scholarly journals Phylogeography ofSwertia perennisin Europe based on cpDNA markers

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5512 ◽  
Author(s):  
Jacek Urbaniak ◽  
Paweł Kwiatkowski ◽  
Paweł Pawlikowski
Keyword(s):  
Genetic Variability ◽  
Haplotype Diversity ◽  
Clonal Plant ◽  
Nucleotide Composition ◽  
Molecular Techniques ◽  
Peat Bogs ◽  
Isolated Populations ◽  
The Carpathians ◽  
Europe Today ◽  
High Level

BackgroundSwertia perennis(Gentianaceae) is a perennial diploid and clonal plant species that is discontinuously distributed in peat bogs in the mountains of Europe, Asia and North America as well as in the lowlands of Europe. The current geographical dispersion ofS. perennisis probably the result of quaternary climatic changes that have played an important role in determining the distribution ofSwertiaand other plant and animal species.MethodsIn this study we used molecular techniques and combined data from chloroplast DNA markers (trnLF region andtrnH-psbA spacer) to elucidate the phylogeography ofS. perennisin Europe. Plants were collected from 28 populations in different locations in the lowlands and mountainous areas of Europe (e.g., the Carpathians, Sudetes, Bohemian Forest and Alps). cDNA was analysed to detect the genetic relationship between specimens from different locations.ResultsA total of 20 haplotypeswere identifiedacross the dataset. Theywere characterised by a high level of genetic variability but showed a lack of phylogeographical structure. This pattern may be the result of repeated recolonization and expansion from several areas. Such genetic differentiation may also be attributed to the relatively long-term isolation ofS. perennisin Pleistocene refugia in Europe, which resulted in independent separation of different cpDNA phylogenetic lineages and variation in the nucleotide composition of cpDNA.DiscussionThe lack of strong phylogeographical structure makes it impossible to indicate the centre of haplotype diversity; however, refugia located in the Carpathians, Sudetes or Alps are the most probable sites whereS. perennisexisted in Europe. This lack of structure may also indicate a high level of gene flow in times when the landscape and fen systems were not fragmented in numerous geographically-isolated populations. This makes it difficult to speculate about the relationships between Asiatic and European plant populations and the origin and distribution of this species in Europe. Today, it seems to be restricted due to the occurrence of plants which clearly reflects the genetic variability from the ancient period.

scholarly journals Phylogeography of Swertia perennis in Europe based on cpDNA markers

2018 ◽  
Author(s):  
Jacek Urbaniak ◽  
Paweł Kwiatkowski ◽  
Paweł Pawlikowski
Keyword(s):  
Genetic Variability ◽  
Haplotype Diversity ◽  
Clonal Plant ◽  
Nucleotide Composition ◽  
Phylogeographic Structure ◽  
Peat Bogs ◽  
Mountain Areas ◽  
Cdna Sequences ◽  
Chloroplast Dna Markers ◽  
High Level

Abstract Background. Swertia perennis (Gentianaceae) is a perennial diploid and clonal plant species found discontinuously distributed in the peat bogs in mountains of Europe, Asia and North America as well as in European lowlands. The current geographical dispersion of S. perennis is probably an effect of Quaternary climatic changes that played an important role in determining the present-day distribution of Swertia and numerous other plant and animal species. Methods. A presented survey of molecular studies based on combined data from chloroplast DNA markers (trnL-trnF and trnH-psbA) that were conducted to elucidate the phylogeography of S. perennis in European localities. Plants were collected from 28 populations that represent different localities in lowlands as well as in mountain areas of Europe (Carpathians, Sudetes, Bohemian Forest and Alps). The cDNA sequences were statistically analysed according to phylogenetical relationships in between specimens collected in separate localities. Results. During the study, 20 haplotypes were characterized representing a high level of genetic variability, but showing a lack of phylogeographical structure. This pattern can be a result of repeated recolonization and expansion from several areas. Such genetic differentiation may also have been due to the relatively long-term isolation of S. perennis in Pleistocene refugia in Europe, resulting in independent separation of different cpDNA phylogenetic lineages. Discussion. The lack of phylogeographical structure makes it impossible to indicate the centre of haplotype diversity, but refugia located between the ice sheets in the lowlands, Carpathians, Sudetes or the Alps are the most probable sites, where S. perennis existed in Europe. The lack of evidence for phylogeographic structure possibly indicates a high level of gene flow in the recent. The variation in nucleotide composition of cpDNA may reflect the genetic variability from the ancient period, when the landscape and the fen systems were not fragmented, especially on the lowlands, however, at present, it is difficult to speculate about relations between northern and mountain parts of its distribution range in Europe.

