scholarly journals BetaScan2: Standardized Statistics to Detect Balancing Selection Utilizing Substitution Data

2020 ◽  
Vol 12 (2) ◽  
pp. 3873-3877 ◽  
Author(s):  
Katherine M Siewert ◽  
Benjamin F Voight
Keyword(s):  
Software Package ◽  
Balancing Selection ◽  
Summary Statistics ◽  
Missense Mutations ◽  
1000 Genomes ◽  
Polymorphism Data

Abstract Long-term balancing selection results in a build-up of alleles at similar frequencies and a deficit of substitutions when compared with an outgroup at a locus. The previously published β(1) statistics detect balancing selection using only polymorphism data. We now propose the β(2) statistic which detects balancing selection using both polymorphism and substitution data. In addition, we derive the variance of all β statistics, allowing for their standardization and thereby reducing the influence of parameters which can confound other selection tests. The standardized β statistics outperform existing summary statistics in simulations, indicating β is a well-powered and widely applicable approach for detecting balancing selection. We apply the β(2) statistic to 1000 Genomes data and report two missense mutations with high β scores in the ACSBG2 gene. An implementation of all β statistics and their standardization are available in the BetaScan2 software package at https://github.com/ksiewert/BetaScan.

scholarly journals Recent Selection Changes in Human Genes under Long-Term Balancing Selection

2016 ◽  
Vol 33 (6) ◽  
pp. 1435-1447 ◽  
Author(s):  
Cesare de Filippo ◽  
Felix M. Key ◽  
Silvia Ghirotto ◽  
Andrea Benazzo ◽  
Juan R. Meneu ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Human Genes ◽  
Recent Selection

Supergene degeneration opposes polymorphism: The curious case of balanced lethals

2021 ◽  
Author(s):  
Emma Berdan ◽  
Alexandre Blanckaert ◽  
Roger K Butlin ◽  
Thomas Flatt ◽  
Tanja Slotte ◽  
...  
Keyword(s):  
Equilibrium State ◽  
Balancing Selection ◽  
Mutation Accumulation ◽  
Small Population ◽  
Quasi Equilibrium ◽  
Deleterious Mutations ◽  
Critical Factors ◽  
Critical Aspect ◽  
Allopatric Divergence

Supergenes offer some of the most spectacular examples of long-term balancing selection in nature but their origin and maintenance remain a mystery. A critical aspect of supergenes is reduced recombination between arrangements. Reduced recombination protects adaptive multi-trait phenotypes, but can also lead to degeneration through mutation accumulation. Mutation accumulation can stabilize the system through the emergence of associative overdominance (AOD), destabilize the system, or lead to new evolutionary outcomes. One such outcome is the formation of balanced lethal systems, a maladaptive system where both supergene arrangements have accumulated deleterious mutations to the extent that both homozygotes are inviable, leaving only heterozygotes to reproduce. Here, we perform a simulation study to understand the conditions under which these different outcomes occur, assuming a scenario of introgression after allopatric divergence. We found that AOD aids the invasion of a new supergene arrangement and the establishment of a polymorphism. However, this polymorphism is easily destabilized by further mutation accumulation. While degradation may strengthen AOD, thereby stabilizing the supergene polymorphism, it is often asymmetric, which is the key disrupter of the quasi-equilibrium state of the polymorphism. Furthermore, mechanisms that accelerate degeneration also tend to amplify asymmetric mutation accumulation between the supergene arrangements and vice versa. As the evolution of a balanced lethal system requires symmetric degradation of both arrangements, this leaves highly restricted conditions under which such a system could evolve. We show that small population size and low dominance coefficients are critical factors, as these reduce the efficacy of selection. The dichotomy between the persistence of a polymorphism and degradation of supergene arrangements likely underlies the rarity of balanced lethal systems in nature.

scholarly journals Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching

2019 ◽  
Author(s):  
Zachary L. Fuller ◽  
Veronique J.L. Mocellin ◽  
Luke Morris ◽  
Neal Cantin ◽  
Jihanne Shepherd ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Genome Wide Association ◽  
Conservation Strategies ◽  
Genome Sequences ◽  
Acropora Millepora ◽  
Genome Wide ◽  
A Genome ◽  
In The Wild

AbstractAlthough reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

Quantitative Analysis of Agricultural and Food Products: A New Instrumental and Computerized Approach

1992 ◽  
Vol 75 (1) ◽  
pp. 18-25 ◽  
Author(s):  
Bertrand S Lanher
Keyword(s):  
Fourier Transform ◽  
Quantitative Analysis ◽  
Software Package ◽  
Flow Cell ◽  
Infrared Spectrometry ◽  
Fourier Transform Infrared Spectrometry ◽  
Calibration And Validation ◽  
Study Results ◽  
Validation Standard

Abstract A new software package, ANAQUANT, was specifically designed for a long-term approach to the quantitation of compounds In biological products. Its functionality and validity were tested by measuring fat and protein contents In liquid cow's milk using Fourier transform Infrared spectrometry and a handcrafted transmission flow cell. Calibration and validation standard deviations were 0.2484 and 0.3987 g/kg, respectively, for the prediction of proteins, and 0.3163 and 0.4222 g/L, respectively, for the prediction of butterfat. One month elapsed between calibration of the Instrument and the validation study. Results are consistent with those proposed in the literature.

