scholarly journals Genetic diversity and spatial genetic structure in populations of Orbignya phalerata Mart. under different exploitation intensities in the Brazilian savanna

2015 ◽  
Vol 64 (1-6) ◽  
pp. 201-211 ◽  
Author(s):  
Bruna Ibanes ◽  
A.M. Sebbenn ◽  
V.C.R. Azevedo ◽  
M.A. Moreno ◽  
F.B. Gandara ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Spatial Distance ◽  
Null Alleles ◽  
Fixation Index ◽  
Genetic Studies ◽  
Expected Heterozygosity ◽  
Adult Trees ◽  
Diversity Structure

Abstract Genetic studies in tropical tree species have found signs of decreased genetic diversity and increased levels of inbreeding and spatial genetic structure (SGS) in fragmented and exploited populations. The aim of this paper was to investigate genetic diversity, structure, and intrapopulation SGS using eight microsatellite loci for three Orbignya phalerata populations that have undergone different intensities of seed harvesting. From each population, we georeferenced and sampled 30 seedlings, 30 juveniles, and 30 adult trees. The total number of alleles over all loci (k), and observed (Ho) and expected heterozygosity (He) presented lower values for the population experiencing more intense fruit harvesting than less heavily exploited populations, suggesting that fruit harvesting may decrease genetic diversity. Null alleles were detected in practically all loci among seedlings, juveniles, and adults in all populations, indicating that the estimates of Ho, He, and fixation index (F) are biased. When corrected for null alleles (FNull), the fixation index decreased for all samples, resulting in significantly higher than zero results for seedlings of all populations, but not for juveniles and adults of all populations. The comparison of FNull values between cohorts in the most heavily exploited population (ESP) suggests that inbred individuals are eliminated between seedling and adult stages. Significant SGS was detected up to 60 m in all populations, which indicates short distance seed dispersal. Genetic differentiation (G’ST) between pairwise populations was related to spatial distance between populations, with the greatest difference between more distant populations.

scholarly journals Genetic diversity of Anadenanthera colubrina Vell. (Brenan) var cebil, a tree species from the South American subtropical forest as revealed by cpSSR markers

2011 ◽  
Vol 60 (1-6) ◽  
pp. 123-132 ◽  
Author(s):  
M. E. Barrandeguy ◽  
M.V. García ◽  
C. F. Argüelles ◽  
G. D. L. Cervigni
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Tree Species ◽  
Evolutionary Dynamics ◽  
Pairwise Comparison ◽  
Fixation Index ◽  
Haplotypic Diversity ◽  
Adult Trees ◽  
Minimum Spanning Network ◽  
Subdivided Populations

Abstract Anadenanthera colubrina var cebil is a tree species native to the Upper Parana Atlantic Forest where human activities have severely impacted causing deep fragmentation. Microsatellites are not available in this species. Therefore, the first objective of this study was to generate chloroplast simple sequence repeats (cpSSR) by cross-species transfer. Understanding the evolutionary dynamics of subdivided populations is an important matter. In this way, a first approach to the characterization of the haplotypic diversity within and between populations as well as the genetic structure of native Argentinean populations were the main goals of this study. Twenty four individuals from two populations of the Misiones province were studied and four cpSSR loci were tested. Two of them exhibited polymorphic patterns leading to the identification of 11 cpDNA haplotypes with high mean genetic diversity (GD=0.73). The minimum spanning network defined three clear groups which can be assigned to at least three subpopulations. AMOVA indicated that the total variance showed the highest percentage of variation (48%) within subpopulations with a fixation index (FST) statistically significant (FST=0.520; p<0.05). Brown’s two loci component analysis indicated that substructure population is present. Jost’s differentiation global index (Dest) was 0.049 while Dest pairwise comparison reflected a certain level of genetic structure. The high diversity level detected in the adult trees of A. colubrina var cebil from the populations under study could be due to recent human influence. In this way, the reduction in population size caused a reduction in the number of trees leading to surviving trees showing the historical diversity of the populations analyzed.

