scholarly journals Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10327
Author(s):  
Ricardo M. Landínez-García ◽  
Juan Carlos Narváez ◽  
Edna J. Márquez
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Freshwater Fish ◽  
Microsatellite Loci ◽  
Natural Populations ◽  
Genetic Stock ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Genetic Stocks ◽  
Species Specific

Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.

scholarly journals Using Random Amplified Polymorphic DNA to Assess Genetic Diversity and Structure of NaturalCalophyllum brasiliense(Clusiaceae) Populations in Riparian Forests

2014 ◽  
Vol 2014 ◽  
pp. 1-8
Author(s):  
Evânia Galvão Mendonça ◽  
Anderson Marcos de Souza ◽  
Fábio de Almeida Vieira ◽  
Regiane Abjaud Estopa ◽  
Cristiane Aparecida Fioravante Reis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Random Amplified Polymorphic Dna ◽  
Natural Populations ◽  
Rio Grande ◽  
Shannon Index ◽  
High Genetic Diversity ◽  
Family Structures ◽  
Genetic Diversity And Structure ◽  
Kinship Coefficients

The objective of this study was to assess the genetic variability in two natural populations ofCalophyllum brasilienselocated along two different rivers in the state of Minas Gerais, Brazil, using RAPD molecular markers. Eighty-two polymorphic fragments were amplified using 27 primers. The values obtained for Shannon index (I) were 0.513 and 0.530 for the populations located on the margins of the Rio Grande and Rio das Mortes, respectively, demonstrating the high genetic diversity in the studied populations. Nei’s genetic diversity (He) was 0.341 for the Rio Grande population and 0.357 for the Rio das Mortes population. These results were not significantly different between populations and suggest a large proportion of heterozygote individuals within both populations. AMOVA showed that 70.42% of the genetic variability is found within populations and 29.58% is found among populations (ФST=0.2958). The analysis of kinship coefficients detected the existence of family structures in both populations. Average kinship coefficients between neighboring individuals were 0.053 (P<0.001) in Rio das Mortes and 0.040 (P<0.001) in Rio Grande. This could be due to restricted pollen and seed dispersal and the history of anthropogenic disturbance in the area. These factors are likely to contribute to the relatedness observed among these genotypes.

scholarly journals Genetic Structure and Connectivity of the Red Mangrove at Different Geographic Scales through a Complex Transverse Hydrological System from Freshwater to Marine Ecosystems

Diversity ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 48 ◽  
Author(s):  
Landy R. Chablé Iuit ◽  
Salima Machkour-M’Rabet ◽  
Julio Espinoza-Ávalos ◽  
Héctor A. Hernández-Arana ◽  
Haydée López-Adame ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Rhizophora Mangle ◽  
Inter Simple Sequence Repeat ◽  
Interesting Case ◽  
High Dispersion ◽  
Mangrove Forests ◽  
Fine Scale ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure

Mangrove forests are ecologically and economically valuable resources composed of trees morphologically and physiologically adapted to thrive across a range of habitats. Although, mangrove trees have high dispersion capacity, complexity of hydrological systems may lead to a fine-scale genetic structure (FSGS). The Transverse Coastal Corridor (TCC) is an interesting case of hydrological systems from fresh to marine waters where mangrove forests dominate. We evaluated genetic diversity and structure of Rhizophora mangle across a range of hydrological conditions within the TCC using inter-simple sequence repeat molecular markers. Sampling included four hydrological systems, two localities inside each system, and fringe and dwarf trees. Genetic differentiation was evaluated at local (<100 km) and fine (<10 km) scales through a set of analyses, and genetic diversity was evaluated at all scale levels and between fringe and dwarf physiognomic types. Rhizophora mangle exhibited a high genetic structure at both scales with high genetic diversity. The genetic structure observed among hydrological systems likely reflects the historical dispersion of mangroves, whereas the FSGS reflect contemporary processes such as seed dispersal restriction, habitat fragmentation, and local water flow regimes. A higher genetic diversity for dwarf than for fringe trees and differentiation between both physiognomic types at a fine-scale were observed and discussed.

scholarly journals Diversity and genetic structure in natural populations of Geonoma schottiana Mart (arecaceae): implications for conservation

