Sea Turtle Population Genomic Discovery: Global and Locus-Specific Signatures of Polymorphism, Selection, and Adaptive Potential

Abstract In the era of genomics, single-nucleotide polymorphisms (SNPs) have become a preferred molecular marker to study signatures of selection and population structure and to enable improved population monitoring and conservation of vulnerable populations. We apply a SNP calling pipeline to assess population differentiation, visualize linkage disequilibrium, and identify loci with sex-specific genotypes of 45 loggerhead sea turtles (Caretta caretta) sampled from the southeastern coast of the United States, including 42 individuals experimentally confirmed for gonadal sex. By performing reference-based SNP calling in independent runs of Stacks, 3,901–6,998 SNPs and up to 30 potentially sex-specific genotypes were identified. Up to 68 pairs of loci were found to be in complete linkage disequilibrium, potentially indicating regions of natural selection and adaptive evolution. This study provides a valuable SNP diagnostic workflow and a large body of new biomarkers for guiding targeted studies of sea turtle genome evolution and for managing legally protected nonmodel iconic species that have high economic and ecological importance but limited genomic resources.

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Association of multiple nucleotide variations in the pituitary glutaminyl cyclase gene QPC with low radial BMD in adult women.

10.31234/osf.io/93fcq ◽

2020 ◽

Author(s):

Lungwani Muungo

Keyword(s):

Linkage Disequilibrium ◽

Multiple Regression ◽

Genetic Variations ◽

Strong Linkage Disequilibrium ◽

Adult Women ◽

Nucleotide Polymorphisms ◽

Haplotype Estimation ◽

Factors Affecting ◽

Glutaminyl Cyclase ◽

Strong Linkage

Correlation between 13 genetic variations of the glutaminyl-peptide cyclotransferase gene andadjusted aBMD was tested among 384 adult women. Among 13 variations with strong linkage disequilibrium,R54W showed a prominent association (p ? 0.0003), which was more striking when examined among 309 eldersubjects (>50 years; p ? 0.0001). Contribution for postmenopausal bone loss was suggested.Introduction: Alterations in homeostatic regulation of estrogen through the hypothalamus-pituitary-gonadal axis(HPG axis) importantly affect the pathogenesis of osteoporosis. Osteoporosis-susceptibility genes have beenproposed in this hormonal axis, such as estrogen receptor genes and the gonadotropin-releasing hormone gene(GnRH). Here we report another example of genes: glutaminyl-peptide cyclotransferase gene (QPCT), an essentialmodifier of pituitary peptide hormones, including GnRH.Materials and Methods: Analyses of association of 13 single nucleotide polymorphisms (SNPs) at the QPCT locuswith adjusted areal BMD (adj-aBMD) were carried out among 384 adult women. Linkage disequilibrium (LD) wasanalyzed by haplotype estimation and calculation of D? and r2. Multiple regression analysis was applied forevaluating the combined effects of the variations.Results and Conclusions: LD analysis indicated strong linkage disequilibrium within the entire 30-kb region of theQPCT gene. Significant correlations were observed between the genotypes of the six SNPs and the radial adj-aBMD,among which R54W (nt ? 160C?T) presented the most prominent association (p ? 0.0003). Striking associationwas observed for these SNPs among the 309 subjects ?50 years of age (R54W, p ? 0.0001; ?1095T?C, p ?0.0002; ?1844C?T, p ? 0.0002). Multiple regression analyses indicated that multiple SNPs in the gene might actin combination to determine the radial adj-aBMD. These results indicate that genetic variations in QPCT are theimportant factors affecting the BMD of adult women that contribute to susceptibility for osteoporosis. The datashould provide new insight into the etiology of the disease and may suggest a new target to be considered duringtreatment.J Bone Miner

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The Oxford Handbook of IPOs

10.1093/oxfordhb/9780190614577.001.0001 ◽

2018 ◽

Keyword(s):

