scholarly journals Enhanced genetic differentiation of Japanese chum salmon identified from a meta-analysis of allele frequencies

2019 ◽  
Author(s):  
Shuichi Kitada ◽  
Hirohisa Kishino
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Chum Salmon ◽  
Meta Analysis ◽  
Distribution Range ◽  
Allele Frequencies ◽  
Geographical Information ◽  
Data Sets ◽  
Nucleotide Polymorphisms ◽  
Athletic Ability

AbstractThe number of individuals returning to Japan, the location of the world’s largest chum salmon hatchery program, has declined substantially over two decades. To find the genetic cause of this severe decline never previously experienced, we analyzed published genetic data sets for adult chum salmon, namely, 10 microsatellites, 53 single nucleotide polymorphisms (SNPs) and a combined mitochondrial DNA locus (mtDNA3), and three isozymes, from 576 locations in the distribution range (n = 76,363). The SNPs were selected for stock identification to achieve high accuracy, were highly differentiated in the distribution range and included important genes related to reproduction, growth and immune responses. By contrasting the genetic differentiation of these genes with the population structure estimated from the neutral microsatellite markers, we identified genes that distort the neutral population structure. We matched the sampling locations of SNPs and isozymes with those of microsatellites based on geographical information, and performed regression analyses of SNP and isozyme allele frequencies of matched locations on the population structure. TreeMix analysis indicated two admixture events, from Japan/Korea to Russia and the Alaskan Peninsula. Meta-analysis of allele frequencies identified three outliers, mtDNA3 (control region and NADH-3), GnRH373 (gonadotropin-releasing hormone) and U502241 (unknown), which showed enhanced differentiation in Japanese/Korean populations compared with the others. GnRH improves stream odor discrimination and has increased expression in adult chum salmon brains during homing migration, suggesting that the current admixture was caused by GnRH373 differentiation. mtDNA plays a key role in endurance exercise training, energy metabolism and oxygen consumption, suggesting that the significant reduction in mtDNA3 allele frequencies reduced aerobic athletic ability, as observed in YouTube videos. Our analyses relied on limited data sets, though they were the best available. Clearly, genome-wide data will be needed to fully address this issue.

scholarly journals A whole-genome scan for association with invasion success in the fruit fly Drosophila suzukii using contrasts of allele frequencies corrected for population structure

2019 ◽  
Author(s):  
Laure Olazcuaga ◽  
Anne Loiseau ◽  
Hugues Parrinello ◽  
Mathilde Paris ◽  
Antoine Fraimout ◽  
...  
Keyword(s):  
Population Structure ◽  
Genome Wide Association Study ◽  
Evolutionary Model ◽  
Population Level ◽  
Allele Frequencies ◽  
Invasion Success ◽  
Nucleotide Polymorphisms ◽  
Drosophila Suzukii ◽  
A Genome ◽  
Invasive Status

AbstractEvidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we called C2, that contrasts allele frequencies corrected for population structure. This new statistical framework has been implemented in an upgraded version of the program BayPass. We identified a relatively small set of single nucleotide polymorphisms (SNPs) that show a highly significant association with the invasive status of populations. In particular, two genes RhoGEF64C and cpo, the latter contributing to natural variation in several life-history traits (including diapause) in Drosophila melanogaster, contained SNPs significantly associated with the invasive status in the two separate main invasion routes of D. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by non-equilibrium demographic conditions for which binary covariables of interest can be defined at the population level.

scholarly journals A Whole-Genome Scan for Association with Invasion Success in the Fruit Fly Drosophila suzukii Using Contrasts of Allele Frequencies Corrected for Population Structure

2020 ◽  
Vol 37 (8) ◽  
pp. 2369-2385 ◽  
Author(s):  
Laure Olazcuaga ◽  
Anne Loiseau ◽  
Hugues Parrinello ◽  
Mathilde Paris ◽  
Antoine Fraimout ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Genome Wide Association Study ◽  
Allele Frequencies ◽  
Invasion Success ◽  
Nucleotide Polymorphisms ◽  
Drosophila Suzukii ◽  
Single Nucleotide ◽  
A Genome ◽  
Invasive Status

Abstract Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here, we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we called C2, that contrasts allele frequencies corrected for population structure. We evaluated this new statistical framework using simulated data sets and implemented it in an upgraded version of the program BayPass. We identified a relatively small set of single-nucleotide polymorphisms that show a highly significant association with the invasive status of D. suzukii populations. In particular, two genes, RhoGEF64C and cpo, contained single-nucleotide polymorphisms significantly associated with the invasive status in the two separate main invasion routes of D. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by nonequilibrium demographic conditions for which binary covariables of interest can be defined at the population level.

