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1

Determination of genetic diversity between natural and cultured populations of Common Dentex (Dentex dentex) fish in the East Aegean Sea

Kayaci Ali, Can Mehmet Fatih, Güner Yusuf, Güleç Fartih

Oceanological and Hydrobiological Studies

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2023

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Vol. 52, No. 1

52--67

EN

Common dentex (Dentex dentex) is a commercial species of fish that is a highly valuable food source living naturally near Mediterranean and Atlantic Coasts. Therefore, monitoring and maintaining common dentex habitats are of high importance. A total of 53 specimens were collected from 6 natural habitats (from the Eastern Aegean and from the Antalya coast, which is the closest coast to the Western Mediterranean), and one aquaculture facility in the Eastern Aegean Sea. The mitochondrial Cytochrome Oxidase I (COI) gene was used to detect a total of 26 haplotypes. Along with the COI gene sequence, real-time PCR and high-resolution melting analyses were performed as rapid and inexpensive alternatives. Sequence analysis showed that the highest haplotype diversity was obtained from the aquaculture facility in Karaburun and Antalya Locations, Turkey. Analysis of Molecular Variance (AMOVA)based on the haplotype frequencies resulted in 92.54% genetic variation within localities and 7.46% genetic variation between/among localities. The mean fixation index (Fst) was calculated as 0.0746 (p < 0.001). Genetic distances were primarily in collaboration with geographical distances and were efficiently confirmed by high resolution melting (HRM) analysis. The results will be valuable in monitoring and maintaining natural habitats as well as aquaculture facilities where common dentex are grown.

2

Genetic variation of arta populations (Calligonum polygonoides subsp. comosum) in Egypt : Genepools for biodiversity and afforestation

Mahdy Ehab M.B., Rizk Rehab M.

Journal of Water and Land Development

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2023

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no. 56

81--90

EN

Genetic diversity manipulates a prime and vital role in the sustainable use of genetic resources. The data highlighted more insights into the genetic diversity of the arta plant (Calligonum polygonoides subsp. comosum) populations collected from three localities, Qalabshu (QQ), Mutubas (MM) and Gamasa (GG), in Egypt as gene pool for biodiversity conservation and afforestation. Random amplified polymorphic DNA (RAPD) markers investigated the population pattern and structure. A total of 129-amplicons oscillated from 145 to 1505 bp and a total of 19-amplicons were specific markers with an average of nine bands for each population. The Shannon index (I) scored at an average of 0.3. The diversity (h) oscillated from 0.11 to 0.25. The similarity matrices based on Jaccard coefficient recorded positive values. A higher correlation (r = 0.83) was between the combined Qalabshu (QQ) and Mutubas (MM) matrices using the Mantel test with 1,000 permutations. This species has higher adaptability for their regions. This gene pool is a valuable reservoir for enriching genetic diversity and provides basal information for the biodiversity conservation of a dominant species. The dominant species can be utilised in afforestation in the same region or another region which has the same environmental conditions.

3

Genetic Diversity in Salix gordejevii Populations from Different Environmental Gradients in Horqin Sandy Land, Northern China

Huang Wen-Da, Zhao Xue-Yong, Zhao Xin, Luo Ya-Yong, Feng Jing, Su Na, He Yuan-Zheng

Polish Journal of Ecology

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2019

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Vol. 67, nr 3

175--185

EN

Salix gordejevii (Salicaceae) is a climax and dominant sand-fixing shrub species native to the northern China. We assessed S. gordejevii population genetic variation in different environmental gradients in Horqin Sandy Land, Northern China using inter-simple sequence repeat (ISSR) markers, and investigated the possible existence of relationships between genetic diversity and environmental gradients. The results showed that S. gordejevii populations in general have high genetic diversity. An analysis of molecular variation (AMOVA) revealed relatively high levels (> 89.91%) of within-population genetic variation. Based on cluster analysis, the 12 studied S. gordejevii populations can be clustered into three clades. Genetic diversity and differentiation of S. gordejevii populations are affected from different environmental gradients. Genetic diversity of all populations was affected by habitat environment change, and was well-correlated with the humidity gradients. These results have important implications for restoration and management of degraded ecosystems in arid and semi-arid areas.