scholarly journals Phylogeography of Swertia perennis in Europe based on cpDNA markers

2018 ◽  
Author(s):  
Jacek Urbaniak ◽  
Paweł Kwiatkowski ◽  
Paweł Pawlikowski
Keyword(s):  
Genetic Variability ◽  
Haplotype Diversity ◽  
Clonal Plant ◽  
Nucleotide Composition ◽  
Phylogeographic Structure ◽  
Peat Bogs ◽  
Mountain Areas ◽  
Cdna Sequences ◽  
Chloroplast Dna Markers ◽  
High Level

Abstract Background. Swertia perennis (Gentianaceae) is a perennial diploid and clonal plant species found discontinuously distributed in the peat bogs in mountains of Europe, Asia and North America as well as in European lowlands. The current geographical dispersion of S. perennis is probably an effect of Quaternary climatic changes that played an important role in determining the present-day distribution of Swertia and numerous other plant and animal species. Methods. A presented survey of molecular studies based on combined data from chloroplast DNA markers (trnL-trnF and trnH-psbA) that were conducted to elucidate the phylogeography of S. perennis in European localities. Plants were collected from 28 populations that represent different localities in lowlands as well as in mountain areas of Europe (Carpathians, Sudetes, Bohemian Forest and Alps). The cDNA sequences were statistically analysed according to phylogenetical relationships in between specimens collected in separate localities. Results. During the study, 20 haplotypes were characterized representing a high level of genetic variability, but showing a lack of phylogeographical structure. This pattern can be a result of repeated recolonization and expansion from several areas. Such genetic differentiation may also have been due to the relatively long-term isolation of S. perennis in Pleistocene refugia in Europe, resulting in independent separation of different cpDNA phylogenetic lineages. Discussion. The lack of phylogeographical structure makes it impossible to indicate the centre of haplotype diversity, but refugia located between the ice sheets in the lowlands, Carpathians, Sudetes or the Alps are the most probable sites, where S. perennis existed in Europe. The lack of evidence for phylogeographic structure possibly indicates a high level of gene flow in the recent. The variation in nucleotide composition of cpDNA may reflect the genetic variability from the ancient period, when the landscape and the fen systems were not fragmented, especially on the lowlands, however, at present, it is difficult to speculate about relations between northern and mountain parts of its distribution range in Europe.

Assessment of genetic variability amongst cultivated populations of Khasi mandarin (Citrus reticulata Blanco) detected by ISSR

2021 ◽  
pp. 1-11
Author(s):  
Karishma Kashyap ◽  
Rasika M. Bhagwat ◽  
Sofia Banu
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Inter Simple Sequence Repeat ◽  
Northeast India ◽  
Issr Markers ◽  
Citrus Reticulata ◽  
Brahmaputra Valley ◽  
Indian Food ◽  
Cultivated Populations ◽  
High Level

Abstract Khasi mandarin (Citrus reticulata Blanco) is a commercial mandarin variety grown in northeast India and one of the 175 Indian food items included in the global first food atlas. The cultivated plantations of Khasi mandarin grown prominently in the lower Brahmaputra valley of Assam, northeast India, have been genetically eroded. The lack in the efforts for conservation of genetic variability in this mandarin variety prompted diversity analysis of Khasi mandarin germplasm across the region. Thus, the study aimed to investigate genetic diversity and partitioning of the genetic variations within and among 92 populations of Khasi mandarin collected from 10 cultivated sites in Kamrup and Kamrup (M) districts of Assam, India, using Inter-Simple Sequence Repeat (ISSR) markers. The amplification of genomic DNA with 17 ISSR primers yielded 216 scorable DNA amplicons of which 177 (81.94%) were polymorphic. The average polymorphism information content was 0.39 per primer. The total genetic diversity (HT = 0.28 ± 0.03) was close to the diversity within the population (HS = 0.20 ± 0.01). A high mean coefficient of gene differentiation (GST = 0.29) reflected a high level of gene flow (Nm = 1.22), indicating high genetic differentiation among the populations. Analysis of Molecular Variance (AMOVA) showed 78% of intra-population differentiation, 21% among the population and 1% among the districts. The obtained results indicate the existence of a high level of genetic diversity in the cultivated Khasi mandarin populations, indicating the need for preservation of each existing population to revive the dying out orchards in northeast India.