scholarly journals Gene flow in an overexploited population of Swietenia macrophylla King (Meliaceae) in the Bolivian Amazon

2012 ◽  
Vol 61 (1-6) ◽  
pp. 212-220 ◽  
Author(s):  
A. M. Sebbenn ◽  
J. C. Licona ◽  
B. Mostacedo ◽  
B. Degen
Keyword(s):  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Pollen Dispersal ◽  
Dispersal Distance ◽  
Fixation Index ◽  
Permanent Plots ◽  
Swietenia Macrophylla ◽  
Genetic Structure Of Populations ◽  
Bolivian Amazon ◽  
Adult Trees

Abstract Pollen and seed movement among and within populations connect individuals and populations, and therefore are among the most important evolutionary processes determining the genetic structure of populations. Seven microsatellite loci were used to investigate the realized pollen dispersal and intra-population spatial genetic structure (SGS) in four permanent plots located in an overexploited big-leaf mahogany (Swietenia macrophylla King) population in the Bolivian Amazon. All adult trees found in the plots were mapped, sampled and genotyped. Seedlings were sampled below the canopy of reproductive trees. Private alleles in the sub-population of the adults and the seedlings were observed. The observed heterozygosity was significantly lower and fixation index was significantly higher for the seedlings (Ho=0.697, F=0.068) compared to the adults (Ho=0.761, F=-0.023). In one plot, seed immigration was observed (18%). Realized pollen immigration ranged among the plots from zero to 41% and selfing ranged from zero to 5.8%. We observed an average pollen dispersal distance from 75 to 255 m, with the maximum reaching 576 m. We found a significant SGS up to 150 m, showing that near neighbour individuals are relatives. The observed data on pollen- and seed dispersal provides important information for the sustainable management of the endangered mahogany species.

scholarly journals Population structure and phylogenetic relationships in Brassica rapa L. subspecies by using isozyme markers

2020 ◽  
Author(s):  
R. H. Sammour ◽  
M. A. Karam ◽  
Y. S. Morsi ◽  
R. M. Ali
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Brassica Rapa ◽  
Phylogenetic Relationships ◽  
Fixation Index ◽  
Distribution Area ◽  
Enzyme Analysis ◽  
Breeding Programs ◽  
Expected Heterozygosity ◽  
Wide Range

Abstract The present study aimed to assess population structure and phylogenetic relationships of nine subspecies of Brassica rapa L. represented with thirty-five accessions cover a wide range of species distribution area using isozyme analysis in order to select more diverse accessions as supplementary resources that can be utilized for improvement of B. napus. Enzyme analysis resulted in detecting 14 putative polymorphic loci with 27 alleles. Mean allele frequency 0.04 (rare alleles) was observed in Cat4A and Cat4B in sub species Oleifera accession CR 2204/79 and in subspecies trilocularis accessions CR 2215/88 and CR 2244/88. The highest genetic diversity measures were observed in subspecies dichotoma, accession CR 1585/96 (the highest average of observed (H0) and expected heterozygosity (He), and number of alleles per locus (Ae)). These observations make this accession valuable genetic resource to be included in breeding programs for the improvement of oilseed B. napus. The average fixation index (F) is significantly higher than zero for the analysis accessions indicating a significant deficiency of heteozygosity. The divergence among subspecies indicated very great genetic differentiation (FST = 0.8972) which means that about 90% of genetic diversity is distributed among subspecies, while 10% of the diversity is distributed within subspecies. This coincides with low value of gene flow (Nm = 0.0287). B. rapa ssp. oleifera (turnip rape) and B. rapa ssp. trilocularis (sarson) were grouped under one cluster which coincides with the morphological classification.

scholarly journals GENOMIC DETERMINATION OF THE MOST IMPORTANT FATHER LINES OF SLOVAK PINZGAU COWS

