scholarly journals Genome-wide developed microsatellites reveal a weak population differentiation in the hoverflyEupeodes corollae(Diptera: Syrphidae) across China

2019 ◽  
Author(s):  
Meng-Jia Liu ◽  
Xiao-qiang Wang ◽  
Ling Ma ◽  
Li-Jun Cao ◽  
Hong-Ling Liu ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Northern China ◽  
High Rate ◽  
Genomic Sequences ◽  
Genome Wide ◽  
Geographical Populations ◽  
Plant Pollinator ◽  
Strict Selection

AbstractThe hoverfly,Eupeodes corollae,is a worldwide natural enemy of aphids and a plant pollinator. To provide insights into the biology of this species, we examined its population genetic structure by obtaining 1.15-GB random genomic sequences using next-generation sequencing and developing genome-wide microsatellite markers. A total of 79,138 microsatellite loci were initially isolated from the genomic sequences; after strict selection and further testing of 40 primer pairs in eight individuals, 24 polymorphic microsatellites with high amplification rates were developed. These microsatellites were used to examine the population genetic structure of 96 individuals from four field populations collected across southern to northern China. The number of alleles per locus ranged from 5 to 13 with an average of 8.75; the observed and expected heterozygosity varied from 0.235 to 0.768 and from 0.333 to 0.785, respectively. Population genetic structure analysis showed weak genetic differentiation among the four geographical populations ofE. corollae, suggesting a high rate of gene flow reflecting likely widespread migration ofE. corollaein China.

scholarly journals Population genetic structure and genetic diversity study in Lallemantia royleana (Benth.) Benth.: identification of potential gene pools in Iran

Hacquetia ◽  
2019 ◽  
Vol 18 (1) ◽  
pp. 97-104
Author(s):  
Fahimed Koohdar ◽  
Masoud Sheidai ◽  
Seyed Mehdi Talebi
Keyword(s):  
Genetic Structure ◽  
Medicinal Plants ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Point Of View ◽  
Gene Pools ◽  
Economic Point ◽  
Geographical Regions ◽  
Geographical Populations ◽  
Genetic Diversity Study

Abstract Lallemantia royleana (Benth.) Benth. (Family Lamiaceae), is one of the most popular medicinal plants in Iran. It is an herbaceous pant that is commonly known as “Lady mantle”. The vernacular name of Lallemantia royleana’s seed is Balangu or Balangu Shirazi that is used as a source of medicine. Medicinal plants are very important from economic point of view in Iran and several large industries are focused on medicinal plants cultivation, extraction and export. Therefore, providing data on the biology of these plants is important for the country. Lallemantia royleana grows in different parts of Iran and forms several local populations. Genetic, morphological and biochemical divergence of geographical populations are well known in plant species. We have no report on population genetic structure, genetic fragmentation, local adaptation and gen flow of Lallemantia royleana populations in the country. Therefore, the present population genetics investigation was programmed to produce data on above said questions. Randomly collected plants of 7 geographical regions were studied by ISSR molecular markers. This information can be used in hybridization and gene conservation of this medicinal plant in Iran.

scholarly journals Genome-wide analysis clarifies the population genetic structure of wild gilthead sea bream (Sparus aurata)

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0236230
Author(s):  
Francesco Maroso ◽  
Konstantinos Gkagkavouzis ◽  
Sabina De Innocentiis ◽  
Jasmien Hillen ◽  
Fernanda do Prado ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Gilthead Sea Bream ◽  
Sea Bream ◽  
North East ◽  
Genome Wide ◽  
Distribution Ranges ◽  
In The Wild ◽  
The Mediterranean

Gilthead sea bream is an important target for both recreational and commercial fishing in Europe, where it is also one of the most important cultured fish. Its distribution ranges from the Mediterranean to the African and European coasts of the North-East Atlantic. Until now, the population genetic structure of this species in the wild has largely been studied using microsatellite DNA markers, with minimal genetic differentiation being detected. In this geographically widespread study, 958 wild gilthead sea bream from 23 locations within the Mediterranean Sea and Atlantic Ocean were genotyped at 1159 genome-wide SNP markers by RAD sequencing. Outlier analyses identified 18 loci potentially under selection. Neutral marker analyses identified weak subdivision into three genetic clusters: Atlantic, West, and East Mediterranean. The latter group could be further subdivided into an Ionian/Adriatic and an Aegean group using the outlier markers alone. Seascape analysis suggested that this differentiation was mainly due to difference in salinity, this being also supported by preliminary genomic functional analysis. These results are of fundamental importance for the development of proper management of this species in the wild and are a first step toward the study of the potential genetic impact of the sea bream aquaculture industry.

scholarly journals A genome-wide data assessment of the African lion (Panthera leo) population genetic structure and diversity in Tanzania

PLoS ONE ◽  
2018 ◽  
Vol 13 (11) ◽  
pp. e0205395 ◽  
Author(s):  
Nathalie Smitz ◽  
Olivia Jouvenet ◽  
Fredrick Ambwene Ligate ◽  
William-George Crosmary ◽  
Dennis Ikanda ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Panthera Leo ◽  
African Lion ◽  
Genome Wide ◽  
A Genome ◽  
Data Assessment ◽  
Genome Wide Data ◽  
Genetic Structure And Diversity

Gene-ecological zonation and population genetic structure of Tectona grandis L.f. in India revealed by genome-wide SSR markers