scholarly journals EVALUACIÓN DE AMPLIFICACIÓN CRUZADA DE MICROSATÉLITES PARA ESTUDIOS DE GENÉTICA POBLACIONAL DEL CAZÓN ANTILLANO RHIZOPRIONODON POROSUS (CARCHARHINIDAE) EN EL CARIBE COLOMBIANO

2016 ◽  
Vol 45 (1) ◽  
Author(s):  
Mónica Almanza Bernal ◽  
Edna J. Márquez ◽  
Luis Chasqui
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Distribution Range ◽  
Small Scale ◽  
Formulation Development ◽  
Significant Genetic Differentiation ◽  
Fishery Resource ◽  
Genotype Frequencies ◽  
Population Structure Analysis ◽  
The Caribbean

The Caribbean sharpnose shark, Rhizoprionodon porosus is an important resource for artisanal small-scale fisheries. It is one of the most abundant coastal sharks within its distribution range, and plays an important role as a predator in coastal marine ecosystems. For its coastal habits, it is susceptible to intensive extraction, especially the juveniles. To accomplish proper management and conservation of exploited Rhizoprionodon populations, knowledge about its genetic diversity and its population structure within their distribution range is needed. The ability of heterologous primers developed for other requiem sharks to amplify microsatellite molecular markers in R. porosus was tested in this study (cross amplification). The change in allele frequency of four microsatellite loci served to assess the genetic structure of R. porosus in the Colombian Caribbean. Analysis of molecular variance Amova and population structure analysis using the Фst statistical of genotype frequencies indicate low but significant genetic differentiation among R. porosus from the departments analyzed (Фst (3,165) = 0.002; p = 0.000). Besides, the analysis of pairs of departments indicates that there is significant genetic differentiation among La Guajira and the other samples analyzed of the Antillean sharpnose shark (all p values = 0.000). The information obtained helps to understand the dynamics of natural populations of the Caribbean sharpnose shark, serving as a baseline for the formulation, development of conservation strategies and management of this fishery resource; however, due the low number of heterologous loci useful for population genetics studies, research efforts on the development of specific markers for the species should be done for further population genetic studies of this species.

scholarly journals Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 822 ◽  
Author(s):  
Kyung Jun Lee ◽  
Jung-Ro Lee ◽  
Raveendar Sebastin ◽  
Myoung-Jae Shin ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Discriminant Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Differentiation ◽  
Principal Components ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs

Watermelon is an economically important vegetable fruit worldwide. The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future breeding programs.

scholarly journals “Theory, practice, and conservation in the age of genomics: the Galápagos giant tortoise as a case study”

2017 ◽  
Author(s):  
Stephen J Gaughran ◽  
Maud C Quinzin ◽  
Joshua M Miller ◽  
Ryan C Garrick ◽  
Danielle L Edwards ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Sampling Design ◽  
Natural Populations ◽  
Molecular Techniques ◽  
Model Organisms ◽  
Strong Impact ◽  
Nucleotide Polymorphisms ◽  
Distinct Structure ◽  
Snp Data

AbstractHigh-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in non-model species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that represent three species of Galápagos giant tortoises (Chelonoidisspp.). Though microsatellite and mitochondrial DNA analyses have supported the distinctiveness of these species, a recent study called into question how well these markers matched with data from genomic SNPs, thereby questioning decades of studies in non-model organisms. Using >20,000 genome-wide SNPs from 30 individuals from three Galápagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNPs and 2-5 individuals, or hundreds of SNPs and 10 individuals, but only if the units of analysis are delineated in a way that is consistent with evolutionary history. We show that the lack of structure in the recent SNP-based study was likely due to unnatural grouping of individuals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few samples per population, and underscores the importance of sampling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions.“Modern molecular techniques provide unprecedented power to understand genetic variation in natural populations. Nevertheless, application of this information requires sound understanding of population genetics theory.”- Fred Allendorf (2017, p. 420)

scholarly journals Genetic Basis of Aerobically Supported Voluntary Exercise: Results from a Selection Experiment with House Mice

Genetics ◽  
2020 ◽  
Vol 216 (3) ◽  
pp. 781-804
Author(s):  
David A. Hillis ◽  
Liran Yadgary ◽  
George M. Weinstock ◽  
Fernando Pardo-Manuel de Villena ◽  
Daniel Pomp ◽  
...  
Keyword(s):  
Wheel Running ◽  
Allele Frequencies ◽  
Limb Bud ◽  
Exercise Behavior ◽  
Voluntary Exercise ◽  
Selection Experiment ◽  
Nucleotide Polymorphisms ◽  
Athletic Ability ◽  
Laboratory Rodents ◽  
Genomic Regions