United States ◽

Initial Public Offerings ◽

Financial Regulation ◽

Large Body ◽

Public Information ◽

The United States ◽

Minimum Size ◽

Stock Exchanges ◽

Public Offerings ◽

Firm’S Life Cycle

Firms generally begin as privately owned entities. When they grow large enough, the decision to go public and its consequences are among the most crucial times in a firm’s life cycle. The first time a firm is a reporting issuer gives rise to tremendous responsibilities about disclosing public information and accountability to a wide array of retail shareholders and institutional investors. Initial public offerings (IPOs) offer tremendous opportunities to raise capital. The economic and legal landscape for IPOs has been rapidly evolving across countries. There have been fewer IPOs in the United States in the aftermath of the 2007–2009 financial crisis and associated regulatory reforms that began in 2002. In 1980–2000, an average of 310 firms went public every year, while in 2001–2014 an average of 110 firms went public every year. At the same time, there are so many firms that seek an IPO in China that there has been a massive waiting list of hundreds of firms in recent years. Some countries are promoting small junior stock exchanges to go public early, and even crowdfunding to avoid any prospectus disclosure. Financial regulation of analysts and investment banks has been evolving in ways that drastically impact the economics of going public—in some countries, such as the United States, drastically increasing the minimum size of a company before it can expect to go public. This Handbook not only systematically and comprehensively consolidates a large body of literature on IPOs, but provides a foundation for future debates and inquiry.

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Protein Variation in ADH and ADH-RELATED in Drosophila pseudoobscura: Linkage Disequilibrium Between Single Nucleotide Polymorphisms and Protein Alleles

Genetics ◽

10.1093/genetics/159.2.673 ◽

2001 ◽

Vol 159 (2) ◽

pp. 673-687

Author(s):

Stephen W Schaeffer ◽

C Scott Walthour ◽

Donna M Toleno ◽

Anna T Olek ◽

Ellen L Miller

Keyword(s):

Linkage Disequilibrium ◽

Single Nucleotide Polymorphisms ◽

Drosophila Pseudoobscura ◽

Linkage Disequilibrium Mapping ◽

Nucleotide Polymorphisms ◽

Neutral Model ◽

Significant Linkage Disequilibrium ◽

Single Nucleotide ◽

Synonymous Sites ◽

Significant Linkage

Abstract A 3.5-kb segment of the alcohol dehydrogenase (Adh) region that includes the Adh and Adh-related genes was sequenced in 139 Drosophila pseudoobscura strains collected from 13 populations. The Adh gene encodes four protein alleles and rejects a neutral model of protein evolution with the McDonald-Kreitman test, although the number of segregating synonymous sites is too high to conclude that adaptive selection has operated. The Adh-related gene encodes 18 protein haplotypes and fails to reject an equilibrium neutral model. The populations fail to show significant geographic differentiation of the Adh-related haplotypes. Eight of 404 single nucleotide polymorphisms (SNPs) in the Adh region were in significant linkage disequilibrium with three ADHR protein alleles. Coalescent simulations with and without recombination were used to derive the expected levels of significant linkage disequilibrium between SNPs and 18 protein haplotypes. Maximum levels of linkage disequilibrium are expected for protein alleles at moderate frequencies. In coalescent models without recombination, linkage disequilibrium decays between SNPs and high frequency haplotypes because common alleles mutate to haplotypes that are rare or that reach moderate frequency. The implication of this study is that linkage disequilibrium mapping has the highest probability of success with disease-causing alleles at frequencies of 10%.

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PSV-13 Genetic parameters and quantitative trait loci for heat stress related traits in sheep

Journal of Animal Science ◽

10.1093/jas/skaa054.289 ◽

2020 ◽

Vol 98 (Supplement_3) ◽

pp. 163-164

Author(s):

Devin R Jacobs ◽

Claudia E Silvera-Rojas ◽

Jennifer M Bormann ◽

Terry A Gipson ◽

Arthur L Goetsch ◽

...

Keyword(s):