2021 ◽  
Vol 17 (4) ◽  
Author(s):  
Swathi Balakrishnan ◽  
Suma Arun Dev ◽  
Ambothi Rathnasamy Sakthi ◽  
Balasubramanian Vikashini ◽  
Reshma Bhasker T ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Ssr Markers ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Tectona Grandis ◽  
Genome Wide ◽  
Ecological Zonation ◽  
Tectona Grandis L.F

scholarly journals Population Genetic Structure and Contribution of Philippine Chickens to the Pacific Chicken Diversity Inferred From Mitochondrial DNA

2021 ◽  
Vol 12 ◽  
Author(s):  
Cyrill John P. Godinez ◽  
Peter June D. Dadios ◽  
Dinah M. Espina ◽  
Megumi Matsunaga ◽  
Masahide Nishibori
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Structure ◽  
Southeast Asia ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
The Philippines ◽  
Population History ◽  
High Rate ◽  
Haplotypic Diversity ◽  
Neutrality Tests

The Philippines is considered one of the biodiversity hotspots for animal genetic resources. In spite of this, population genetic structure, genetic diversity, and past population history of Philippine chickens are not well studied. In this study, phylogeny reconstruction and estimation of population genetic structure were based on 107 newly generated mitochondrial DNA (mtDNA) complete D-loop sequences and 37 previously published sequences of Philippine chickens, consisting of 34 haplotypes. Philippine chickens showed high haplotypic diversity (Hd = 0.915 ± 0.011) across Southeast Asia and Oceania. The phylogenetic analysis and median-joining (MJ) network revealed predominant maternal lineage haplogroup D classified throughout the population, while support for Philippine–Pacific subclade was evident, suggesting a Philippine origin of Pacific chickens. Here, we observed Philippine red junglefowls (RJFs) at the basal position of the tree within haplogroup D indicating an earlier introduction into the Philippines potentially via mainland Southeast Asia (MSEA). Another observation was the significantly low genetic differentiation and high rate of gene flow of Philippine chickens into Pacific chicken population. The negative Tajima’s D and Fu’s Fs neutrality tests revealed that Philippine chickens exhibited an expansion signal. The analyses of mismatch distribution and neutrality tests were consistent with the presence of weak phylogeographic structuring and evident population growth of Philippine chickens (haplogroup D) in the islands of Southeast Asia (ISEA). Furthermore, the Bayesian skyline plot (BSP) analysis showed an increase in the effective population size of Philippine chickens, relating with human settlement, and expansion events. The high level of genetic variability of Philippine chickens demonstrates conservation significance, thus, must be explored in the future.

scholarly journals Population genomic SNPs from epigenetic RADs: gaining genetic and epigenetic data from a single established next-generation sequencing approach

2019 ◽  
Author(s):  
M. Crotti ◽  
C.E. Adams ◽  
K.R. Elmer
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
List Type ◽  
Summary Statistics ◽  
Next Generation ◽  
Population Genomic ◽  
Genome Wide ◽  
Generation Sequencing

SummaryEpigenetics is increasingly recognised as an important molecular mechanism underlying phenotypic variation. To study DNA methylation in ecological and evolutionary contexts, epiRADseq is a cost-effective next-generation sequencing technique based on reduced representation sequencing of genomic regions surrounding non-/methylated sites. EpiRADseq for genome-wide methylation abundance and ddRADseq for genome-wide SNP genotyping follow very similar library and sequencing protocols, but to date these two types of dataset have been handled separately. Here we test the performance of using epiRADseq data to generate SNPs for population genomic analyses.We tested the robustness of using epiRADseq data for population genomics with two independent datasets: a newly generated single-end dataset for the European whitefish Coregonus lavaretus, and a re-analysis of publicly available, previously published paired-end data on corals. Using standard bioinformatic pipelines with a reference genome and without (i.e. de novo catalogue loci), we compared the number of SNPs retained, population genetic summary statistics, and population genetic structure between data drawn from ddRADseq and epiRADseq library preparations.We find that SNPs drawn from epiRADseq are similar in number to those drawn from ddRADseq, with a 55-83% of SNPs being identified by both methods. Genotyping error rate was <5% in both approaches. For summary statistics such as heterozygosity and nucleotide diversity, there is a strong correlation between methods (Spearman’s rho > 0.88). Furthermore, identical patterns of population genetic structure were recovered using SNPs from epiRADseq and ddRADseq approaches.We show that SNPs obtained from epiRADseq are highly similar to those from ddRADseq and are equivalent for estimating genetic diversity and population structure. This finding is particularly relevant to researchers interested in genetics and epigenetics on the same individuals because using a single epigenomic approach to generate two datasets greatly reduces the time and financial costs compared to using these techniques separately. It also efficiently enables correction of epigenetic estimates with population genetic data. Many studies will benefit from a combinatorial approach with genetic and epigenetic markers and this demonstrates a single, efficient method to do so.

Comparative population genetic structure in a plant-pollinator/seed predator system

2011 ◽  
Vol 20 (22) ◽  
pp. 4618-4630 ◽  
Author(s):  
ISABEL S. MAGALHAES ◽  
GABRIELA GLEISER ◽  
ANNE-MARIE LABOUCHE ◽  
GIORGINA BERNASCONI
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Seed Predator ◽  
Plant Pollinator ◽  
Predator System ◽  
Comparative Population
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