scholarly journals Characterization of diversity and genetic structure in natural populations of Stryphnodendron adstringens (Mart.) Coville by means of allozyme markers

2014 ◽  
Vol 16 (2) ◽  
pp. 216-224 ◽  
Author(s):  
J.S. Glasenapp ◽  
E.R. Martins ◽  
V.W.D. Casali ◽  
C.D. Cruz ◽  
P.B. Barbosa
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Polymorphic Locus ◽  
Local Level ◽  
Natural Populations ◽  
Tropical Trees ◽  
The Other ◽  
Fixation Index ◽  
Brazilian Savannah ◽  
Average Proportion

The S. adstringens, a typical Cerrado (Brazilian savannah) tree, is used because of its medicinal and tanning properties. Because of the still incipient genetic knowledge of the species, the objective of this work was to characterize the diversity and genetic structure of S. adstringens by using allozyme markers. Seeds were collected in five Brazilian mesoregions, in which 627 individuals in 16 populations in the states of Minas Gerais and Goiás were sampled. Fourteen isoenzyme systems were assessed, out of which seven were polymorphic with a total of 10 loci and 28 alleles. Average genetic diversity (H) was 0.226, average proportion of polymorphic loci (P) was 68.75, average number of alleles per polymorphic locus (AP) was 2.65 and effective number of alleles (Ae) was equal to 1.29. The results of total fixation index (F= 0.003), within population fixation index (f =-0.114) and genetic differentiation measure (θ =0.105) were not significant, which shows the inexistence of genetic structure. Two principal groups were found in the cluster analysis (UPGMA), where the first one was formed by the population of State Park (PE) of Rio Preto (MG) and the other, by the other populations. If the population of PE of Rio Preto is excluded from the analysis, G ST is drastically reduced from 0.077 to 0.026. Thus, approximately 2/3 of the total value of G ST found in S. adstringens was due to the variation among the population of PE of Rio Preto and the other populations. Overall, the values of H and P found in S. adstringens are compatible with the ones found in typically distributed tropical trees. On the other hand, by excluding the population of PE of Rio Preto, the value of the G ST genetic differentiation measure was smaller than the one found in native tropical trees from temperate zones. The similarity between the assessed populations shows that the gene flow is still high enough to avoid genetic differentiation, at the local level, at least.

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.

Phenotypic and genetic diversities are not correlated in strains of the cyanobacterium Microcystis aeruginosa isolated in SW Spain. Las diversidades fenotípica y genética de cepas de la cianobacteria Microcystis aeruginosa aisladas en el SW de España no están correlacionadas

2013 ◽  
Vol 38 ◽  
pp. 5-12
Author(s):  
Victoria López-Rodas ◽  
Eduardo Costas ◽  
Antonio Flores-Moya
Keyword(s):  
Genetic Structure ◽  
Microcystis Aeruginosa ◽  
National Park ◽  
Natural Populations ◽  
Toxin Production ◽  
The Other ◽  
Water Bodies ◽  
Phenotypic Traits ◽  
Doñana National Park ◽  
Sw Spain

English.  The cyanobacterium Microcystis aeruginosa (Kützing) Kützing is notorious for forming extensive and toxic blooms but the genetic structure of natural populations, and in particular during blooms, remains to be explored. In order to add more knowledge about the genetic structure of M. aeruginosa, we compared phenotypic and genetic variabilities in seventeen strains of M. aeruginosa isolated from three adjacent water bodies in SW Spain (the consecutive reservoirs La Minilla and El Gergal, and small pools in Doñana National Park). For this purpose, a phenetic tree, based on six phenotypic traits (including morphology of cells, photosynthetic and respiratory performance, and toxin production) was compared with a phylogenetic tree built by using the 16S-23S rDNA Internal Transcribed Spacer sequence. Whereas the strains isolated from La Minilla showed a relatively homogeneous phenotype, the phenotypic traits of the remaining strains did not discriminate between the other two water bodies. On the other hand, only a strain isolated in Doñana National Park showed a slightly different ITS sequence, but the sequences from the remaining strains were similar. Possible explanations for this discrepancy between phenotypic and genetic diversities are discussed.Español.  La cianobacteria Microcystis aeruginosa (Kützing) Kützing puede dar lugar a extensas floraciones tóxicas pero la estructura genética de las poblaciones naturales, y en particular durante las floraciones, ha sido escasamente estudiada. Con el objeto de profundizar en la estructura genética de M. aeruginosa, se han comparado las variabilidades fenotípica y genética de diecisiete cepas aisladas de tres cuerpos de agua adyacentes en el SW de España (los embalses consecutivos de La Minilla y El Gergal, y charcas en el Parque Nacional de Doñana). Para este fin, un árbol de similitud fenética basado en seis caracteres fenotípicos (que incluyen la morfología de las células, el rendimiento fotosintético y respiratorio y la producción de toxina) se comparó con un árbol filogenético construido mediante el uso de la secuencia de ITS 16S - 23S del ADNr. Las cepas aisladas en La Minilla mostraron un fenotipo relativamente homogéneo pero no se detectó un patrón de fenotipos que discriminase los otros dos cuerpos de agua. Por otro lado, sólo una cepa aislada en el Parque Nacional de Doñana mostró una secuencia ITS diferente, pero las secuencias de las cepas restantes fueron idénticas. Se discuten las posibles explicaciones para esta discrepancia entre la diversidad fenotípica y genética en M. aeruginosa.