Genetic variability and demographic history of Heliothis virescens (Lepidoptera: Noctuidae) populations from Brazil inferred by mtDNA sequences

2011 ◽  
Vol 102 (3) ◽  
pp. 333-343 ◽  
Author(s):  
K.C. Albernaz ◽  
K.L. Silva-Brandão ◽  
P. Fresia ◽  
F.L. Cônsoli ◽  
C. Omoto
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Heliothis Virescens ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Low Frequency ◽  
Haplotype Network ◽  
Demographic Expansion ◽  
Significant Genetic Structure ◽  
History Of

AbstractIntra- and inter-population genetic variability and the demographic history of Heliothis virescens (F.) populations were evaluated by using mtDNA markers (coxI, coxII and nad6) with samples from the major cotton- and soybean-producing regions in Brazil in the growing seasons 2007/08, 2008/09 and 2009/10. AMOVA indicated low and non-significant genetic structure, regardless of geographical scale, growing season or crop, with most of genetic variation occurring within populations. Clustering analyzes also indicated low genetic differentiation. The haplotype network obtained with combined datasets resulted in 35 haplotypes, with 28 exclusive occurrences, four of them sampled only from soybean fields. The minimum spanning network showed star-shaped structures typical of populations that underwent a recent demographic expansion. The recent expansion was supported by other demographic analyzes, such as the Bayesian skyline plot, the unimodal distribution of paired differences among mitochondrial sequences, and negative and significant values of neutrality tests for the Tajima's D and Fu's FS parameters. In addition, high values of haplotype diversity (Ĥ) and low values of nucleotide diversity (π), combined with a high number of low frequency haplotypes and values of θπ<θW, suggested a recent demographic expansion of H. virescens populations in Brazil. This demographic event could be responsible for the low genetic structure currently found; however, haplotypes present uniquely at the same geographic regions and from one specific host plant suggest an initial differentiation among H. virescens populations within Brazil.

CITY PARK AS A NATURAL-ANTHROPOGENIC OBJECT (ON THE EXAMPLE OF THE PARK OF THE 50th ANNIVERSARY OF VLKSM IN THE CITY OF YEKATERINBURG)

2021 ◽  
pp. 133-140
Author(s):  
L. I. ATKINA ◽  
◽  
L. V. BULATOVA ◽  
L. P. ABRAMOVA
Keyword(s):  
Soil Cover ◽  
Negative Impact ◽  
50Th Anniversary ◽  
Ground Cover ◽  
Peat Bogs ◽  
Anthropogenic Transformation ◽  
History Of ◽  
High Level ◽  
The City ◽  
City Park

Based on a comprehensive assessment of the state of the park landscape, the level of its anthropogenic transformation is determined, which is necessary to identify the potential for restoring the natural biodiversity of the object. It is reported that the plantations and soil cover of the park of the 50th anniversary of VLKSM are very heterogeneous; they reflect the history of park establishment. The soil cover consists of three main types: sod, bog and urbanozem. It should be stressed that the best preserved part of the park is the plot with boggy soils around the pond. Herbaceous plants growing on the plot are very similar to the species composition of the ground cover of overgrown peat bogs. Over the 40 years since the foundation of the park, a high level of pollutants has been accumulated in the soil, which allows us to state that the negative impact occurs constantly. Consequently, the existing plantings are insufficient to protect visitors from vehicle emissions from the roads along Yasnaya and Shaumyana streets. There are enough natural elements in the park of the 50th anniversary of VLKSM; this should be taken into account in its redevelopment. There is an opportunity to restore the reservoir and return the plantings to their natural appearance. It is proposed to add elements of landscape decoration in the park.

Genetic variability in the natural populations of Lasioderma serricorne (F.) (Coleoptera: Anobiidae), detected by RAPD markers and by esterase isozymes

2015 ◽  
Vol 106 (1) ◽  
pp. 47-53 ◽  
Author(s):  
T. Coelho-Bortolo ◽  
C.A. Mangolin ◽  
A.S. Lapenta
Keyword(s):  
Genetic Variability ◽  
Random Amplified Polymorphic Dna ◽  
Natural Populations ◽  
Electrophoretic Analysis ◽  
Effective Control ◽  
Lasioderma Serricorne ◽  
Control Programs ◽  
Dried Fruit ◽  
High Level ◽  
High Degree