CERNE ◽  
2011 ◽  
Vol 17 (2) ◽  
pp. 195-201 ◽  
Author(s):  
Mirian de Sousa Silva ◽  
Fábio de Almeida Vieira ◽  
Dulcinéia de Carvalho
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Natural Populations ◽  
Diversity Indices ◽  
Tropical Species ◽  
High Genetic Diversity ◽  
Minas Gerais State ◽  
Isozyme Loci ◽  
Important Food Source

Geonoma schottiana is an underbrush palm which is found in high densities in tropical forests. This species is known for having an asynchronous fruit producing pattern, over all seasons of the year, thus being an important food source for frugivores. This work aims to determine the diversity and spatial genetic structure of two natural populations, referred to as MC I and MC II, of which 60 individuals were sampled, in Poço Bonito Biological Reserve, Lavras, Minas Gerais state. Results of 10 polymorphic isozyme loci indicated a high genetic diversity for the species (Ĥe= 0.428 and Ĥo = 0.570), with an mean number of alleles per locus of 2.0. Estimates of Cockerham's coancestry coefficients indicated an absence of intrapopulation (<img border=0 width=28 height=24 src="../../../../../../img/revistas/cerne/v17n2/a06car02.jpg" > or = -0.343) and interpopulation inbreeding (<img border=0 width=26 height=26 src="../../../../../../img/revistas/cerne/v17n2/a06car01.jpg" > or = -0.161), suggesting that on average populations are not endogamous. A high genetic divergence was found between populations (<img border=0 width=26 height=27 src="../../../../../../img/revistas/cerne/v17n2/a06car03.jpg"> = 13.5%), in comparison to most tropical species (<5%). Consequently, the estimated historical gene flow was low (<img border=0 width=26 height=27 src="../../../../../../img/revistas/cerne/v17n2/a06car04.jpg">m = 0.40). The analysis of spatial distribution of G. schottiana genotypes in MCI revealed a random distribution of genotypes. The high genetic diversity indices found suggest that the populations in question favor in situ genetic conservation, consequently favoring the conservation of riparian environments.

scholarly journals Genetic diversity and structure of Astrocaryum jauari (Mart.) palm in two Amazon river basins

2014 ◽  
Vol 14 (3) ◽  
pp. 166-173 ◽  
Author(s):  
Liliane D. Santos Oliveira ◽  
Santiago L. Ferreyra Ramos ◽  
Maria T. Gomes Lopes ◽  
Gabriel Dequigiovanni ◽  
Elizabeth Ann Veasey ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Microsatellite Loci ◽  
Plant Material ◽  
Spatial Genetic Structure ◽  
River Basins ◽  
Genetic Analyses ◽  
Main River ◽  
Genetic Diversity And Structure

Astrocaryum jauari is a non-domesticated palm that is exploited by poachers. Our objective was to investigate the organization of the geneticdiversity and structure of three A. jauari populations. The study was carried out in the state of Amazonas, between the municipalities of Coari and Manaus. Nine microsatellite loci were used for the genetic analyses. High genetic variation was found, with a mean number of alleles per locus varying from 3.9 to 4.4. The average observed heterozygosity, varying from 0.71 to 0.78, was higher than expected. No spatial genetic structure was detected, since only one cluster was observed. Our results indicate a possible dispersion strategy and suggest that conservation measures of this species should focus mainly on the populations found at the end of the main river (Solimões) where most of the plant material originating from the headwaters of the tributaries of this river is concentrated.

scholarly journals Genetic diversity and structure among natural populations of Mytilaria laosensis (Hamamelidaceae) revealed by microsatellite markers

2018 ◽  
Vol 67 (1) ◽  
pp. 93-98 ◽  
Author(s):  
Niu Yu ◽  
Jie Yuan ◽  
Guangtian Yin ◽  
Jinchang Yang ◽  
Rongsheng Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Geographic Distance ◽  
Natural Populations ◽  
Magnetic Bead ◽  
Mantel Test ◽  
High Genetic Diversity ◽  
Information Index ◽  
Genetic Diversity And Structure ◽  
High Level ◽  
Mytilaria Laosensis