Heat Stress ◽

Quantitative Trait Loci ◽

Rectal Temperature ◽

Quantitative Trait ◽

Fixed Effects ◽

Univariate Analysis ◽

Average Daily Gain ◽

The United States ◽

Nucleotide Polymorphisms ◽

Trait Loci

Abstract Greater selection emphasis has been placed on efficiency than on fitness in livestock populations over the last several decades. Heat stress is a concern in production systems due to the negative effects on production, reproduction, and immunity. The objective of the study was to estimate variance components and identify quantitative trait loci (QTL) for heat stress related traits in sheep. A total of 125 Dorper, Katahdin, and St. Croix ewes originating from four regions of the United States were selected for the experiment. Animals were separated into four trials due to facility limitations. Data were collected for each trial over four consecutive two-week periods in an environmentally controlled facility with targeted heat load index (HLI) for daytime/nighttime of 70/70, 85/77, 90/77, and 95/81. Body weight was collected three times per week and rectal temperature was collected weekly. Black globe temperature and humidity were measured every 15 minutes. Animals were genotyped using the Illumina OvineSNP50 BeadChip. After quality control, 49,396 effective single nucleotide polymorphisms were included in the univariate analysis performed with the BLUPF90 suite of programs. Fixed effects in the models included region of origin, breed, trial, and age as a covariate. Traits analyzed included rectal temperature at 95 HLI (RT95), feed intake at 95 HLI (FI95), and average daily gain for the period for HLI between 90 and 95 (ADG). Heritabilities for RT95, FI95, and ADG were 0.35, 0.10, and 0.10, respectively. Largest effect QTL were identified on chromosomes 23, 9, and 6 for RT95, chromosomes 9, 2, and 20 for FI95, and chromosomes 6, 1, and 5 for ADG. Many of the regions identified have also been associated with weight and carcass traits in other studies, but few had obvious connections to the heat stress related response. In conclusion, results suggest selection could improve heat tolerance in sheep.

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Genomic selection in French dairy cattle

Animal Production Science ◽

10.1071/an11119 ◽

2012 ◽

Vol 52 (3) ◽

pp. 115 ◽

Cited By ~ 63

Author(s):

D. Boichard ◽

F. Guillaume ◽

A. Baur ◽

P. Croiseau ◽

M. N. Rossignol ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Genomic Selection ◽

Reference Population ◽

Specific Reference ◽

Nucleotide Polymorphisms ◽

Genomic Evaluation ◽

Linear Unbiased Prediction ◽

Best Linear Unbiased ◽

Estimated Breeding Values ◽

Restricted Use

Genomic selection is implemented in French Holstein, Montbéliarde, and Normande breeds (70%, 16% and 12% of French dairy cows). A characteristic of the model for genomic evaluation is the use of haplotypes instead of single-nucleotide polymorphisms (SNPs), so as to maximise linkage disequilibrium between markers and quantitative trait loci (QTLs). For each trait, a QTL-BLUP model (i.e. a best linear unbiased prediction model including QTL random effects) includes 300–700 trait-dependent chromosomal regions selected either by linkage disequilibrium and linkage analysis or by elastic net. This model requires an important effort to phase genotypes, detect QTLs, select SNPs, but was found to be the most efficient one among all tested ones. QTLs are defined within breed and many of them were found to be breed specific. Reference populations include 1800 and 1400 bulls in Montbéliarde and Normande breeds. In Holstein, the very large reference population of 18 300 bulls originates from the EuroGenomics consortium. Since 2008, ~65 000 animals have been genotyped for selection by Labogena with the 50k chip. Bulls genomic estimated breeding values (GEBVs) were made official in June 2009. In 2010, the market share of the young bulls reached 30% and is expected to increase rapidly. Advertising actions have been undertaken to recommend a time-restricted use of young bulls with a limited number of doses. In January 2011, genomic selection was opened to all farmers for females. Current developments focus on the extension of the method to a multi-breed context, to use all reference populations simultaneously in genomic evaluation.

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Linkage and linkage disequilibrium analysis of the lipoprotein lipase gene with lipid profiles in Chinese hypertensive families

Clinical Science ◽

10.1042/cs20040101 ◽

2005 ◽

Vol 108 (2) ◽

pp. 137-142 ◽

Cited By ~ 5

Author(s):

Wenjie YANG ◽

Jianfeng HUANG ◽

Cailiang YAO ◽

Shaoyong SU ◽

Donghai LIU ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Lipoprotein Lipase ◽

