scholarly journals Genetic Differentiation Studies among Natural Populations of Tilapia zillii

2015 ◽  
Vol 7 (4) ◽  
pp. 423-429
Author(s):  
Tofunmi E. OLADIMEJI ◽  
Michael O. AWODIRAN ◽  
Olaniyi O. KOMOLAFE
Keyword(s):  
Genetic Differentiation ◽  
Random Amplified Polymorphic Dna ◽  
Natural Populations ◽  
Principal Component ◽  
Genetic Distances ◽  
Morphological Studies ◽  
Tilapia Zillii ◽  
Meristic Counts ◽  
Ctab Method ◽  
Group Relationships

The population structure of Tilapia zillii (Gervais 1848) from three reservoirs in Nigeria, Osun State (Opa, Osu and Igun) was determined by employing morphological and molecular (Random Amplified Polymorphic DNA) methods. For morphological studies, 25 morphometric measurements and six meristic counts were recorded on 40 individuals within each population. Principal Component Analysis (PCA) was performed on the morphometric and meristic data using the PAST software. For RAPD studies, genomic DNA was extracted from caudal fin tissue using CTAB method and five primers were used to initiate PCR amplifications. All the clusters produced by the Principal components analysis (PCA) of the morphometric and meristic parameters overlapped indicating a low level of genetic differentiation between the three populations of T. zillii studied. The UPGMA cluster diagram from RAPD analysis identified two major genotypic groups with inter and intra group relationships. All individuals in the first cluster were from the Osu reservoir, while individuals from Opa and Igun reservoirs constituted the second cluster. Nei’s unbiased measure of genetic distances was 0.8532, 0.7321 and 0.7111 for Osu, Igun and Opa populations respectively. This revealed that Opa and Igun populations were genetically closer, while Osu populations is distant from them. The results suggest that the RAPD technique could be used to differentiate populations of T. zillii. However, additional methods such as microsatellite and sequence analysis can be used to maximize the efficiency of genetic differentiation studies.

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

The use of RAPD markers to distinguish among juniper and cedar cultivars

2000 ◽  
Vol 78 (5) ◽  
pp. 655-659 ◽  
Author(s):  
Tom Hsiang ◽  
Junbin Huang
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Unknown Origin ◽  
Genetic Distances ◽  
Group Method ◽  
Pair Group ◽  
Juniperus Chinensis ◽  
Juniperus Scopulorum ◽  
Close Relatives

Two species of Chamaecyparis and six cultivars each of Juniperus chinensis L. and Juniperus scopulorum Sarg. (Cupressaceae) were subjected to random amplified polymorphic DNA (RAPD) analysis using seven primers. Unweighted pair group method with averages (UPGMA) and principal component analyses of genetic distances between cultivars showed that 42 polymorphic RAPD bands could distinguish among all cultivars and properly group them by species and genera. Where the origin of a specific juniper cultivar is uncertain, analysis of genetic distance can pinpoint close relatives. For example, we were unable to trace the origin of J. chinensis 'Alps', and we initially thought it was a mislabeled J. chinensis 'Blue Alps'. However, we found 'Alps' to be closer to J. chinensis 'Fairview' and 'Mountbatten' than to 'Blue Alps'. Similarly, 'Wichita Blue' has an unknown origin, but it had the highest genetic similarity with 'Medora'.Key words: juniper, cedar, RAPD, cultivars, phylogenetics.

scholarly journals Genetic Differentiation Studies among Natural Populations of Tilapia zillii

2015 ◽  
Vol 7 (4) ◽  
Author(s):  
Tofunmi E. OLADIMEJI ◽  
Michael O. AWODIRAN ◽  
Olaniyi O. KOMOLAFE
Keyword(s):  
Genetic Differentiation ◽  
Natural Populations ◽  
Tilapia Zillii

scholarly journals GENETIC CHANGE AND RATES OF CLADOGENESIS

Genetics ◽  
1975 ◽  
Vol 81 (4) ◽  
pp. 757-773
Author(s):  
John C Avise ◽  
Francisco J Ayala
Keyword(s):  
Genetic Differentiation ◽  
Genetic Distance ◽  
Genetic Divergence ◽  
Natural Populations ◽  
Genetic Distances ◽  
Genetic Change ◽  
The Other ◽  
Limited Information ◽  
History Of ◽  
The Relationship

