We have developed a genotyping “chip” for the iconic and endangered Araucaria angustifolia tree containing 3,400 SNPs, discovered from RNAseq and RAD-sequencing data. Of these, 1,643 were polymorphic in a sample of 192 individuals from a provenance/progeny collection involving 15 populations from Brazil (SP, MG, PR and SC). These same 192 individuals were genotyped with 30 microsatellites (SSR). Analysis of the population genetic structure with SSR and SNPs revealed substantial differences in the magnitude of population differentiation: Fst was 0.13 with SSR and 0.28 with an equivalent number of SNPs. This pattern was maintained with different estimators (Gst, G’st, Dst) or Rst for microsatellites. Using all 1,643 SNPs covering the entire spectrum of allelic frequencies Fst was slightly higher (0.31).  These results corroborate the recognized fact that the multiallelism of SSR restricts the maximum Fst value even in the absence of gene flow, and allele homoplasy tends to overestimate gene flow and homogeneity among populations resulting in largely underestimated population differentiation. Conversely, although bi-allelic and less informative individually, SNPs have a considerably lower mutation rate and a negligible mutation reversal rate, providing robust, accurate, genome-wide estimates of genetic differentiation. These results raise important questions about the validity of the low levels of genetic differentiation between natural populations typically reported for Araucaria based on microsatellites.  An underestimated Fst has critical repercussions on inferences of genetic structure and gene flow and, more importantly, on strategic decisions about the conservation of natural populations and enrichment of  germplasm banks of this ecologically keystone tree.

05 - A genotyping array of 3,400 Single Nucleotide Polymorphisms (SNPs) advances the genetic analysis of the iconic tree Araucaria angustifolia, showing that the natural populations are more differentiated than previously reported