Lipid Profiles ◽

Strong Linkage Disequilibrium ◽

Nucleotide Polymorphisms ◽

Linkage Disequilibrium Analysis ◽

Lipid Levels ◽

Lipase Gene ◽

Significant Independent Risk Factor ◽

Lpl Gene

Elevated TG [triacylglycerol (triglyceride)] is a significant independent risk factor for cardiovascular disease. LPL (lipoprotein lipase) is one of the key enzymes in the metabolism of the TG-rich lipoproteins which hydrolyses TG from the chylomicrons and very-LDL (low-density lipoprotein). To investigate the relationship between the LPL gene and lipid profiles, especially TG, in 148 hypertensive families, we have chosen seven flanking microsatellite markers and four internal markers of the LPL gene and conducted linkage analysis by SOLAR and S.A.G.E. (statistical analysis for genetic epidemiology)/SIBPAL 2 programs, and linkage disequilibrium analysis by QTDT (quantitative transmission/disequilibrium test) and GOLD (graphical overview of linkage disequilibrium). There were statistically significant differences in lipid levels between subjects without and with hypertension within families. A maximum LOD score of 1.3 with TG at the marker D8S261 was observed by SOLAR. Using S.A.G.E./SIBPAL 2, we identified a linkage with TG at the marker ‘ATTT’ located within intron 6 of the LPL gene (P=0.0095). Two SNPs (single nucleotide polymorphisms), HindIII and HinfI, were found in linkage disequilibrium with LDL-cholesterol levels (P=0.0178 and P=0.0088 respectively). A strong linkage disequilibrium was observed between the HindIII in intron 8 and HinfI in the exon 9 (P<0.00001, D′=0.895). Linkage disequilibrium was also found between the ‘ATTT’ polymorphism in intron 6 and two SNPs (P=0.0021 and D′=0.611 for HindIII; and P=0.00004, D′=0.459 for HinfI). The present study in the Chinese families with hypertension suggested that the LPL gene might influence lipid levels, especially TG metabolism. Replication studies both in Chinese and other populations are warranted to confirm these results.

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Cyber Place Management and Crime Prevention: The Effectiveness of Cybersecurity Awareness Training Against Phishing Attacks

Journal of Contemporary Criminal Justice ◽

10.1177/10439862211001628 ◽

2021 ◽

pp. 104398622110016

Author(s):

Sinchul Back ◽

Rob T. Guerette

Keyword(s):

Crime Prevention ◽

Research University ◽

Management Strategies ◽

Large Body ◽

The United States ◽

Place Management ◽

Online Setting ◽

Using Data ◽

Virtual Domain ◽

The Impact

Criminologists and crime prevention practitioners recognize the importance of geographical places to crime activities and the role that place managers might play in effectively preventing crime. Indeed, over the past several decades, a large body of work has highlighted the tendency for crime to concentrate across an assortment of geographic areas, where place management tends to be absent or weak. Nevertheless, there has been a paucity of research evaluating place management strategies and cybercrime within the virtual domain. The purpose of this study was to investigate the effectiveness of place management techniques on reducing cybercrime incidents in an online setting. Using data derived from the information technology division of a large urban research university in the United States, this study evaluated the impact of an anti-phishing training program delivered to employees that sought to increase awareness and understanding of methods to better protect their “virtual places” from cybercrimes. Findings are discussed within the context of the broader crime and place literature.

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Manage the Risk of Turbine Rotor Failure

ASME 2010 Power Conference ◽

10.1115/power2010-27161 ◽

2010 ◽

Author(s):

David Yates ◽

Angelo Tarantino ◽

Joop Kraijesteijn

Keyword(s):

Ultrasonic Transducer ◽

Large Body ◽

The United States ◽

Turbine Rotor ◽

Operational Reliability ◽

Ultrasonic Transducers ◽

Economic Costs ◽

Utility Industry ◽

Power Generation Equipment ◽

Accepted Practice

Turbine rotors failure has resulted in a broad spectrum of events ranging from catastrophic burst to prolonged forced outages that ultimately have significant economic costs for affected utilities. Avoiding turbine rotor failure and its associated cost requires a detailed understanding of the operational reliability of power generation equipment. Nearly all large body turbine and generator rotors manufactured in the United States typically have a central bore hole that provides suitable access from which to conduct various material inspections. The term “boresonics” has become synonymous with the procedure for performing ultrasonic examination of turbine rotor material as conducted from the surface of a central bore cavity. Boresonics is now a fairly common and accepted practice throughout the utility industry. In general, boresonics involves passing ultrasonic transducers through the rotor bore to search a given volume of material for flaws at different locations and orientations within a rotor forging. Each individual ultrasonic transducer has specific inherent performance characteristics based on known wave physics that governs the art of ultrasonic testing. The results of boresonic inspections offer utility engineers a basis for making intelligent decisions on the condition of turbine and generator rotors. This paper describes how boresonic inspections are typically performed in the industry. Furthermore, the paper will give a description of the equipment and required skills of the system operators and will present examples of findings based on KEMA’s experience in this field.