AbstractLasioderma serricorne (F.) is a small cosmopolitan beetle regarded as a destructive pest of several stored products such as grains, flour, spices, dried fruit and tobacco. Chemical insecticides are one of the measures used against the pest. However, intensive insecticide use has resulted in the appearance of resistant insect populations. Therefore, for the elaboration of more effective control programs, it is necessary to know the biological aspects of L. serricorne. Among these aspects, the genetic variability knowledge is very important and may help in the development of new control methods. The objective of this study was to evaluate the genetic variability of 11 natural populations of L. serricorne collected respectively in three and four towns in the states of Paraná and São Paulo, Brazil, using 20 primers random amplified polymorphic DNA (RAPD) and polymorphisms of esterases. These primers produced 352 polymorphic bands. Electrophoretic analysis of esterases allowed the identification of four polymorphic loci (Est-2, Est-4, Est-5 and Est-6) and 18 alleles. Results show that populations are genetically differentiated and there is a high level of genetic variability within populations. The high degree of genetic differentiation is not directly correlated to geographical distance. Thus, our data indicate that movement of infested commodities may contribute to the dissemination of L. serricorne, facilitating gene flow.

scholarly journals Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

2016 ◽  
Vol 24 (2) ◽  
pp. 85-97 ◽  
Author(s):  
Sylvanus A. Nwafili ◽  
Tian-Xiang Gao
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Control Region ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Recent Population Expansion ◽  
Base Pair Fragment ◽  
Population Structures ◽  
High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

scholarly journals Analysis of Genetic Diversity in three Kazakh Sheep using 12 Microsatellites

2018 ◽  
Vol 7 (4.38) ◽  
pp. 122
Author(s):  
Kairat Dossybayev ◽  
Aizhan Mussayeva ◽  
Bakytzhan Bekmanov ◽  
Beibit Kulataev
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Mean Value ◽  
Fixation Index ◽  
Merino Sheep ◽  
Str Markers ◽  
Sheep Breeds ◽  
Str Loci ◽  
High Level ◽  
Two Populations

The genetic structure of three Kazakh sheep breeds was examined by using 12 microsatellite loci. A total of 144 alleles were detected from the 12 STR loci, with a mean value of 12.0. The highest allele diversity was found at the locus CSRD247 (16 alleles). PIC value showed that all studied STR markers are more informative and appropriate for genetic analysis of three Kazakh sheep populations. Beside of INRA006, all markers had high level of genetic variability. As Fixation index shows, the excess of the heterozygosity was observed only in loci MAF065. Obtained number of private alleles in Edilbai, Kazakh Arkhar Merino and Kazakh Fine-wool sheep were 25, 17 and 15 respectively. Genetic diversity was higher in Edilbai population than in other two populations. The genetic variability was lower in Kazakh Arkhar Merino sheep than in the Edilbai and Kazakh Fine-wool sheep breeds. The genetic distance was the largest between Edilbai and Kazakh Arkhar Merinos. Also, the moderate differentiation was observed between Edilbai and Kazakh Arkhar Merinos.   

scholarly journals Genetic diversity of the Neotropical otter (Lontra longicaudis Olfers, 1818) in Southern and Southeastern Brazil

2007 ◽  
Vol 67 (4 suppl) ◽  
pp. 813-818 ◽  
Author(s):  
CS. Trinca ◽  
HF. Waldemarin ◽  
E. Eizirik
Keyword(s):  
Molecular Diversity ◽  
Single Point ◽  
Haplotype Diversity ◽  
Point Mutations ◽  
Conservation Strategies ◽  
Southeastern Brazil ◽  
Nucleotide Variability ◽  
Single Point Mutations ◽  
High Level ◽  
Lontra Longicaudis

The Neotropical otter is one of the least known otter species, and it is considered to be threatened to various degrees throughout its geographic range. Little information exists on the ecological characteristics of this species, and no genetic study has been published about it until now, hampering the design of adequate conservation strategies for its populations. To contribute with genetic information to comprehensive conservation efforts on behalf of L. longicaudis, we characterized the molecular diversity of the 5’ portion of the mtDNA control region in samples from this species collected in Southern and Southeastern Brazil. The sequence analysis revealed a high level of haplotype diversity (h = 0.819; SE = 0.0052) and nucleotide variability ranging from 0.0039 to 0.0067. One of the sampled haplotypes was the most common in both regions and, from this sequence, several other (locally occurring) haplotypes could be derived by single point mutations. No significant genetic differentiation was observed between the Southern and Southeastern regions.

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