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 Genetic Structure in Populations of Euterpe precatoria Mart. in the Brazilian Amazon

2021 ◽  
Vol 8 ◽  
Author(s):  
Santiago Linorio Ferreyra Ramos ◽  
Gabriel Dequigiovanni ◽  
Maria Teresa Gomes Lopes ◽  
Ananda Virginia de Aguiar ◽  
Ricardo Lopes ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Bayesian Analysis ◽  
Management Strategies ◽  
Geographic Distance ◽  
Natural Populations ◽  
Population Level ◽  
Brazilian Amazon ◽  
The State ◽  
Fixation Index ◽  
Palm Tree

Euterpe precatoria is a palm tree belonging to the Arecaceae family, occurring in Western and Central Brazilian Amazonia. Its fruit, which is very appreciated in the Amazon region, produces pulp that is consumed in fresh form. Its production is carried out almost exclusively by extractive farmers. In order to establish adequate strategies to sustain this genetic resource, we need knowledge about the diversity and genetic structure in natural populations. This study aimed to evaluate the influence of geographic distance on genetic structure in the main extractive populations of E. precatoria in the Brazilian Amazon. Leaves from 377 plants were collected in 19 populations located in 16 municipalities in the State of Amazonas and three in the State of Rondônia. Twelve microsatellite loci were used to genotype the plants. The diversity and genetic structure among populations were estimated. The average number of alleles per locus was 5.97. The observed heterozygosity means (HO) were higher than expected (HE) at the population level (HO = 0.72, HE = 0.66) and fixation index (f = -0.100) was negative. The FST value (0.1820) and the AMOVA results (Φ = 0.1796) showed population structure. The populations were clustered into three groups (K = 3) in the Bayesian analysis. The Discriminant Analysis of Principal Components (DAPC) confirmed eight clusters, with the populations close to those identified by the Bayesian analysis. The geographic differentiation was confirmed by the groupings obtained in the Structure analysis and the DACP function. Information related to phenotypic, genetic and environmental characterization of populations is important to guide conservation and management strategies and the formulation of public species management policies in Amazonia.

scholarly journals GENETIC VARIATION IN NATURAL POPULATIONS OF FIVE DROSOPHILA SPECIES AND THE HYPOTHESIS OF THE SELECTIVE NEUTRALITY OF PROTEIN POLYMORPHISMS

Genetics ◽  
1974 ◽  
Vol 77 (2) ◽  
pp. 343-384
Author(s):  
Francisco J Ayala ◽  
Martin L Tracey ◽  
Lorraine G Barr ◽  
John F McDonald ◽  
Santiago Pérez-Salas
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Natural Populations ◽  
Evolutionary Divergence ◽  
Average Value ◽  
Local Populations ◽  
Selective Neutrality ◽  
Average Proportion ◽  
Substantial Degree ◽  
Protein Polymorphisms

ABSTRACT We have studied genetic variation at 30-32 loci coding for enzymes in natural populations of five species of Drosophila. The average proportion of heterozygous loci per individual is 17.7 ± 0.4%. The average proportion of polymorphic loci per population is 69.2 ± 2.6% or 49.8 ± 2.2%, depending on what criterion of polymorphism is used. The following generalizations are advanced: (1) The amount of genetic polymorphism varies considerably from locus to locus. (2) At a given locus, populations of the same species are very similar in the amount and pattern of genetic variation. (3) However, at some loci large differences sometimes occur between local populations of the same species. (4) The amount of variation at a given locus is approximately the same in all five species. (5) When different species are compared, the pattern of the variation is either essentially identical or totally different at a majority of loci. We have tested the hypothesis that protein polymorphisms are selectively neutral by examining four predictions derived from the hypothesis. Our results are at variance with every one of the predictions. We have measured the amount of genetic differentiation, D, between taxa of various degrees of evolutionary divergence. The average value of D is 0.033 for local populations, 0.228 for subspecies, 0.226 for semispecies, 0.538 for sibling species, and 1.214 for morphologically distinguishable species. Our results indicate that a substantial degree of genetic differentiation (22.8 allelic substitutions for every 100 loci) occurs between allopatric populations that have diverged to the point where they might become different species if they were to become sympatric. However, very little additional genetic change is required for the development of complete reproductive isolation. After the speciation process is completed, species continue to diverge genetically from each other.