AGROFOR ◽  
2016 ◽  
Vol 1 (3) ◽  
Author(s):  
Veronika KUKUČKOVÁ ◽  
Nina MORAVČÍKOVÁ ◽  
Radovan KASARDA
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
The State ◽  
Most Probable Number ◽  
Pedigree Data ◽  
Probable Number ◽  
Expected Heterozygosity ◽  
High Level ◽  
The Bayesian Approach

The aim of this study was to assess genetic structure of Slovak Pinzgau populationbased on polymorphism at molecular markers using statistical methods. Femaleoffspring of 12 most frequently used bulls in Slovak Pinzgau breeding programmewere investigated. Pinzgau cattle were found to have a high level of diversity,supported by the number of alleles observed across loci (average 5.31, range 2-11)and by the high within-breed expected heterozygosity (average 0.66, range 0.64-0.73). The state of genetic diversity is satisfying and standard for local populations.Detection of 12 possible subpopulation structures provided us with detailedinformation of the genetic structure. The Bayesian approach was applied, detectingthree, as the most probable number of clusters. The similarity of eachsubpopulation using microsatellites was confirmed also by high-throughputmolecular data. The observed inbreeding (FROH=2.3%) was higher than thatexpected based on pedigree data (FPED=0.4%) due to the limited number ofavailable generations in pedigree data. One of the most important steps indevelopment of efficient autochthonous breed protection programs ischaracterization of genetic variability and assessment of the population structure.The chosen set of microsatellites confirmed the suitability in determination of thesubpopulations of Pinzgau cattle in Slovakia. The state of genetic diversity at moredetailed level was successfully performed using bovineSNP50 BeadChip.

scholarly journals Oceanographic features and limited dispersal shape the population genetic structure of the vase sponge Ircinia campana in the Greater Caribbean

Heredity ◽  
2020 ◽  
Vol 126 (1) ◽  
pp. 63-76
Author(s):  
Sarah M. Griffiths ◽  
Mark J. Butler ◽  
Donald C. Behringer ◽  
Thierry Pérez ◽  
Richard F. Preziosi
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Larval Dispersal ◽  
Population Genetic ◽  
Spatial Genetic Structure ◽  
Florida Keys ◽  
The United States ◽  
Limited Dispersal ◽  
Mass Mortalities

AbstractUnderstanding population genetic structure can help us to infer dispersal patterns, predict population resilience and design effective management strategies. For sessile species with limited dispersal, this is especially pertinent because genetic diversity and connectivity are key aspects of their resilience to environmental stressors. Here, we describe the population structure of Ircinia campana, a common Caribbean sponge subject to mass mortalities and disease. Microsatellites were used to genotype 440 individuals from 19 sites throughout the Greater Caribbean. We found strong genetic structure across the region, and significant isolation by distance across the Lesser Antilles, highlighting the influence of limited larval dispersal. We also observed spatial genetic structure patterns congruent with oceanography. This includes evidence of connectivity between sponges in the Florida Keys and the southeast coast of the United States (>700 km away) where the oceanographic environment is dominated by the strong Florida Current. Conversely, the population in southern Belize was strongly differentiated from all other sites, consistent with the presence of dispersal-limiting oceanographic features, including the Gulf of Honduras gyre. At smaller spatial scales (<100 km), sites showed heterogeneous patterns of low-level but significant genetic differentiation (chaotic genetic patchiness), indicative of temporal variability in recruitment or local selective pressures. Genetic diversity was similar across sites, but there was evidence of a genetic bottleneck at one site in Florida where past mass mortalities have occurred. These findings underscore the relationship between regional oceanography and weak larval dispersal in explaining population genetic patterns, and could inform conservation management of the species.

scholarly journals Development and characterization of microsatellite loci for Cedrela fissilis Vell (Meliaceae), an endangered tropical tree species