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mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

BMC Bioinformatics ◽

10.1186/s12859-020-03945-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Bing Song ◽

August E. Woerner ◽

John Planz

Keyword(s):

Population Genetics ◽

Linkage Disequilibrium ◽

Genetic Markers ◽

Software Package ◽

Tandem Repeats ◽

Population Data ◽

Real Data ◽

R Package ◽

Nucleotide Polymorphisms ◽

Mutual Independence

Abstract Background Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessments. Generally, pairwise non-random associations are tested by linkage disequilibrium; however, the dependence of one panel might be triplet, quartet, or other. Therefore, a compatible and user-friendly software is necessary for testing and assessing the global linkage disequilibrium among mixed genetic data. Results This study describes a software package for testing the mutual independence of mixed genetic datasets. Mutual independence is defined as no non-random associations among all subsets of the tested panel. The new R package “mixIndependR” calculates basic genetic parameters like allele frequency, genotype frequency, heterozygosity, Hardy–Weinberg equilibrium, and linkage disequilibrium (LD) by mutual independence from population data, regardless of the type of markers, such as simple nucleotide polymorphisms, short tandem repeats, insertions and deletions, and any other genetic markers. A novel method of assessing the dependence of mixed genetic panels is developed in this study and functionally analyzed in the software package. By comparing the observed distribution of two common summary statistics (the number of heterozygous loci [K] and the number of share alleles [X]) with their expected distributions under the assumption of mutual independence, the overall independence is tested. Conclusion The package “mixIndependR” is compatible to all categories of genetic markers and detects the overall non-random associations. Compared to pairwise disequilibrium, the approach described herein tends to have higher power, especially when number of markers is large. With this package, more multi-functional or stronger genetic panels can be developed, like mixed panels with different kinds of markers. In population genetics, the package “mixIndependR” makes it possible to discover more about admixture of populations, natural selection, genetic drift, and population demographics, as a more powerful method of detecting LD. Moreover, this new approach can optimize variants selection in disease studies and contribute to panel combination for treatments in multimorbidity. Application of this approach in real data is expected in the future, and this might bring a leap in the field of genetic technology. Availability The R package mixIndependR, is available on the Comprehensive R Archive Network (CRAN) at: https://cran.r-project.org/web/packages/mixIndependR/index.html.

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Phylogeographic Analysis Reveals Multiple International transmission Events Have Driven the Global Emergence of Escherichia coli O157:H7

Clinical Infectious Diseases ◽

10.1093/cid/ciy919 ◽

2018 ◽

Vol 69 (3) ◽

pp. 428-437 ◽

Cited By ~ 8

Author(s):

Eelco Franz ◽

Ovidiu Rotariu ◽

Bruno S Lopes ◽

Marion MacRae ◽

James L Bono ◽

...

Keyword(s):

United States ◽

Disease Outbreaks ◽

The United States ◽

Human Case ◽

Whole Genome Sequencing Data ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

E Coli ◽

Phylogeographic Analysis ◽

International Distribution

AbstractBackgroundShiga toxin–producing Escherchia coli (STEC) O157:H7 is a zoonotic pathogen that causes numerous food and waterborne disease outbreaks. It is globally distributed, but its origin and the temporal sequence of its geographical spread are unknown.MethodsWe analyzed whole-genome sequencing data of 757 isolates from 4 continents, and performed a pan-genome analysis to identify the core genome and, from this, extracted single-nucleotide polymorphisms. A timed phylogeographic analysis was performed on a subset of the isolates to investigate its worldwide spread.ResultsThe common ancestor of this set of isolates occurred around 1890 (1845–1925) and originated from the Netherlands. Phylogeographic analysis identified 34 major transmission events. The earliest were predominantly intercontinental, moving from Europe to Australia around 1937 (1909–1958), to the United States in 1941 (1921–1962), to Canada in 1960 (1943–1979), and from Australia to New Zealand in 1966 (1943–1982). This pre-dates the first reported human case of E. coli O157:H7, which was in 1975 from the United States.ConclusionsInter- and intra-continental transmission events have resulted in the current international distribution of E. coli O157:H7, and it is likely that these events were facilitated by animal movements (eg, Holstein Friesian cattle). These findings will inform policy on action that is crucial to reduce the further spread of E. coli O157:H7 and other (emerging) STEC strains globally.

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