4

Evaluation of genetic diversity and population structure of five yellow catfish Pelteobagrus fulvidraco populations by microsatellite markers

Zhong L., Wang M., Pan J., Li D., Tang S., Bian W., Chen X.

Oceanological and Hydrobiological Studies

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2018

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Vol. 47, No. 2

99--106

EN

Yellow catfish, Pelteobagrus fulvidraco, is an important commercial freshwater species in China. Knowledge about the genetic diversity of the yellow catfish is important to support the management and conservation programs, which would subsequently support the sustainable production of this species. To investigate the genetic diversity and the structure of yellow catfish in the middle and lower reaches of the Yangtze River, 125 individuals from five lakes were genotyped using 13 microsatellite markers. Moderate genetic diversity was determined in all populations, with the observed heterozygosity (HO) ranging from 0.42 to 0.49 and the expected heterozygosity (HE) ranging from 0.51 to 0.61. Low to moderate genetic differentiation among the populations was revealed from pairwise FST values (p < 0.05), as well as from analysis of molecular variance (AMOVA). The UPGMA dendrogram and Bayesian clustering analysis indicated a correlation between genetic differences and geographic distance – four populations from the lower reaches clustered together, whereas the Poyang Lake (PY) population formed a separate cluster. The present study would be helpful in the wild stock management and artificial propagation programs for yellow catfish in the middle and lower reaches of the Yangtze River.

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Assessment of Chosen Reproductive Cycle Processes and Genetic Diversity of Salix myrtilloides L. in Wetlands of Polesie Lubelskie: The Prospects of Its Survival in the Region

Pogorzelec M., Głębocka K., Hawrylak-Nowak B., Bronowicka-Mielniczuk U.

Polish Journal of Ecology

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2015

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Vol. 63, nr 3

352--364

EN

Salix myrtilloides L. is an endangered species whose western limit of range runs through Poland. The main aim of the study was to increase the knowledge on the ecology and biology of S. myrtilloides populations in the Polesie Lubelskie region (Eastern Poland) in order to create an effective protection program. An 80% decrease in its population was found in this area. Our study was conducted to identify the mechanisms responsible for the process of withdrawal of this species from its natural stands by determining whether the processes of generative reproduction (pollen viability and germinability, seed germination ability and dynamics) in the populations occur properly and by characterizing within- and among-population genetic diversity of S. myrtilloides, using ISSR (Inter-Simple Sequence Repeat) primers. The results confirmed that S. myrtilloides pollen viability was high (84.17±8.67), and so were the seed germination ability (76% of the total number of sown seeds/24 h) and dynamics. The within-population genetic diversity was quite high for this species and the inter-population genetic variation was of medium value (ΦPT=0.148). The condition of two populations, their genetic diversity and sex ratio as well as the correctness of the investigated reproductive cycle stages altogether give prospects for their survival. It seems to be very important to start conservation involving the reintroduction and reconstruction of S. myrtilloides populations in the Polesie Lubelskie region. The proposed method for restoration of S. myrtilloides resources would be possible if ex situ cultivation and in vitro methods were used.

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Genetic diversity of the non-native crab Rhithropanopeus harrisii (Brachyura: Panopeidae) in the Polish coastal waters − an example of patchy genetic diversity at a small geographic scale

Hegele-Drywa J., Thiercelin N., Schubart C. D., Normant-Saremba M.

