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Genetic diversity of Gomphocarpus sinaicus Boiss. within and between wadi systems of the St Katherine Protectorate (South Sinai, Egypt)


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Genetic diversity of Gomphocarpus sinaicus Boiss. within and between wadi systems of the St Katherine Protectorate (South Sinai, Egypt) 

 Samy M. Zalat1&3, Somia El-Akkad2&3, Mona A. M. Mahmoud3

1- Department of Zoology, Faculty of Science, Suez Canal University, Ismailia, Egypt

2- Department of Botany, Faculty of Science, Ain Shams University, Abbassia, Egypt

3- Nature & Science Foundation, Ahmed Orabi Association, Line 4North, Land 35A, P.O. 205, Cairo, Egypt


The genetic variation of Gomphocarpus sinaicus plant was assessed within and between populations from seven wadis in the mountaineous area of St Katherine Protectorate using DNA (RAPD) markers. A neighbour-joining tree showed that most individuals from a given population tend to cluster together, and are therefore more genetically similar than individuals from different populations. Low levels of diversity were present within populations, which reflect high gene flow within each valley. There were highly significant differences between the populations of G. sinaicus from the seven sites, using a one-way Anova (F6,65 = 5.823, P<0.000). Furthermore, there was a significant positive correlation between genetic distance and geographical distance (r = 0.549, n = 7, P < 0.05) between the populations of G. sinaicus in different valleys. Significance: The highly significant values of genetic differences reflect limited interpopulation gene flow that could be attributed to the mountainous nature of the St Katherine’s Protectorate acting as natural barriers to gene flow and leading to genetic divergence among different wadis.


Gomphocarpus sinaicus is common plant in Egypt, distributed in both central and southern Sinai. It is a perennial herb with long spreading rhizomes that grows at different wadis of St Katherine in particular terraces of both sides of the wadi bed and gentle slopes of the rocky mountains. This plant is used as food by insects such as aphids, the nymphs and the adults of red spotted bug. This study investigates levels of genetic variation and the process of genetic divergence of populations of Gomphocarpus sinaicus plant both between wadis that isolated physically by high mountain ridges of St Katherine and within wadis without geographical isolation using RAPD technique as a genetic marker.

 Materials & Methods

Study site:  Samples were collected from seven wadis within St Katherine Protectorate (Figure 1).

 Extraction of DNA: Dry leaves were used for DNA extraction using a standard CTAB extraction procedure (Wolff et al., 1994; modified after Saghai-Maroof et al., 1984). Five primers were used and RAPD analysis was performed in 25 μl volume reactions according to Wolff and Peters-Van Rijn (1993). 

Data analysis: RAPD bands were scored as 1 (present) or 0 (absent) using GelDocuAdvanced software. The resulting presence/absence fragment matrix was analyzed using several computer programs. MVSP, Shannon's index of diversity to obtain estimates of within population genetic diversity (Hs) and total genetic diversity between the populations (Ht). Genetic distances were calculated between populations with UPGMA and the significant differences between populations were tested using Anova. SPSS for Windows was used to analyze correlation between genetic and geographical distances between populations.


The results of banding patterns of DNA fragments generated by each primer were recorded. Eighty nine DNA fragments were generated from seven sites within St Katherine Protectorate. Nineteen bands were detected in all populations. Of the 89 bands analyzed, nine DNA fragments were exclusive to wadi Abu Sela, eight to El Dir, three to El Arbaein, two to both El Raha, El Tofaha and El Rasis. And only one DNA fragment was exclusive to wadi Telah (Figure 2).

Shannon’s diversity index: The data obtained from Shannon’s diversity index was showed that all populations contain different levels of diversity with an overall average of Hs = 1.546. Shannon’s diversity index for the total population was estimated to be Ht = 1.703, and the proportion of total diversity distributed within populations (Hs / Ht = 0.909) was found to be greater than that present between populations [(Ht- Hs) / Ht = 0.091].

Neighbour joining tree: The tree of the seven sites showed that most individuals from a given population tend to cluster together, and are therefore more genetically similar than individuals from different populations. In particular, individuals from El Arbaein, El Tofaha, and El Rasis were clustered together by 100% each, while both Abu Sela and Telah population clustered by 90%. It is clearly visible from the tree that population of wadi Abu Sela formed distinct cluster and therefore they are genetically distinct from the other populations (Figure 3).

Statistically, there are highly significant differences between the populations of G. sinaicus from the seven sites, using a one-way Anova (F6, 65 = 5.823, P<0.000). There was a significant positive correlation between genetic distance and geographical distance (r = 0.549, P <  0.05) between populations of G. sinaicus (Figure 4)


Ø G. sinaicus is a species with mainly wind-dispersed seeds that have evolved aids for wind dispersal, such as hairs (Ridley, 1930). Furthermore, the species  is also an insect-pollinated, their pollinia are dispersed by different groups of insects from Hymenoptera and Lepidoptera (Wyatt and Broyles, 1994).
Ø The Anova analysis showed that the seven populations of G. sinaicus may be considered genetically different from each other. These results indicate high genetic isolation between populations in different wadi systems.
Ø There is a great possibility of seeds to move from wadi El Dir to mix with wadi El Raha  and this is clearly visible in the dendogram where 50% of individuals from  wadi El Dir cluster together with 66.7% of individuals from wadi El Raha.
Ø The dendogram showed that population from wadi Abu Sela are separated from the rest of populations and this may be due to the population showed a greater diversity value of all.
Ø The  highest genetic distance values are recorded between wadi Abu Sela and the rest of all wadis. This could be attributed to the outflow of wadi Abu Sela is in opposite direction to the rest of these wadis which makes gene exchange between them very limited. In addition to, Abu Sela is the farthest wadi in relation to other wadis  (2.31-6.07 km).
Ø Results of RAPD analysis suggest that most gene dispersal is between El Rasis, wadi El Raha and El Dir populations. This could be due to the connection of these wadis with El Rasis, where El Rasis bed has the lowest elevation of all
ØFlash floods and seed longevity may give us the answer for the question: why two individuals from each of wadi El Dir and wadi Telah, and one individual from wadi Abu Sela populations were displaced from their corresponding population clusters.
Ø There is a positive significant correlation between the matrix of genetic distances and the matrix of geographical distances between populations from different wadis This indicates that geographical isolation (distance) is an important factor influencing the genetic structure of G. sinaicus populations.
ØPollinators of G. sinaicus  inhabiting wadis around St Katherine prefer to disperse pollen, taking their way straight between the mountains and the possibilities of crossing the mountain with very high altitude (2400m) is difficult. The cross distances between wadis ranges from 1.11 to 5.35 km long,  which is too long distance for the pollinator to fly without consequences.


-Ridley, HN (1930). The dispersal of plants throughout the world. L. Reeve & Co., Ltd., Lloyds Bank Buildings, Ashford, Kent.

-Saghai-Maroof, MA; Soilman, KM; Jorgensen, RA and Allard, RW (1984). Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences of the USA, 81: 8014-8018.

-Wolff, K and Peter-Van Rijn, J (1993). Rapid detection of genetic variability in chrysanthemum (Dendranthema grandiflora. Tzvelen) using random primers. Heredity, 71: 335-341.

-Wolff, K; Peter-Van Rijn, J and Hofstra, H (1994). RFLP analysis in chrysanthermum I. Probe and primer development. Theoretical and Applied Genetics, 88: 472-478.

-Wyatt, R and Broyles, SB (1994). Ecology and evolution of reproduction in milkweeds. Annu. Rev. Ecol. Syst., 25: 423-441.

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