scholarly journals Genetic Differentiation between Sympatric Populations of Bacillus cereus and Bacillus thuringiensis

2002 ◽  
Vol 68 (3) ◽  
pp. 1414-1424 ◽  
Author(s):  
Gislayne Vilas-Boas ◽  
Vincent Sanchis ◽  
Didier Lereclus ◽  
Manoel Victor F. Lemos ◽  
Denis Bourguet
Keyword(s):  
Bacillus Thuringiensis ◽  
Genetic Differentiation ◽  
Bacillus Cereus ◽  
Natural Populations ◽  
The Other ◽  
Small Samples ◽  
Natural Conditions ◽  
Sympatric Populations ◽  
Data Set ◽  
Clonal Proliferation

ABSTRACT Little is known about genetic exchanges in natural populations of bacteria of the spore-forming Bacillus cereus group, because no population genetics studies have been performed with local sympatric populations. We isolated strains of Bacillus thuringiensis and B. cereus from small samples of soil collected at the same time from two separate geographical sites, one within the forest and the other at the edge of the forest. A total of 100 B. cereus and 98 B. thuringiensis strains were isolated and characterized by electrophoresis to determine allelic composition at nine enzymatic loci. We observed genetic differentiation between populations of B. cereus and B. thuringiensis. Populations of a given Bacillus species—B. thuringiensis or B. cereus—were genetically more similar to each other than to populations of the other Bacillus species. Hemolytic activity provided further evidence of this genetic divergence, which remained evident even if putative clones were removed from the data set. Our results suggest that the rate of gene flow was higher between strains of the same species, but that exchanges between B. cereus and B. thuringiensis were nonetheless possible. Linkage disequilibrium analysis revealed sufficient recombination for B. cereus populations to be considered panmictic units. In B. thuringiensis, the balance between clonal proliferation and recombination seemed to depend on location. Overall, our data indicate that it is not important for risk assessment purposes to determine whether B. cereus and B. thuringiensis belong to a single or two species. Assessment of the biosafety of pest control based on B. thuringiensis requires evaluation of the extent of genetic exchange between strains in realistic natural conditions.

scholarly journals DNA polymorphism, genetic originality and identification of sterlet populations and replacement broodstock (Acipenser ruthenus)

2021 ◽  
pp. 53-60
Author(s):  
L. V. Komarova ◽  
◽  
A. R. Peleeva ◽  
N. V. Kostitsyna ◽  
A. G. Melnikova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Gene Pool ◽  
Dna Polymorphism ◽  
Molecular Genetic ◽  
Natural Populations ◽  
Federal District ◽  
Acipenser Ruthenus ◽  
Sterlet Acipenser Ruthenus

DNA polymorphism has been studied, indicators of genetic diversity and genetic originality have been de-termined for three natural populations and three replacement broodstocks of sterlet (Acipenser ruthenus Linnaeus, Acipenseridae) from the Volga Federal District. In the group of A. ruthenus replacement broodstock, 106 ISSR-PСR markers were identified, and in the group of natural populations, 103 ISSR-PСR markers. The indicators of genetic diversity and the coefficient of genetic originality (CGO) were slightly higher in the group of natural populations. Analysis of genetic structure of natural populations and groups of broodstock herds A. ruthenus showed that the coefficient of genetic differentiation are also slightly higher in the group of natural populations and equal 0,377. As a result of molecular genetic iden-tification, generic and species identification fragments of sterlet DNA were revealed, as well as combina-tions of polymorphic fragments for identification of the studied natural populations and stocks. The data obtained can be used to preserve the gene pool of populations, which is characteristic for a particular re-gion.

CONNECTION g.307 G > A SNP POLYMORPHISM OF THE ALPHA-FUKOZYLTRASFERAZA 1 GENE WITH ECONOMIC-USEFUL TRAITS IN THE LARGE WHITE PIG BREED

2017 ◽  
Vol 54 ◽  
pp. 134-140
Author(s):  
H. S. Rudoman ◽  
V. M. Balatsky ◽  
V. Y. Nor ◽  
V. O. Vovk
Keyword(s):  
Genetic Structure ◽  
Information Content ◽  
Analysis Of Variance ◽  
Farm Animals ◽  
Daily Weight Gain ◽  
Fixation Index ◽  
Its Sequencing ◽  
Large White ◽  
Stage Of Development ◽  
High Level