2014 ◽  
Vol 63 (1-6) ◽  
pp. 240-243 ◽  
Author(s):  
F. B. Gandara ◽  
E. V. Tambarussi ◽  
Alexandre Magno Sebbenn ◽  
E. M. Ferraz ◽  
M. A. Moreno ◽  
...  
Keyword(s):  
Genomic Library ◽  
Population Level ◽  
Fixation Index ◽  
Allele Number ◽  
Neotropical Tree ◽  
Expected Heterozygosity ◽  
Adult Trees ◽  
Ssr Loci ◽  
Polymorphic Microsatellite

Abstract The timber of the Neotropical tree Cedrela fissilis is used in construction, shipbuilding, carpentry and for medical purposes. In this study, polymorphic microsatellite (SSR) markers derived from an enriched genomic library were characterized using 120 adult trees from four different C. fissilis populations. No substantial genotypic linkage disequilibrium was detected among all possible pairs of SSR loci. The number of alleles per locus ranged from 2 to 20, the average allele number ranged from 8 to 9.7, depending on the population. The observed heterozygosity among the different SSR loci varied from 0.0 to 1.00 , the expected heterozygosity varied from 0.07 to 0.95 On the population level, the average observed and expected heterozygosities ranged from 0.50 to 0.63 and from 0.64 to 0.70, respectively. The average fixation index among populations ranged from 0.09 to 0.24. Thus, the SSR loci revealed high poly - morphism rates and can be used to study the genetic diversity,structure, mating system, and gene flow in C. fissilis.

The genetic diversity and spatial genetic structure of the Corso-Sardinian endemicFerula arrigoniiBocchieri (Apiaceae)

Plant Biology ◽  
2014 ◽  
Vol 16 (5) ◽  
pp. 1005-1013 ◽  
Author(s):  
C. A. Dettori ◽  
S. Sergi ◽  
E. Tamburini ◽  
G. Bacchetta
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Spatial Genetic Structure

scholarly journals A new set of microsatellite loci for Cattleya walkeriana Gardner, an endangered tropical orchid species and its transferability to Cattleya loddigesii Lindl. and Cattleya nobilior Reichenbach

2017 ◽  
Vol 16 (3) ◽  
pp. 284-287
Author(s):  
Bruno C. Rossini ◽  
Mariá B. Kampa ◽  
Celso L. Marino ◽  
Fernanda Bortolanza Pereira ◽  
Fábio M. Alves ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Null Alleles ◽  
Germplasm Resources ◽  
Significant Linkage Disequilibrium ◽  
Orchid Species ◽  
Expected Heterozygosity ◽  
Tropical Orchid ◽  
Significant Linkage

AbstractIn this study, we isolate and analyse a new set of microsatellite loci for Cattleya walkeriana. Twenty-two primer pairs were screened for C. walkeriana (n = 32) and assessed for their transferability to Cattleya loddigesii (n = 12) and Cattleya nobilior (n = 06). All loci amplified for C. walkeriana; however, for C. loddigesii and C. nobilior, four and five primers, respectively, did not present amplification. The polymorphic loci presented between 2 and 13 alleles per locus for both C. walkeriana and C. loddigesii, with respective averages of 5.1 and 4.2. For C. nobilior, we found between two and five alleles per locus, with an average of 2.6. For C. walkeriana, observed heterozygosity varied from 0.100 to 0.966, whereas expected heterozygosity ranged from 0.097 to 0.900. The observed and expected heterozygosity for C. loddigesii and C. nobilior were also estimated. We found no significant linkage disequilibrium between any pair of loci, and evidence of null alleles at four loci (Cw16, Cw24, Cw30 and Cw31) for C. walkeriana. The combined power to exclude the first parent and combined non-exclusion probability of identity were 0.999 and 2.3 × 10−20, respectively. These new loci can be used in studies of germplasm resources, and assessments of genotypic and genetic diversity and population structure, thus improving the accuracy of such analyses and their applicability in the conservation and protection of these endangered species.

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