Adaptation and Natural Selection

2021 ◽  
pp. 125-154
Author(s):  
Áki J. Láruson ◽  
Floyd A. Reed
Keyword(s):  
Natural Selection ◽  
Allele Frequency ◽  
Levels Of Selection ◽  
Frequency Data ◽  
Selection Coefficient ◽  
Frequency Distributions ◽  
Single Allele ◽  
Selection Strength ◽  
The Difference ◽  
Over Time

Here non-random shifts in allele frequencies over time are introduced, as well as how to incorporate varying levels of selection into a model of a single population through time. This chapter highlights the difference between weak and strong selection, the dynamics of single allele versus genotype-level selection, and how selection strength and population size affect allele frequency distributions over time. Finally the inference of the selection coefficient from allele frequency data is discussed, alongside the concepts of overdominance and underdominance.

scholarly journals An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data

2019 ◽  
Author(s):  
Aaron J. Stern ◽  
Peter R. Wilton ◽  
Rasmus Nielsen
Keyword(s):  
Natural Selection ◽  
Allele Frequency ◽  
Dna Sequence ◽  
Importance Sampling ◽  
Likelihood Function ◽  
Sequence Data ◽  
Lactase Persistence ◽  
Selection Coefficient ◽  
Dna Sequence Data ◽  
Full Likelihood

AbstractMost current methods for detecting natural selection from DNA sequence data are limited in that they are either based on summary statistics or a composite likelihood, and as a consequence, do not make full use of the information available in DNA sequence data. We here present a new importance sampling approach for approximating the full likelihood function for the selection coefficient. The method treats the ancestral recombination graph (ARG) as a latent variable that is integrated out using previously published Markov Chain Monte Carlo (MCMC) methods. The method can be used for detecting selection, estimating selection coefficients, testing models of changes in the strength of selection, estimating the time of the start of a selective sweep, and for inferring the allele frequency trajectory of a selected or neutral allele. We perform extensive simulations to evaluate the method and show that it uniformly improves power to detect selection compared to current popular methods such as nSL and SDS, under various demographic models and can provide reliable inferences of allele frequency trajectories under many conditions. We also explore the potential of our method to detect extremely recent changes in the strength of selection. We use the method to infer the past allele frequency trajectory for a lactase persistence SNP (MCM6) in Europeans. We also study a set of 11 pigmentation-associated variants. Several genes show evidence of strong selection particularly within the last 5,000 years, including ASIP, KITLG, and TYR. However, selection on OCA2/HERC2 seems to be much older and, in contrast to previous claims, we find no evidence of selection on TYRP1.Author summaryCurrent methods to study natural selection using modern population genomic data are limited in their power and flexibility. Here, we present a new method to infer natural selection that builds on recent methodological advances in estimating genome-wide genealogies. By using importance sampling we are able to efficiently estimate the likelihood function of the selection coefficient. We show our method improves power to test for selection over competing methods across a diverse range of scenarios, and also accurately infers the selection coefficient. We also demonstrate a novel capability of our model, using it to infer the allele’s frequency over time. We validate these results with a study of a lactase persistence SNP in Europeans, and also study a set of 11 pigmentation-associated variants.

Detection of natural selection by methods based on models of the behaviour of neutral alleles

1980 ◽  
Vol 12 (4) ◽  
pp. 469-479
Author(s):  
B. K. Averill
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Allele Frequency ◽  
Allele Frequencies ◽  
Frequency Data ◽  
Allele Frequency Data

SummaryThe allele frequency data of artificial populations were examined by several methods which test whether various configurations of allele frequencies are the result of drift or selection. Although no genotypic selective differences were included in these populations the methods indicated that selection was operating in some instances; hence the models are not reliable. Distinguishing between the actions of drift and selection would be facilitated if data for many loci were included, so that a notion of the variance of the genetic variation measure could be obtained.

