201-216	The amino acid sequence that would be coded by the genes sequenced in this study and two GenBank sequences from Florida. The first letter refer to the site of collection (FF:  Fortin de las Flores;  LT:  Los Tuxtlas;  Nan:  Nanciyaga;  Mat:  Mateos de Romero;  Xal:  Xalapa), the first number refers to the individual specimen, and the number after the dash is the sequence identifier for that individual (when two sequences are presented, they are assumed to be separate alleles for a heterozygous individual). The different repeat motifs are identified by the following symbols, where G symbolizes glycine, P proline, and X or Y a variety of amino acids. large oval: XGPGG;  medium oval: XGGY;  small oval: XGG;  box:  low glycine (non-repetitive) spacer.  A colored oval or a bar in the spacer indicates an amino acid substitution.  The nature of the substitution is indicated by the color. Grey: same group;  Purple:  exchange of glycine and long chain residue;  Blue: exchange of hydrophobic and hydrophilic residue;  Green:  exchange of aromatic and straight chain residue;  Yellow: addition or deletion of cysteine;  Red: addition or deletion of proline.