Oceanological and Hydrobiological Studies

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2015

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Vol. 44, No. 3

305--315

EN

The American panopeid crab species Rhithropanopeus harrisii (Gould, 1841) is listed as an non-native species in European waters. In Poland, it occurred in the 1950s at two sites at the Baltic Sea coast, the Dead Vistula River (DVR) and the Vistula Lagoon (VL). Almost 50 years later, two additional populations were identified in the Gulf of Gdańsk (GG) and its inner part, Puck Bay (PB). In the present study, we sequenced and analyzed part of the mitochondrial cytochrome oxidase subunit I gene of the four Polish populations of R. harrisii in order to assess their genetic diversity and connectivity. The analyzed sequences of a length of 989 base pairs revealed eight different haplotypes. The highest number of haplotypes (n=6) was observed in the population from GG, whereas the lowest (n=3) in VL. The most common haplotype was recorded in 37% of the analyzed individuals. Pairwise ΦST values were mostly non-significant, with the exception of the comparison between DVR and VL (ΦST = 0.267; P < 0.05) and between PB and VL (ΦST = 0.194; P < 0.05), indicating a restricted gene flow or different sources of colonization.

7

Chemotypes and geographic distribution of the Fusarium graminearum species complex

Przemieniecki S. W., Kurowski T. P., Korzekwa K.

Environmental Biotechnology

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2014

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Vol. 10, No. 2

45--59

EN

The Fusarium graminearum species complex (FGSC) consists of phylogenetically distinct pathogenic species. Isolates from various regions display genetic variety worldwide. Three type B trichothecene chemotypes have been identified within the FGSC: nivalenol, 3-deoxynivalenol and 15-deoxynivalenol. The variations in morphological, genetic and virulence traits of FGSC fungi can be attributed mainly to their geographic boundaries. The geographic range of host plants, type of farming system and weather conditions also influence the prevalence of FGSC taxa. The geographic distribution of FGSC members may reflect not only their chemotype but also adaptive traits. While 15-acetyl-deoxynivalenol (15-ADON) chemotype is prevalent in most of Europe, the 3-acetyl-deoxynivalenol (3-ADON) chemotype has achieved greater prevalence in parts of North America. The Asian species F. asiaticum has spread into new territories. Isolates of F. asiaticum have been identified in North America and Europe, and the species has recently been reported to be infecting cereal crops in South America. The occurrence of numerous members of the FGSC in those regions and the introduction of F. asiaticum into new areas raise significant food safety concerns and indicate the need for monitoring mycotoxin concentrations in harvested grain.

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Success of wild pear Pyrus pyraster (L.) Burgsd. in colonization of steep sunny slopes : an interdisciplinary study in the Bielinek Reserve (NW Poland)

Antkowiak W., Cedro A., Prajs B., Wolko Ł., Michalak M.

Polish Journal of Ecology

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2012

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Vol. 60, nr 1

57-78

EN

A local population of Pyrus pyraster was studied in dry and warm habitats: xerothermic grasslands Potentillo-Stipetum capillatae and Adonido-Brachypodietum, as well as thermophilous oak forest Quercetum pubescentipetraeae in the forest-steppe Bielinek Reserve (NW Poland). Our aims were to assess: (1) the ability of this species to adapt to extremely dry sites, as a pioneer woody plant; (2) its phytosociological position; and (3) morphological variation and genetic diversity of the local population. The pear trees in Bielinek Reserve seem to reach an optimum in shrub communities of the class Rhamno-Prunetea, but tree age clearly indicates that the grasslands were colonized by wild pear trees already before the shrub communities developed. This indicates that P. pyraster can colonize very dry, eroded sites, such as steep sunny slopes covered by xerothermic grasslands. Wild pear trees form plant communities that are a seral stage followed by forest-shrub communities or thermophilous forests. The species in xerothermic shrub communities of the reserve shows a high constancy. It is also very resistant to extreme temperatures, insolation, drought, and erosion. Its tree-ring width (on average 1.1 mm per year) was strongly related to precipitation and temperature in spring and summer. High precipitation resulted in wider tree rings, while dry years (associated with high air temperature) caused a decrease in tree-ring width. Another significant factor is precipitation in winter, which had a positive influence on tree-ring width. Microsatellite markers revealed a high level of genetic diversity in this population. Our results suggest that wild pear can be recommended for afforestation of areas affected by droughts and disturbed sites in Central Europe. It can be used to increase the heterogeneity of the landscape, e.g. by creation of forest ecotones and for planting along roads and field margins, especially considering the predicted climate change.