scholarly journals NATURAL SELECTION AND FITNESS ENTROPY IN A DENSITY-REGULATED POPULATION

Genetics ◽  
1982 ◽  
Vol 101 (2) ◽  
pp. 317-329
Author(s):  
R A Desharnais ◽  
R F Costantino
Keyword(s):  
Experimental Data ◽  
Natural Selection ◽  
Allele Frequency ◽  
Equilibrium Density ◽  
Initial Population ◽  
Initial Population Density ◽  
Density Dependent ◽  
Fitness Value ◽  
The Difference ◽  
Density Dependent Selection

ABSTRACT The entropy H(po,p*) of a population with the initial allele frequency po given the equilibrium polymorphic frequency p* has been proposed as a measure of natural selection. In the present paper, we have extended this concept to include a particular aspect of density-dependent selection. We compared size trajectory of a population initially at genetic equilibrium, N(t), with the size trajectories of populations not initially at p*,N(t), but which do eventually converge to a common equilibrium allele frequency and equilibrium density, N*. The following experimentally testable hyopthesis was established. The total area defined by the difference between the trajectories of N(t) and N(t) as they converge to N* is directly proportional to the fitness entropy when population size is transformed using the density-dependent fitness value. Two properties of this relationship were noted. First, it is independent of the magnitude of natural selection and, secondly, it does not depend upon the initial population density as long as the equilibrium and nonequilibrium populations have the same initial numbers. This hypothesis was evaluated with experimental data on the flour beetle Tribolium castaneum.

The Distinction between [P] and [S]

2017 ◽  
Author(s):  
Galen Strawson
Keyword(s):  
Personal Identity ◽  
Radical Change ◽  
Legal Responsibility ◽  
The Difference ◽  
Definition Of ◽  
Over Time

This chapter examines the difference between John Locke's definition of a person [P], considered as a kind of thing, and his definition of a subject of experience of a certain sophisticated sort [S]. It first discusses the equation [P] = [S], where [S] is assumed to be a continuing thing that is able to survive radical change of substantial realization, as well as Locke's position about consciousness in relation to [P]'s identity or existence over time as [S]. It argues that Locke is not guilty of circularity because he is not proposing consciousness as the determinant of [S]'s identity over time, but only of [S]'s moral and legal responsibility over time. Finally, it suggests that the terms “Person” and “Personal identity” pull apart, in Locke's scheme of things, but in a perfectly coherent way.

ANALISIS KOMPARATIF TUTURAN BAHASA INDONESIA PADA MAHASISWA UNIVERSITAS IQRA BURU

2020 ◽  
Author(s):  
HARZIKO
Keyword(s):  
Historical Development ◽  
Qualitative Approach ◽  
Data Selection ◽  
Communication Tool ◽  
Comparative Linguistics ◽  
Data Presentation ◽  
Vocal System ◽  
The Difference ◽  
Bahasa Indonesia ◽  
Over Time

Language is a tool used to convey ideas, ideas, feelings, and thoughts to others. Language, which is an arbiter sound symbol system that is used by members of one community to work together, interact, and identify themselves. In other words, language can be a means to convey intent or purpose so that the desired thing is achieved. As a communication tool, language develops over time. Therefore, language will never die if its speakers still care and love for the language comparative linguistics as a study or study of language which includes the comparison of cognate languages or the historical development of a language. This research aims to elucidate the use of Indonesian language at students of Iqra Buru University with Comparative Analysis. The method used in this research is descriptive with a qualitative approach. Data collected by observation, interview, and documentation techniques. Sources of data in this study were 5 speakers 5 speakers language Analyzing the data by means of data selection, data classification, and data presentation. The results of the study stated that there were phonological differences, namely the Jamee vowel system contained / ɛ / and / ɔ /, while the vocal system was / a / and the consonant system was Jamee / ɣ / or / R /, while the language / r /, then the difference pronunciations include single vowels, for example makɛn, bɔRa in Jamee and eating, bara in Language used by iqra Rush university students. Keywords

scholarly journals Herd-Level and Individual Differences in Fecal Lactobacilli Dynamics of Growing Pigs