The biological basis of exercise behavior is increasingly relevant for maintaining healthy lifestyles. Various quantitative genetic studies and selection experiments have conclusively demonstrated substantial heritability for exercise behavior in both humans and laboratory rodents. In the “High Runner” selection experiment, four replicate lines of Mus domesticus were bred for high voluntary wheel running (HR), along with four nonselected control (C) lines. After 61 generations, the genomes of 79 mice (9–10 from each line) were fully sequenced and single nucleotide polymorphisms (SNPs) were identified. We used nested ANOVA with MIVQUE estimation and other approaches to compare allele frequencies between the HR and C lines for both SNPs and haplotypes. Approximately 61 genomic regions, across all somatic chromosomes, showed evidence of differentiation; 12 of these regions were differentiated by all methods of analysis. Gene function was inferred largely using Panther gene ontology terms and KO phenotypes associated with genes of interest. Some of the differentiated genes are known to be associated with behavior/motivational systems and/or athletic ability, including Sorl1, Dach1, and Cdh10. Sorl1 is a sorting protein associated with cholinergic neuron morphology, vascular wound healing, and metabolism. Dach1 is associated with limb bud development and neural differentiation. Cdh10 is a calcium ion binding protein associated with phrenic neurons. Overall, these results indicate that selective breeding for high voluntary exercise has resulted in changes in allele frequencies for multiple genes associated with both motivation and ability for endurance exercise, providing candidate genes that may explain phenotypic changes observed in previous studies.

Allele frequency stability in large, wild exploited populations over multiple generations: insights from Alaska sockeye salmon (Oncorhynchus nerka)

2012 ◽  
Vol 69 (5) ◽  
pp. 916-929 ◽  
Author(s):  
Daniel Gomez-Uchida ◽  
James E. Seeb ◽  
Christopher Habicht ◽  
Lisa W. Seeb
Keyword(s):  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Temporal Changes ◽  
Allele Frequencies ◽  
Annual Number ◽  
Data Sets ◽  
Nucleotide Polymorphisms ◽  
Snp Data ◽  
Spatial Differences ◽  
The Stability

We genotyped nuclear and mitochondrial single nucleotide polymorphisms (SNPs) in six paired archived and contemporary collections of Alaskan sockeye salmon ( Oncorhynchus nerka ) to evaluate the stability of allele frequencies over 25–42 years (4.9–8.4 generations). First, our results show that temporal changes were dramatically (between 40- and 250-fold) smaller than spatial differences in allele frequencies when based on nuclear SNPs. Second, the magnitude of temporal change was consistent with a model of genetic drift: (i) SNPs with high levels of differentiation (large θ) and candidates for diversifying selection were not more likely to show significant temporal changes than small-θ SNPs; and (ii) the fraction of single-locus significant tests was consistent with theoretical predictions relating sample size and the annual number of breeders (Nb). Third, estimates of Nb were bound by infinitely large upper 95% confidence intervals, except for one paired collection with unique life-history attributes of both a smoltification phase and generation time shorter than the other paired collections. Use of multigenerational SNP data sets seems a safe practice in management of Alaska sockeye salmon that could be extended to other large, wild aquatic populations.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

Race-Related Association between APOE Genotype and Alzheimer’s Disease: A Systematic Review and Meta-Analysis

2021 ◽  
pp. 1-10
Author(s):  
Wei Qin ◽  
Wenwen Li ◽  
Qi Wang ◽  
Min Gong ◽  
Tingting Li ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Black People ◽  
Late Onset ◽  
Meta Analysis ◽  
Group Analysis ◽  
Apoe Genotype ◽  
Cochrane Library ◽  
Data Sets ◽  
Apoe Genotypes

Background: The global race-dependent association of Alzheimer’s disease (AD) and apolipoprotein E (APOE) genotype is not well understood. Transethnic analysis of APOE could clarify the role of genetics in AD risk across populations. Objective: This study aims to determine how race and APOE genotype affect the risks for AD. Methods: We performed a systematic search of PubMed, Embase, Web of Science, and the Cochrane Library since 1993 to Aug 25, 2020. A total of 10,395 reports were identified, and 133 were eligible for analysis with data on 77,402 participants. Studies contained AD clinical diagnostic and APOE genotype data. Homogeneous data sets were pooled in case-control analyses. Odds ratios and 95% confidence intervals for developing AD were calculated for populations of different races and APOE genotypes. Results: The proportion of APOE genotypes and alleles differed between populations of different races. Results showed that APOE ɛ4 was a risk factor for AD, whereas APOE ɛ2 protected against it. The effects of APOE ɛ4 and ɛ2 on AD risk were distinct in various races, they were substantially attenuated among Black people. Sub-group analysis found a higher frequency of APOE ɛ4/ɛ4 and lower frequency of APOE ɛ3/ɛ3 among early-onset AD than late-onset AD in a combined group and different races. Conclusion: Our meta-analysis suggests that the association of APOE genotypes and AD differ between races. These results enhance our understanding of APOE-related risk for AD across race backgrounds and provide new insights into precision medicine for AD.

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