9

Genetic diversity of populations of Brachypodium pinnatum (L.) P. Beauv. : expansive grass in a fragmented landscape

Bąba W., Kurowska M., Kompała-Bąba A., Wilczek A., Długosz J., Szarejko I.

Polish Journal of Ecology

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2012

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Vol. 60, nr 1

31-40

EN

Brachypodium pinnatum belongs to native grasses which could dramatically decrease the biodiversity of calcareous grasslands, therefore, an examination of the mechanisms of its expansion is of prime importance for their conservation. We studied the genetic structure of 12 subpopulations of the expansive grass B. pinnatum in a heterogeneous landscape with AFLP markers, aiming at determination whether spatial isolation influences the genetic diversity and the population genetic structure of this species. A high level of overall (79%) and within population polymorphic loci (38.44%) were found and 220 different genotypes were distinguished among the 252 samples analysed. No significant population structure nor isolation-bydistance were found, despite their long-time fragmentation history. This confirms that isolation of calcareous grasslands in a landscape cannot prevent the expansion of B. pinnatum grasses because of the high generative dispersal ability. Subsequent quick and extensive clonal growth of this species enables the successful establishment. In most cases mowing or grazing is sufficient to keep this species at a low density within ancient grasslands and to prevent seed and pollen dispersal, but not for restoration of species-rich calcareous grasslands.

10

Evaluation of anthropogenic pollution in river water based on the genetic diversity of Aeromonas Hydrophila

Korzekwa K., Gołaś I., Harnisz M.

Archives of Environmental Protection

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2012

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Vol. 38, no. 3

41-50

EN

Aeromonas hydrophila is a valuable indicator of the quality of water polluted by sewage and pathogens that pose a risk for humans and cold-blooded animals, including fi sh. The main aim of this research was to evaluate anthropogenic pollution of river water based on genetic diversity of 82 A. hydrophila strains by means of RAPD, semi-random AP-PCR (ISJ) and the rep-BOX conservative repeats test. Genetic diversity of A. hydrophila was HT = 0.28 (SD = 0.02) for all DNA markers (RAPD, semi random and rep-BOX). None of the analyzed electrophoretic patterns was identical, implying that there were many sources of strain transmission. The presence of genes for aerolysin (aerA), hemolysin (ahh1) and the cytotoxic enzyme complex (AHCYTOGEN) was verifi ed for all tested strains, and drug resistance patterns for tetracycline, enrofl oxacin and erythromycin were determined. The most diverse A. hydrophila strains isolated from river water were susceptible to enrofl oxacine (HS = 0.27), whereas less diverse strains were susceptible to erythromycin (HS = 0.24). The presence of the multidrug resistance marker (ISJ4-25; 1100 bp locus) in the examined strains (resistant to three analyzed drugs) indicates that intensive fi sh cultivation affects the microbiological quality of river water.

PL

Aeromonas hydrophila jest cennym wskaźnikiem jakości wody w przypadku zanieczyszczeń ściekami oraz mikroorganizmami względnie patogennymi dla człowieka i zwierząt zimnokrwistych, w tym ryb. Celem niniejszych badań była ocena zanieczyszczenia antropogenicznego na podstawie zróżnicowania genetycznego 82 szczepów A. hydrophila poprzez analizy RAPD, pół-przypadkowo amplifi kowanej klasy AP-PCR (ISJ) i konserwatywnego powtórzenia rep-BOX. Zróżnicowanie genetyczne A. hydrophila wyniosło HT = 0,28 (SD = 0,02) dla wszystkich markerów DNA (RAPD, pół-przypadkowe i rep-BOX). Wszystkie szczepy dla wszystkich markerów ujawniły indywidualny wzór elektroforetyczny, nie ujawniono jednego źródła rozprzestrzeniania się szczepów. U szczepów potwierdzono obecność genów aerolizyny (aerA), hemolizyny (ahh1) i kompleksu enzymów cytotoksycznych (AHCYTOGEN), jak również określono wzorzec oporności na tetracyklinę, enrofl oksacynę i erytromycynę. Najbardziej zróżnicowane okazały się szczepy A. hydrophila wrażliwe na enrofl oksacynę (HS = 0,27) a najmniej zróżnicowane były szczepy wrażliwe na erytromycynę (HS = 0,24). Wyselekcjonowany marker wielolekooporności (locus ISJ4-25, 1100 pz) obecny u szczepów (opornych na 3 rozpatrywane leki) świadczy o wpływie intensywnej hodowli ryb na jakość mikrobiologiczną wody rzecznej.