Abstract Mytilaria laosensis is a fast-growing tropical broadleaf tree that is extensively used for wood production and has significant ecological benefits. To investigate the genetic diversity and population structure of M. laosensis, eight major natural popu­lations in China were analyzed by using simple sequence repeat (SSR) markers. A total of 88 microsatellite-containing fragments were obtained by the method of magnetic bead enrichment, among which 26 pairs of SSR primers were scree­ned out and used to generate a total of 190 alleles among 152 individuals. The average of observed number of alleles, Shannon’s information index and polymorphism information content per locus were 18.3, 1.1577 and 0.7759, respectively, implying a high level of genetic diversity in M. laosensis popu­lations. The variation within populations accounted for 81.74 % of total variation based on analysis of molecular variance. Clus­ter analysis divided the eight populations into four groups, among which five populations from the southern parts of Guangxi province were classified as one major group. Mantel test showed that there was highly significant correlation bet­ween Euclidean genetic distance and geographic distance, suggesting that geographic isolation contribute to the high genetic diversity of M. laosensis. Together, these could provide support for the feasibility of exploration and utilization of M. laosensis in subtropical areas of East Asia including Jiangxi, Hunan and Fujian province of China.

scholarly journals Genetic structure of the carp population (Cyprinus carpio carpio) grown in the aquaculture in the Republic of Belarus

2021 ◽  
Vol 65 (1) ◽  
pp. 68-75
Author(s):  
V. A. Lemesh ◽  
V. Yu. Ageyets ◽  
A. Yu. Nosova ◽  
V. N. Kipen ◽  
N. I. Tsar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Cyprinus Carpio ◽  
Microsatellite Loci ◽  
High Genetic Diversity ◽  
Total Percentage ◽  
Cyprinus Carpio Carpio ◽  
Rare Alleles ◽  
The Republic ◽  
High Level

In this study, we presented a panel of 14 microsatellite loci (MFW1, MFW2, MFW6, MFW9, MFW10, MFW11, MFW13, MFW16, MFW20, MFW24, MFW26, MFW28, MFW29 and Cid0909), with which we studied the genetic structure of Cyprinus carpio carpio of the breed “Izobelinsky” in the Republic of Belarus. Four offshoots of carp were included in the study: two mirrory (“Smes’ zerkal’naya”, “Tri prim”) and two scaly (“Smes’ cheshujchataya”, “Stolin XVIII”).As a result, it was found that the carp breed “Izobelinsky” exhibits a high level of in-breed genetic variability. In the studied microsatellite loci, 231 alleles were identified, 62 % of the total number of alleles were rare alleles with a frequency of occurrence of less than 5.0 %. The number of effective alleles (Ne) at the loci ranged from 3.082 (MFW10) to 9.754 (MFW26). The Shannon biodiversity index (I) was 2.082 ± 0.075. The highest value of the expected heterozygosity index (He) was noted for the MFW26 locus (0.897), the lowest – for the MFW10 locus (0.676).The greatest genetic diversity is characteristic of the scaly carp “Smes’ cheshujchataya” and “Stolin XVIII”. The highest total percentage of rare alleles was determined for fishes from “Stolin XVIII”. The minimum values of this parameter were found for specimens of the carp “Smes’ zerkal’naya” and “Tri prim”.The results of this study indicate a fairly high genetic diversity of four offshoots of the carp breed “Izobelinsky”, which was established using the marker loci optimally selected for analysis. This makes it possible to differentiate the layering among themselves.

scholarly journals GENETIC DIVERSITY AND STRUCTURE OF Oenocarpus mapora GERMPLASM CONSERVED AT EASTERN AMAZON

2015 ◽  
Vol 37 (4) ◽  
pp. 984-992
Author(s):  
ELISA FERREIRA MOURA ◽  
MARIA DO SOCORRO PADILHA DE OLIVEIRA ◽  
DIEHGO TULOZA DA SILVA ◽  
LÍGIA CRISTINE GONÇALVES PONTES
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Microsatellite Loci ◽  
Natural Populations ◽  
Brazilian Amazon ◽  
Germplasm Bank ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Total Genetic Diversity ◽  
Genetic Diversity And Structure

ABSTRACT The aim of this study was to evaluate the genetic diversity and structure in the germoplasm of Oenocarpus mapora conserved at Eastern Amazon. Thus, 88 individuals were genotyped with five microsatellite loci. These individuals belong to 24 accessions that were sampled in eight sample places of three Brazilian Amazon states conserved at the Active Germplasm Bank (AGB) of Embrapa Eastern Amazon. All loci were polymorphic and they generated 85 alleles with an average of 17 alleles per loci. Total genetic diversity (HE) was 0.48. Sample places were considered genetically distinct, with ?p = 0.354. The analysis of molecular variance (AMOVA) identified that the genetic portion among areas was of 36.14% and within 63.86%. The Nei distances varied from 0.091 between Abaetetuba and Santo Antônio do Tauá, both in the state of Pará (PA), to 4.18, between Parintins, AM and Rio Branco, AC. By means of Bayesian analysis, it was identified nine clusters that compose the accessions of the germplasm bank, with different distributions among individuals. The study showed high fixation rates per sample area, which indicates that there may have been significant inbreeding or crossing among parental individuals. It suggests that future samples should be made of different plants in natural populations. Even though, it was verified that there is considerable genetic variation in the germplasm of O. mapora.