ABSTRACT Models are introduced which predict ratios of mean levels of genetic divergence in species-rich versus species-poor phylads under two competing assumptions: (1) genetic differentiation is a function of time, unrelated to the number of cladogenetic events and (2) genetic differentiation is proportional to the number of speciation events in the group. The models are simple, general, and biologically real, but not precise. They lead to qualitatively distinct predictions about levels of genetic divergence depending upon the relationship between rates of speciation and amount of genetic change. When genetic distance between species is a function of time, mean genetic distances in speciose and depauperate phylads of equal evolutionary age are very similar. On the contrary, when genetic distance is a function of the number of speciations in the history of a phylad, the ratio of mean genetic distances separating species in speciose versus depauperate phylads is greater than one, and increases rapidly as the frequency of speciations in one group relative to the other increases. The models may be tested with data from natural populations to assess (1) possible correlations between rates of anagenesis and cladogenesis and (2) the amount of genetic differentiation accompanying the speciation process. The data collected in electrophoretic surveys and other kinds of studies can be used to test the predictions of the models. For this purpose genetic distances need to be measured in speciose and depauperate phylads of equal evolutionary age. The limited information presently available agrees better with the model predicting that genetic change is primarily a function of time, and is not correlated with rates of speciation. Further testing of the models is, however, required before firm conclusions can be drawn.

scholarly journals Diversity and genetic structure of Ornithogalum L. (Hyacinthaceae) populations as revealed by RAPD-PCR markers

Genetika ◽  
2015 ◽  
Vol 47 (1) ◽  
pp. 275-288
Author(s):  
Andrijana Andric ◽  
Natasa Kocis-Tubic ◽  
Milica Rat ◽  
Dragana Obreht-Vidakovic
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Distances ◽  
Shannon Index ◽  
Similarity Coefficients ◽  
Additional Tool ◽  
Population Genetic Differentiation ◽  
Rapd Pcr

Random amplified polymorphic DNA (RAPD) PCR method was used to assess the level of diversity and genetic structure in Ornithogalum L. populations from Serbia and Hungary with the main goal of improving the knowledge of this genus in the given region. The material was collected from 19 populations and identified as two morphologically similar and phylogenetically close taxa: O. umbellatum L. 1753 and O. divergens Boreau 1887. All ten RAPD primers used for the analysis gave PCR products, with length between 3000bp and 300bp. There were 101 amplified fragments in total; number of polymorphic bands per primer varied between seven and 13. Percentage of polymorphic loci was 96% in total and 12% in average in each population. Genetic variation statistics for all loci also showed that genetic diversity for all populations was 0.29 and Shannon index 0.45, while mean values for these parameters calculated for each population were 0.04 and 0.06, respectively. Analysis of molecular variance demonstrated high population genetic differentiation; however Mantel test showed no significant correlation between geographic distances of populations and genetic distances expressed through population pairwise FST. UPGMA dendrogram based on Jaccard genetic similarity coefficients showed subclustering and principal coordinate analysis based on Nei and Li coefficients of genetic distances indicated grouping. Analysis of populations genetic structure was in accordance with these results and clearly separated populations of O. umbellatum from O. divergens. RAPDs proved to be a reliable and rapid method suitable for distinguishing genetic differentiation in Ornithogalum, thus could be applied as a useful additional tool in resolving taxonomic problems.

scholarly journals Barrier to Gene Flow Between Eastern and Western Populations of Cronartium ribicola in North America

2000 ◽  
Vol 90 (10) ◽  
pp. 1073-1078 ◽  
Author(s):  
R. C. Hamelin ◽  
R. S. Hunt ◽  
B. W. Geils ◽  
G. D. Jensen ◽  
V. Jacobi ◽  
...  
Keyword(s):  
Gene Flow ◽  
New Mexico ◽  
North America ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Genetic Distances ◽  
Group Method ◽  
Cronartium Ribicola ◽  
Western North America ◽  
Pair Group