11

Genetic variation and molecular evolution of endangered Kozlov.s pika (Ochotona koslowi Buchner) based on mitochondrial cytochrome b gene

Lin G., Ci H., Thirgood S., Zhang T., Su J.

Polish Journal of Ecology

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2010

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Vol. 58, nr 3

563-568

EN

Kozlov's pika is a rare and endangered lagomorph species with a limited distribution in the southern Kunlun Mountains in western China. Because of its endangered status, Kozlov's pika is considered a priority species for research and conservation action. Genetic variation and molecular evolution of the Kozlov's pika were studied based on a total of 14 individuals from four locations along the eastern boundary between Xinjiang and Tibet province (35.20-36.48[degrees]N, 86.08-83.04[degrees]E) on extremely high elevation (usually over 4800 m a.s.l.). The density of local populations was about 3-4 per ha, living in a typical alpine desert grassland habitat. The complete mitochondrial cytochrome b (cytb) gene was amplified and sequenced. Based on the cytb gene sequences the genetic variation and molecular evolution were analyzed. Unexpected high haplotype diversity (0.956 [plus or minus] 0.045) but low nucleotide diversity (0.00537 [plus or minus] 0.00126) was found, indicating past demographic expansion. Significant partitioning of variance (P <0.01) among populations (46.7%), and within populations (53.3%), indicating low level of genetic differentiations among local populations. Our results gave an optimistic survival status of Kozlov's pika at the genetic level. Bayes Empirical Bayes analysis with model M2a and M8 detected three positively selected amino acid sites at the significance level of 0.05. The mutant types with either or both of the mutations aspartic acid to asparagine and glutamic acid to lysine had higher isoelectric point values. We suggested these mutant types might have biological significance to help individuals to adapt to the extremely high elevation habitats.

12

Demographic versus genetic (RAPD) variation between and without two populations of the clonal plant Paris quadrifolia L. (Liliaceae)

Kosiński I., Stefanowicz-Hajduk J., Ochocka R.

Polish Journal of Ecology

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2009

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Vol. 57, nr 2

303-311

EN

The two populations of Paris quadrifolia L. were studied in isolated habitats in a currently fragmented landscape. Both populations were located in deciduous forests, the first (A) - on fresh mineral and acidic soil, and the second (B) - on wet organogenic, less acidic and more fertile soil. We hypothesized that genetic variation should be higher within population of more fecund plants, and that genetic distance between the two populations that occupy different isolated habitats in a fragmented landscape should be high. Demographic characteristics of populations were studied in the 2000-2005 period. In patches of both populations, 22 permanent plots measuring 1m[^2] each were designated. For molecular testing 41 samples from both populations were selected. The share of generative shoots was higher in the population A than population B (0.35 and 0.20, respectively). However, the fecundity of ramets expressed as the number of seeds in the ripe fruit was lower in A than in the B population (15 versus 21 seeds). The germination ability was significantly higher for the seeds from A than from the B population (79% versus 44%). The survival of the juveniles was high in both populations (54 and 76%). The Random Amplified Polymorphic DNA (RAPD) analysis with the application of five primers permitted identifying 91 loci. The estimation of genetic diversity was based on polymorphic loci, the share of which was average 44%. Nei.s gene diversity (h) was higher in the A than B population (0.28 versus 0.22). The genetic diversity between the populations was not large (G[ST] = 0.14). Clonal diversity was very high, G/N ratio = 1, and cluster analysis showed intermingling between samples from both the populations. There were quite a small genetic distance (D = 0.10), and a rather high level of gene flow (Nm = 1.51) between the populations from currently isolated habitats. The obtained results indicate that the genetic diversity was lower within population of more fecund plants from more productive habitat.