scholarly journals Effect of Human Disturbance on Genetic Structure of Rare and Endangered Paphiopedilum micranthum Implied the Habitat Status

2020 ◽  
Vol 13 ◽  
pp. 194008292094201
Author(s):  
Zongyan Li ◽  
Jing Li ◽  
Minyang Li
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Human Disturbance ◽  
Natural Populations ◽  
Species Level ◽  
High Genetic Diversity ◽  
Orchid Species ◽  
Southeast China ◽  
Rare And Endangered

Seven populations of Paphiopedilum micranthum from Southeast China were used to assess the influence of human disturbance on genetic structure through analysis with sequence-related amplified polymorphism technology. The results indicated that there was high genetic diversity at species level ( p =  81.25%; I =  0.3709) and a significantly higher differentiation level compared to that those of other outcrossing orchid species, and that moderately disturbed populations sustained higher genetic diversity indexes than the natural populations. This study revealed that human disturbance and population size did not significantly affect the populations’ genetic diversity but aggravated their differentiation. This may suggest that the habitat had a much greater influence on genetic variation.

scholarly journals Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Fehintola V. Ajogbasile ◽  
Adeyemi T. Kayode ◽  
Paul E. Oluniyi ◽  
Kazeem O. Akano ◽  
Jessica N. Uwanibe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Control Strategies ◽  
Population Diversity ◽  
Parasite Population ◽  
Nested Polymerase Chain Reaction ◽  
Public Health Burden ◽  
Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

The spatial genetic structure of bank vole (Myodes glareolus) and yellow-necked mouse (Apodemus flavicollis) populations: The effect of distance and habitat barriers

2009 ◽  
Vol 59 (2) ◽  
pp. 169-187 ◽  
Author(s):  
Michal Kozakiewicz ◽  
Alicja Gryczyńska–Siemiątkowska ◽  
Hanna Panagiotopoulou ◽  
Anna Kozakiewicz ◽  
Robert Rutkowski ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Bank Vole ◽  
Microsatellite Loci ◽  
Myodes Glareolus ◽  
Apodemus Flavicollis ◽  
Island Populations ◽  
Local Populations ◽  
Bank Vole Myodes Glareolus ◽  
Yellow Necked Mouse

AbstractHabitat barriers are considered to be an important factor causing the local reduction of genetic diversity by dividing a population into smaller sections and preventing gene flow between them. However, the “barrier effect” might be different in the case of different species. The effect of geographic distance and water barriers on the genetic structure of populations of two common rodent species – the yellow-necked mouse (Apodemus flavicollis) and the bank vole (Myodes glareolus) living in the area of a lake (on its islands and on two opposite shores) was investigated with the use of microsatellite fragment analysis. The two studied species are characterised by similar habitat requirements, but differ with regard to the socio-spatial structure of the population, individual mobility, capability to cross environmental barriers, and other factors. Trapping was performed for two years in spring and autumn in north-eastern Poland (21°E, 53°N). A total of 160 yellow-necked mouse individuals (7 microsatellite loci) and 346 bank vole individuals (9 microsatellite loci) were analysed. The results of the differentiation analyses (FST and RST) have shown that both the barrier which is formed by a ca. 300 m wide belt of water (between the island and the mainland) and the actual distance of approximately 10 km in continuous populations are sufficient to create genetic differentiation within both species. The differences between local populations living on opposite lake shores are the smallest; differences between any one of them and the island populations are more distinct. All of the genetic diversity indices (the mean number of alleles, mean allelic richness, as well as the observed and expected heterozygosity) of the local populations from the lakeshores were significantly higher than of the small island populations of these two species separated by the water barrier. The more profound “isolation effect” in the case of the island populations of the bank vole, in comparison to the yellow-necked mouse populations, seems to result not only from the lower mobility of the bank vole species, but may also be attributed to other differences in the animals' behaviour.

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