The population structure of Cronartium ribicola from eastern and western North America was studied to test the null hypothesis that populations are panmictic across the continent. Random amplified polymorphic DNA markers previously characterized in eastern populations were mostly fixed in western populations, yielding high levels of genetic differentiation between eastern and western populations (φst = 0.55; θ = 0.36; P < 0.001). An unweighted pair-group method, arithmetic mean dendro-gram based on genetic distances separated the four eastern and four western populations into two distinct clusters along geographic lines. Similarly, a principal component analysis using marker frequency yielded one cluster of eastern populations and a second cluster of western populations. The population from New Mexico was clearly within the western cluster in both analyses, confirming the western origin of this recent introduction. This population was completely fixed (Hj = 0.000; n = 45) at all loci suggesting a severe recent population bottleneck. Genetic distances were low among populations of western North America (0.00 to 0.02) and among eastern populations (0.00 to 0.02), indicating a very similar genetic composition. In contrast, genetic distances between eastern and western populations were large, and all were significantly different from 0 (0.07 to 0.19; P < 0.001). Indirect estimates of migration were high among western populations, including the number of migrants among pairs of populations (Nm > 1) between New Mexico and British Columbia populations, but were smaller than one migrant per generation between eastern and western populations. These results suggest the presence of a barrier to gene flow between C. ribicola populations from eastern and western North America.

Strong genetic differentiation among populations of Fosterella rusbyi (Bromeliaceae) in Bolivia

2019 ◽  
Vol 192 (4) ◽  
pp. 744-759 ◽  
Author(s):  
Tina Wöhrmann ◽  
Ingo Michalak ◽  
Georg Zizka ◽  
Kurt Weising
Keyword(s):  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Haplotype Diversity ◽  
Natural Populations ◽  
Population Expansion ◽  
Genetic Distances ◽  
Allopatric Speciation ◽  
Seasonally Dry ◽  
Nuclear Microsatellite ◽  
Suitable Habitats

Abstract The terrestrial bromeliad Fosterella rusbyi is endemic to the Bolivian Andes, where it mainly grows on steep, exposed slopes along roadsides and riverbeds in the seasonally dry tropical forest (SDTF) and the mesic montane forest (Yungas) biomes. We hypothesize that allopatric speciation may have been a main driver of diversification in Fosterella since the Miocene and that the scattered distribution of suitable habitats fostered the evolution of the high degree of endemism observed today. To provide further information relating to this hypothesis, we analysed the partition of genetic diversity and the extent of gene flow among natural populations of F. rusbyi using plastid and nuclear microsatellite markers. Nineteen plastid haplotypes were found, but the mean haplotype diversity per population was low. Nuclear microsatellite markers revealed 177 different multilocus genotypes (MLGs), of which 31 occurred in more than one plant. Recurrent MLGs were found in 76 plants that were therefore identified as clones. A considerable deficit of heterozygotes was detected at all nuclear loci. Geographical and genetic distances between populations were only weakly correlated with each other. Genetic divergence between populations was extremely high for both marker classes, suggesting that seed and pollen flow are low, even over short distances. The observed patterns are consistent with our hypothesis that newly available sites are sporadically colonized by one or a few founders, followed by in situ population expansion via vegetative propagation, self-pollination and/or biparental inbreeding, genetic differentiation among persistent populations and, ultimately, allopatric speciation.

scholarly journals Genetic Differentiation between Quercus frainetto Ten. and Q. pubescens Willd. in Romania

2011 ◽  
Vol 39 (1) ◽  
pp. 275 ◽  
Author(s):  
Alexandru Lucian CURTU ◽  
Ioan Calin MOLDOVAN ◽  
Mihai Cristian ENESCU ◽  
Iacob CRACIUNESC ◽  
Nicolae SOFLETEA
Keyword(s):  
Genetic Differentiation ◽  
Natural Populations ◽  
Introgressive Hybridization ◽  
Genetic Distances ◽  
Assignment Test ◽  
Quercus Frainetto ◽  
Marker Loci ◽  
Genetic Clusters ◽  
Individual Trees ◽  
Expressed Sequence

Little is known about genetic differences among Quercus frainetto and Q. pubescens, two species of section Dascia Kotschy (subgenus Lepidobalanus, white oaks) that reach in Romania the margins of their natural distribution range. A set of genomic SSRs (simple sequence repeats) and EST (expressed sequence tags)-SSRs was used to estimate the genetic differentiation among four natural populations of the two species. Q. pubescens had higher values of genetic diversity than Q. frainetto, although the differences were not significant. Two out of seven marker-loci, QrZAG112 and QpZAG110, displayed very high FST values. Averaged across loci, the genetic differentiation was high and significant (FST = 0.067). Genetic distances were much higher among species than among populations within species. A Bayesian analysis indicated that two is the most appropriate number of genetic clusters. Using a blind procedure (i.e. based on multilocus genotypes only) the vast majority of sampled individuals (90%) could be assigned to the cluster corresponding to their phenotypes. When information about sampling localities was introduced in the assignment test, all individual trees were correctly classified. The higher degree of admixture in Q. frainetto as compared to Q. pubescens may be explained by different rates of introgressive hybridization.

