A Pleistocene legacy of gene pools, ecodemes and admixtures of Stuckenia pectinata (L.) Börner as evidenced from microsatellites, complete chloroplast genomes and ribosomal RNA cistron (Europe, Africa)

Stuckenia pectinata (L.) Börner is a widely distributed submerged plant well-studied for its ecology, distribution, and molecular diversity. Globally, various genotypic lineages and hybrids of Stuckenia species have been identified using nuclear rRNA (ITS) and chloroplast sequences (notably rpl20–5’rps12 and trnT-trnL). These studies have shown intraspecific variability in S. pectinata, with two gene pools ('genotype 1a' and '1b') reported for Europe and Africa. Moreover, former isozyme research suggested distinct freshwater and brackish water gene pools. Therefore, our primary objective was to determine whether these ecodemes correspond to either 'genotype 1a' or '1b'. Using fifteen nuclear microsatellite loci, complete chloroplast genome sequences (156,677 bp), and the rRNA cistron (7178 bp), we analyzed the genetic identity of 313 S. pectinata samples (representing 124 unique clones) from 12 populations in Europe and Africa. Chloroplast genomes of three African Rift lake populations corresponded to ‘genotype 1b’, while those of nine European populations to ‘genotype 1a’. Microsatellites also clearly distinguished ‘genotype 1a’ from ‘1b’ in an individual PCoA and STRUCTURE analysis, whereas incomplete homogenization of 5S-rRNA sequences suggested either ongoing differentiation or intraspecific hybridization between ‘genotype 1a’ and ‘1b’. Haplotype lineages, rRNA cistron mutations, and microsatellites revealed an additional subdivision within ‘genotype 1a’, potentially distinguishing a freshwater gene pool from a brackish water one. Approximate Bayesian computation analyses using nuclear microsatellites supported a demographic expansion model and a time of divergence, for the African Rift lake populations as well as for the European freshwater and brackish water populations, dating back to the Late Pleistocene. Divergent chloroplast lineages appeared to be already present during the Last Glacial Maximum. Stuckenia pectinata from Lake Hora (Ethiopia), Lake Balaton (Hungary) and the Camargue (France) each harbored two distinct maternal haplotypes, from Selinunte (Italy) indicated F1 hybrids whereas from Lake Peipsi (Estonia), amongst others, showed incomplete rRNA homogenization. It is hypothesized that contemporary S. pectinata populations, especially in Europe, retained a legacy of ancient gene pool differentiation despite a history of hybridization, admixture, and chloroplast capture. It is recommended that studies on the ecology and reproductive strategies of this seemingly common and widespread species should take into account its genetic identity.