scholarly journals Long-Term Balancing Selection at the Blood Group-Related Gene B4galnt2 in the Genus Mus (Rodentia; Muridae)

2011 ◽  
Vol 28 (11) ◽  
pp. 2999-3003 ◽  
Author(s):  
Miriam Linnenbrink ◽  
Jill M. Johnsen ◽  
Inka Montero ◽  
Christine R. Brzezinski ◽  
Bettina Harr ◽  
...  
Keyword(s):  
Blood Group ◽  
Balancing Selection ◽  
Related Gene

scholarly journals Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect

2017 ◽  
Vol 26 (22) ◽  
pp. 6189-6205 ◽  
Author(s):  
Dorothea Lindtke ◽  
Kay Lucek ◽  
Víctor Soria-Carrasco ◽  
Romain Villoutreix ◽  
Timothy E. Farkas ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Stick Insect ◽  
Chromosomal Variants

Unraveling Human Cleft Lip and Palate Research

2008 ◽  
Vol 87 (2) ◽  
pp. 119-125 ◽  
Author(s):  
A.R. Vieira
Keyword(s):  
Statistical Power ◽  
Cleft Lip ◽  
Cleft Lip And Palate ◽  
Current Knowledge ◽  
Missense Mutations ◽  
Definitive Evidence ◽  
Maternal Cigarette Smoking ◽  
Gene Environment ◽  
Functional Variant

The focus of this work is to highlight the most recent advances in the understanding of cleft lip and palate occurrence. Information regarding research on long-term outcomes, genes and their interactions with other genes, and gene-environment interactions is compiled to provide the reader with a critical and up-to-date overview on the current knowledge of the etiology of cleft lip and palate. Recent epidemiological evidence strongly suggests that individuals born with clefts have a shorter lifespan and may have a higher incidence of cancer and psychological disorders. IRF6 has been shown to be an important contributor to cleft lip and palate, but the functional variant leading to the defect has not yet been defined. Inactivation of MSX1 and genes in the FGF family has also been shown to lead to cleft lip and palate. In addition, missense mutations in several candidate genes may cause cleft lip and palate, but definitive evidence regarding the biological consequences of these mutations is yet to be unraveled. Maternal cigarette smoking increases the risk of a baby born with clefts, in particular when the mother carries the GSTT1-null variants. The latest approaches in cleft research include the analysis of several additional phenotypical features of the population, with the goal of increasing the statistical power of genetics studies.

scholarly journals Ancestral polymorphisms in Drosophila pseudoobscura and Drosophila miranda

2011 ◽  
Vol 93 (4) ◽  
pp. 255-263 ◽  
Author(s):  
REUBEN W. NOWELL ◽  
BRIAN CHARLESWORTH ◽  
PENELOPE R. HADDRILL
Keyword(s):  
Balancing Selection ◽  
Molecular Data ◽  
Sequence Polymorphism ◽  
Substantial Proportion ◽  
Drosophila Pseudoobscura ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Speciation Event ◽  
Ancestral Polymorphisms ◽  
Polymorphism Data

SummaryAncestral polymorphisms are defined as variants that arose by mutation prior to the speciation event that generated the species in which they segregate. Their presence may complicate the interpretation of molecular data and lead to incorrect phylogenetic inferences. They may also be used to identify regions of the genome that are under balancing selection. It is thus important to take into account the contribution of ancestral polymorphisms to variability within species and divergence between species. Here, we extend and improve a method for estimation of the proportion of ancestral polymorphisms within a species, and apply it to a dataset of 33 X-linked and 34 autosomal protein-coding genes for which sequence polymorphism data are available in both Drosophila pseudoobscura and Drosophila miranda, using Drosophila affinis as an outgroup. We show that a substantial proportion of both X-linked and autosomal synonymous variants in these two species are ancestral, and that a small number of additional genes with unusually high sequence diversity seem to have an excess of ancestral polymorphisms, suggestive of balancing selection.

scholarly journals Methodology of making organizational and technological decisions at the stage of operational management of construction operations based on the forecasting system

2021 ◽  
Vol 2131 (2) ◽  
pp. 022114
Author(s):  
L Zelentsov ◽  
L Mailyan ◽  
D Pirko
Keyword(s):  
Software Package ◽  
Complex Dynamic ◽  
Short Term ◽  
Current Management ◽  
Construction Operations ◽  
Construction Products ◽  
Forecasting System ◽  
High Level ◽  
Cost Parameters

Abstract The article discusses the issues of forecasting two key parameters of an investment and construction project: time and cost, while the building company is considered as a complex dynamic system. Taking into account the long-term nature of the creation of construction products and, as a consequence, the high level of work in progress, the need to use forecasting models is justified, both at short-term planning intervals (week, month) and at longer intervals (quarter, year). The article examines the formalized forecasting methods, gives a characteristic of the methods most widely used in practice. These methods include forecasting based on ARIMA models. DSTU has developed a pilot software package for an intelligent construction management system, which includes a software package for forecasting the time and cost parameters of a construction object at the stages of operational and current management.

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