One of the top priorities at the present stage of development of pig breeding remains the development of a set of measures aimed at increasing the resistance animals to various diseases, especially – to colibacteriosis .One of the recent and effective approaches to prevent colibacillosis is using markers of selection; it involves pig genotyping by genome locuses. Chosen locuses are associated with animal sensitivity to the disease and selection of the results of genotyping of animals with increased resistance. Due to researches, one of such locuses is alpha-fukozyltrasferаza 1 gene (FUT1). Gene FUT1 is located in chromosome 6. As a result of its sequencing in the swine breeds of Large White and Swedish Landrace, single-nucleotide polymorphism (g.307 G > A SNP) has been detected. AA genotype determines the resistance of animals to colibacteriosis, while AG and GG genotypes are susceptible to this disease. According to the results of previous studies, the positive effect of allele A was determined not only on the resistance of pigs to colibacteriosis, but also on indicators of fattening and meat productivity and on reproductive performance. In Ukraine, the studies of polymorphism FUT1 g.307 G > A SNP were held fragmentedly and only on certain populations of Ukrainian Meat and Large White breed but without establishing its association with the indicators of productivity of pigs. The aim of our work was to study the genetic structure of Ukrainian Large White breeds, type 1 and the establishment of association. g. 307 G > A SNP FUT1 gene with pigs indicators of productivity. For research the 96 samples of hair were used. DNA isolation from samples with biomaterial were carried out using ion exchange resin Chelex-100. Genotyping was performed by PCR-RFLP by method of Jorgensen et al. (2006). Using DNA analysis of this breeds locus FUT1 was determined by genetic structure. Allele frequency of allele G (0,573) and allele A (0,427) was established The distribution of genotype frequencies was not statistically significantly different from the theoretically expected, calculated by the Hardy-Weinberg criterion. Thus, according to the locus of FUT1 g.307 G > A, the breeds investigated are in a state close to the genetic equilibrium. The negative value of the fixation index by the locus FUT1 g.307 G > A indicates an excess of heterozygotes in the population, and hence the lack of targeted selection for this marker. The valuation was performed by calculating the PIC (polymorphic information content) – information content of polymorphism marker. In the analyzed pig herd for this marker, the PIC has an average value (0,367), which indicates the high level of polymorphism of the given locus and is favorable for the possibility of conducting a search for links between individual genotypes and indicators of productivity. To establish the association g.307 G > A SNP FUT1 gene with indicators of animal productivity, a one-way analysis of variance of the experimental data was used. Based on the results of a one-way analysis of variance, a significant effect of the genotypes of the FUT1gene (g.1849 G > C) on the indicator of the average daily weight gain (р ≤ 0,001), the thickness of the bacon at the level of the VI-VII vertebrae (p ≤ 0.01), reaching live weight of 100 kg (р ≤ 0,001) and breeding index of fattening qualities (р ≤ 0,01) was found. The parameter of the influence of the genetic factor on the test feature was 28,54%, 10,4%, 33,4% and 8,8% respectively. According to the investigated indicators of productivity, animals with genotype AA, which determines resistance to colibacteriosis, dominated the animals with genotypes GG and AG. Based on the results of our research and pre-published data, the multiple effect of the g.307 G > A SNP FUT1 gene is observed, which is associated with the indicators of productivity, which again confirms the polygenicity of the quantitative trait loci of farm animals. Taking into account a high level of polymorphism of the investigated gene and reliable associations of genotypes with indicators of productivity found, it can be recommended to carry out breeding of pigs using genetic information of the g.307 G > A SNP gene FUT1.

scholarly journals GENETIC LOAD IN NATURAL POPULATIONS: IS IT COMPATIBLE WITH THE HYPOTHESIS THAT MANY POLYMORPHISMS ARE MAINTAINED BY NATURAL SELECTION?

Genetics ◽  
1974 ◽  
Vol 77 (3) ◽  
pp. 569-589
Author(s):  
Martin L Tracey ◽  
Francisco J Ayala
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Selection ◽  
Natural Population ◽  
Natural Populations ◽  
Genetic Load ◽  
Structural Genes ◽  
Invertebrate Species ◽  
Average Proportion ◽  
Mean Fitness ◽  
The Mean

ABSTRACT Recent studies of genetically controlled enzyme variation lead to an estimation that at least 30 to 60% of the structural genes are polymorphic in natural populations of many vertebrate and invertebrate species. Some authors have argued that a substantial proportion of these polymorphisms cannot be maintained by natural selection because this would result in an unbearable genetic load. If many polymorphisms are maintained by heterotic natural selection, individuals with much greater than average proportion of homozygous loci should have very low fitness. We have measured in Drosophila melanogaster the fitness of flies homozygous for a complete chromosome relative to normal wild flies. A total of 37 chromosomes from a natural population have been tested using 92 experimental populations. The mean fitness of homozygous flies is 0.12 for second chromosomes, and 0.13 for third chromosomes. These estimates are compatible with the hypothesis that many (more than one thousand) loci are maintained by heterotic selection in natural populations of D. melanogaster.

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