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 (7,178 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..., 2.1 Plant materials
A total of 313 individual shoots were collected in twelve populations and ranged from 5-50 per population (Table 1). Collections from Estonia, the Netherlands, Belgium, France, Hungary, Spain, Italy, Ethiopia, and Kenya (Fig. 1) were built up from 2007 – 2018 by the authors using a similar methodology. Samples were taken at 2 m intervals along a transect and approximately 1 m depth, using a rake from a boat or by wading parallel to the edge. Leaves were dried and preserved in individual bags with silica gel until further analysis.
2.2 Nuclear microsatellite analysis
Primers were fluorescence-labelled with four different dye-labels (6FAM, VIC, NED, and PET). DNA concentration was 20–50µg/ml. A primer mix was made by mixing 0.2 µM of each primer together. Multiplex PCRs consisted of 6.25 µl master mix (Qiagen Multiplex PCR kit), 1.25 µl primer mix, 2.5µl H2O, and 2.5µl of genomic DNA. PCR was performed in a thermal cycler (Bio-Rad MyCycler, Hercules, California, USA) w..., , # 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)

[https://doi.org/10.5061/dryad.jwstqjqjb](https://doi.org/10.5061/dryad.jwstqjqjb)

## Description of the data and file structure

* Original_data_Microsatellites.xlsx

Stuckenia pectinata microsatellite scores are provided in GenAlex format : 

A1 = number of microsatellite loci

B1 = total number of individuals

C1 = number of populations

D1 to O1 = number of individuals within each population

D2 to O2 = population codes

C3 to AF3 = names of 15 microsatellite loci with colors  (green, yellow, blue, red) corresponding to the fluorescent labels used in multiplex PCR

From row 4 onwards: Column A = individual sample codes; B = population codes; C to  AF = length of microsatellite allele (biallelic) for each microsatellite locus 

* Stuckenia_chloroplast_sequences_TRIEST_ET_AL_2025_Aq...,