The genus Senecio L. (Asteraceae) includes ca. 1250 species and is one of the largest genera of flowering plants (Bremer 1994, Calvo et al. 2015). In Iran, some species of Senecio have a widespread distribution in the different geographical regions, such as S. vulgaris L., S. glaucus L., and S. leucanthemifolius subsp. vernalis (Waldst. et Kit.) Greuter.

Senecio vulgaris, commonly called groundsel or old-man-in-the-Spring, is an annual herb that grows in a variety of habitats from open grassland to woodland. It is usually regarded as a temperate weed and although it is almost cosmopolitan it appears to be more localized in temperate regions of America and Asia, Mediterranean areas and South Africa (Chater and Walters 1976).

Senecio vulgaris has a long history of herbal use and is widely used as an anthelmintic, antiscorbutic, diaphoretic, diuretic, emmenagogue and purgative (Hatfield 1977, Launert 1981,). A homeopathic remedy is made from aerial parts of the plant. The therapeutic activity of groundsel is related to a variety of biologically active substances such as phenols and flavonoids, essential oils, polysaccharides, triterpenes, amines, saponins, tannins and mucilage (Uzun et al. 2004, Conforti et al. 2006).

A population genetics survey plays the main role in the planning of genetic and breeding programs. It provides data about genetic diversity, gene migration, allelic drift, genetic fragmentation, genetic bottleneck and any other evolutionary forces acting on population divergence (Sheidai et al. 2013).

Intraspecific taxonomic entities can be identified after a detailed population-based investigation within plant species. In general, extensive morphological and genetic divergences among populations result in speciation events. Intraspecific variation occurs within both wild and cultivated crop plants (Maxted and Hunter 2011).

In Iran, S. vulgaris grows in different areas and forms numerous local geographical populations. There is no information about its genetic diversity and adaptation against population divergence. Population genetic studies not only can provide information on these aspects but can also unravel the speciation process of Senecio in general. One method for the study of genetic diversity employs morphological characteristics, but molecular markers are the potential tools to study genetic relations, phylogeny, population dynamics or gene- and genome mapping. .

The advent of molecular markers resulted in an improved ability to track evolution through a good understanding of genetic diversity among populations and new phylogenetic viewpoints (Müller-Schärer and Fischer 2001, Stuessy et al. 2014). Among molecular markers, inter simple sequence repeat (ISSR) deserves special attention as a tool for analyzing diversity. ISSR is easy to use, quick, simple and highly reproducible (Azizi et al. 2014, Eftekharian et al. 2016). ISSR markers usually show high polymorphism and have the very important advantage that no prior information about the genomic sequence is required (Kojima et al. 1998, Bornet and Branchard 2001).

This study aimed to investigate the genetic variation between S. vulgaris populations collected from different geographic regions by using ISSR and morphological characters. Also, gene flow and correlation of genetic and geographical distances were estimated.

Population genetic investigations are useful in understanding genetic variability, allele flow, inbreeding against outbreeding and effective population size. This information is valuable in choosing effective management in conservative plans and also throws light on the presence of intraspecific taxonomic forms and suggests an appropriate hybridization strategy (Freeland et al. 2011, Sheidai et al. 2013, 2014).

Genetic diversity of S. vulgaris was studied by Müller-Schärer and Fischer (2001). According to their investigation different geographical areas include different habitats and populations representing different habitats varied in their sizes.

In our recent study, the genetic structure of S. glaucus showed that population fragmentation, restricted gene flow, genetic drift, and local adaptation have played a role in the genetic divergence of S. glaucus populations in Iran (Eftekharian et al. 2016).

In the present investigation, S. vulgaris populations presented a high degree of genetic variability. Species that are dispersed over a wide area face different environmental conditions and therefore can possess a wide genetic and morphological variability to manage ecological challenges (Freeland et al. 2011, El-Amier et al. 2014, Eftekharian et al. 2015, 2016).

In this study, population fragmentation in S. vulgaris is revealed by PCoA. However, some degree of gene flow and genetic admixture occurred among populations as shown by a reticulogram. The probable loss of genetic variation within these populations can be prevented by this limited gene flow due to the action of genetic drift (Habibollahi et al. 2015).

According to the Mantel test, which presented a pattern of isolation-by-distance in the studied S. vulgaris populations, adjacent populations have more chance for gene exchange than more distant populations, which is why more genetic similarities have been shown in closely situated populations.

Comparison of the two datasets indicated that in some cases, the grouping of populations based on the morphological method was consistent with molecular groupings.

Therefore, the PCoA plot based on molecular and morphological data showed two groups of populations.

Genetic and morphological differences between the two groups may be related to different ecological conditions. Ecological and environmental factors (e.g., temperature, humidity, and soil factors) can be significantly effective in shaping genetic diversity patterns (Huang et al. 2016). According to Müller-Schärer and Fischer (2001) different habitats can affect the genetic structure of S. vulgaris populations. Tang et al. (2015) showed that there was a strong relationship between the soil factors (especially salinity and soil texture) and plant diversity. In our study, the habitat of studied populations varied from mountain meadows (Populations 5, 7 and 9) to roadsides (Populations 2, 3, 4, 6 and 10) and waste grounds (Populations 1 and 8). The mountain meadow habitats had gravelly soils while loamy soils were predominant in the waste ground and roadside habitats. However, the effects of some factors in plant population genetic diversity remain unclear and more investigations have to be done.

Morphological characters revealed that two groups of the studied geographical populations differed from each other in two qualitative morphological features (black tips of calyculus bracts and type of stem), as evidenced in Fig. 3 and three quantitative characters (capitula number, length of the cauline leaf and plant height). Therefore, in these populations, morphological changes accompanied genetic differences and this pattern of arrangement has confirmed the existence of possible intraspecific taxonomic ranks within this species.