scholarly journals Assessment of Genetic Diversity in Five Nicaraguan Populations of Cedrela odorata L. (Meliaceae) using RAPD Markers

Encuentro ◽  
2016 ◽  
pp. 28-39
Author(s):  
Arlen Tijerino ◽  
Lourdes Callejas ◽  
David A. Cerda-Granados
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Rapd Markers ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Natural Populations ◽  
Cedrela Odorata ◽  
Total Genetic Diversity ◽  
Geographical Distances ◽  
The Mean

The goal of this study was to assess the genetic diversity of Nicaraguan populations of Cedrela odorata using Random Amplified Polymorphic DNA (RAPD) markers. Thus, genomic DNA was isolated from leaf samples collected from ninety-two trees belonging to five Nicaraguan natural populations of C. odorata. The mean number of alleles per locus, effective number of alleles per locus, percentage of polymorphic loci, genetic diversity (He ) of Nei and diversity index (Ho ) of Shannon were estimated for each population assuming that the populations were in HardyWeinberg equilibrium. Total genetic diversity was partitioned in intrapopulational and interpopulational diversity using Nei’s genetic differentiation (GST) and through an Analysis of Molecular Variance (AMOVA). The ΦST matrix was used to construct a dendrogram by the neighbor-joining method. According to values of both He and Ho , Esquipulas (Deparment of Matagalpa) presented the lowest diversity level; while La Trinidad (Department of Estelí) showed the highest diversity level. Genetic differentiation was calculated obtaining a GST value of 13.36%. AMOVA also showed a similar differentiation value ΦST =13.81%). Neighbour-joining dendrogram clustered the five populations in two groups, where the group formed by La Trinidad and El Refugio (Department of Granada) presented the biggest differentiation. Correlation between genetic and geographical distances was not found.

scholarly journals Genetic structure and diversity among three Greek sheep breeds using Random Amplified Polymorphic DNA-PCR

2017 ◽  
Vol 62 (4) ◽  
pp. 301 ◽  
Author(s):  
I. MASTRANESTASIS (Ι. ΜΑΣΤΡΑΝΕΣΤΑΣΗΣ) ◽  
Ch. LIGDA (Χρ. ΛΙΓΔΑ) ◽  
K. THEODOROU (Κ. ΘΕΟΔΩΡΟΥ) ◽  
L. V. EKATERINIADOU (Λ.Β. ΑΙΚΑΤΕΡΙΝΙΑΔΟΥ)
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Phylogenetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Distances ◽  
Genetic Identity ◽  
Rapd Pcr ◽  
Pcr Method ◽  
Genetic Structure And Diversity

Genetic structure and diversity of 120 animals from three Greek local breeds were investigated by Random Amplified Polymorphic DNA (RAPD) - PCR method. Sheep samples originated from the Lesvos, Chios and Karagouniko breeds were treated with 11 random primers to estimate their genetic diversity and phylogenetic relationships. Our analysis comprised two levels of the breeds' genetic structure: i) the genetic differentiation among the three breeds and ii) the genetic differentiation among the flocks within each breed. This combined approach gave two main findings: i) the study of genetic distances and identity revealed that the Karagouniko sheep breed is genetically distinct from Chios (GD=0.1979) and Lesvos (GD=0.1691) breeds, while ii) the Chios and Lesvos breeds are genetically similar (GI=0.9631); half of the flocks of Lesvos have a relatively closer relationship with those of Chios than with the other Lesvos flocks. This is the first study that reports the close genetic relationship between the Chios and Lesvos breeds and gives strong evidence to hypotheses about their related origin. Furthermore, the study of polymorphic loci revealed particular indicators located in Karagouniko breed, as definitional datum of genetic identity or as a fingerprint of breed. Therefore, RAPD-DNA methods can be an efficient tool for the determination of phylogenetic relationships and genetic identity among the bloodstock breed of sheep.

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