13

Variables diversity in systems identification based on extended genetic programming

Winkler S., Affenzeller M., Wagner S.

Systems Science

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2008

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Vol. 34, no 2

35-41

EN

There are several methods that are frequently used for solving data based system identification problems; genetic programming (GP) has already been used successfully for solving data mining problems in the context of several scientific domains. Extended functional bases, additional optimization phases and further developed selection mechanisms essentially contribute to the method's ability to generate high quality results for various kinds of data based identification scenarios. Even though there has already been a lot of investigation regarding the optimization of the method and its parameter settings, there is still rather little systematic analysis of internal processes regarding genetic dynamics and the progress of genetic diversity during the execution of genetic programming based identification using these algorithmic extensions. In this paper, we report on results of investigations regarding exactly these aspects: We have developed methods and statistical features that are able to describe genetic diversity and dynamics of GP-based structure identification algorithms; here, we introduce statistic analysis of genetic diversity regarding variables and time offset settings within GP populations. Genetic diversity is (amongst other aspects) characterized by the occurrence of variables for the models in which they are used; statistical methods for estimating respective impact features are also presented here. Data sets representing two different kinds of systems (complex mechatronical systems as well as medical benchmark data) have been used for empirical tests; furthermore, standard implementations of genetic programming are compared to extended techniques including offspring selection as well as sliding window techniques.

14

Genetic variability in the Antarctic hairgrass Deschampsia antarctica Desv. From maritime Antarctic and Subantarctic sites

Chwedorzewska K., Bednarek P.

Polish Journal of Ecology

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2008

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Vol. 56, nr 2

209-216

EN

The level of polymorphism, genetic variability and relatedness of the Antarctic hairgrass Deschampsia antarctica Desv. populations from South Shetlands Is. (King George I., Penguin I., Livingstone I.), from vicinity of Antarctic Peninsula (Galindez I., Uruguay I.), and Falklands Is. (Jason Is., Sealion I.) were studied using the AFLP approach. Six EcoRI/MseI type selective primer pairs combinations were used for AFLP profiling and amplified scoreable DNA fragments; than AMOVA and PCA were performed. The level of molecular variability among all individuals from all the analysed populations was low and reach only 5.4 % irrespective of the distance between the localities and it was not significant at a broader geographical scale, even among the three groups of populations (South Shetlands Is., vicinity of Antarctic Peninsula, and Falklands Is.). PCA analysis shows that all populations formed uniform groups according to their locations.

15

Genetic diversity test of re-established population of Allium angulosum L.

Zeidler M., Čurn V.

Polish Journal of Ecology

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2003

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Vol. 51, nr 1

45-51

EN

The genetic diversity of re-established population of endangered species Allium angulosum L. was tested as a one part of rescue program. Founder individuals were picked in Chropyně - Zářiči area (North Moravia, Czech Republic) and new population was set in Protected Landscape Area Litovelské Pomoravi (North Moravia, Czech Republic). The task was whether the newly founded population was made by representative individuals to cover (include) the genetic variability of source (mother) population. Items were tested with variability assay of six isozyme systems (G-6-PDH, AAT, PGM, EST, ACP, PGI) using discontinuous polyacrylamide gel electrophoresis (PAGE). The method stated relatively sufficient level of variability on condition that new population would be raised to prevent genetic changes. Application of more tests checking the genetic diversity within population could be uself during reintroduction and management of endangered plant species.