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 113
Author(s):  
Emilia König ◽  
Virpi Sali ◽  
Paulina Heponiemi ◽  
Seppo Salminen ◽  
Anna Valros ◽  
...  
Keyword(s):  
Species Diversity ◽  
Growing Pigs ◽  
General Management ◽  
Immune Parameters ◽  
Sampling Points ◽  
Sequencing Technique ◽  
Piglet Serum ◽  
The Difference ◽  
Over Time ◽  
Fecal Sampling

We studied the fecal lactobacilli count and species diversity of growing pigs along with immune parameters associated with intestinal lactobacilli. Thirty pigs categorized as small (S, n = 12) or large (L, n = 18) at birth were followed from birth to slaughter in two commercial herds, H1 and H2. Herds differed in terms of their general management. We determined sow colostrum quality, colostrum intake, piglet serum immunoglobulins, and pig growth. We took individual fecal samples from pigs in the weaning and finishing units. We studied lactobacilli count and identified their diversity with 16S PCR. Total lactobacilli count increased in H1 and decreased in H2 between samplings. Lactobacilli species diversity was higher in H1 in both fecal sampling points, whereas diversity decreased over time in both herds. We identified altogether seven lactobacilli species with a maximum of five (one to five) species in one herd. However, a relatively large proportion of lactobacilli remained unidentified with the used sequencing technique. Small pigs had higher lactobacilli counts in both herds but the difference was significant only in H2 (p = 0.01). Colostrum quality was numerically better in H1 than in H2, where colostrum intake tended to be associated with total lactobacilli count (p = 0.05).

scholarly journals 152. Applying A Difference-in-Difference Analysis to Assess Effect of Antimicrobial Stewardship Strategies on Changes in Antimicrobial Use

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S86-S86
Author(s):  
Ann F Chou ◽  
Yue Zhang ◽  
Makoto M Jones ◽  
Christopher J Graber ◽  
Matthew B Goetz ◽  
...  
Keyword(s):  
Antimicrobial Stewardship ◽  
Clinical Pharmacist ◽  
Antibiotic Use ◽  
Feedback Mechanism ◽  
Health Care Facilities ◽  
Antimicrobial Use ◽  
Time Points ◽  
The Difference ◽  
The Impact ◽  
Over Time

Abstract Background About 30–50% of inpatient antimicrobial therapy is sub-optimal. Health care facilities have utilized various antimicrobial stewardship (AS) strategies to optimize appropriate antimicrobial use, improve health outcomes, and promote patient safety. However, little evidence exists to assess relationships between AS strategies and antimicrobial use. This study examined the impact of changes in AS strategies on antimicrobial use over time. Methods This study used data from the Veterans Affairs (VA) Healthcare Analysis & Informatics Group (HAIG) AS survey, administered at 130 VA facilities in 2012 and 2015, and antimicrobial utilization from VA Corporate Data Warehouse. Four AS strategies were examined: having an AS team, feedback mechanism on antimicrobial use, infectious diseases (ID) attending physicians, and clinical pharmacist on wards. Change in AS strategies were computed by taking the difference in the presence of a given strategy in a facility between 2012–2015. The outcome was the difference between antimicrobial use per 1000 patient days in 2012–2013 and 2015–2016. Employing multiple regression analysis, changes in antimicrobial use was estimated as a function of changes in AS strategies, controlling for ID human resources in and organizational complexity. Results Of the 4 strategies, only change in availability of AS teams had an impact on antimicrobial use. Compared to facilities with no AS teams at both time points, antibiotic use decreased by 63.9 uses per 1000 patient days in facilities that did not have a AS team in 2012 but implemented one in 2015 (p=0.0183). Facilities that had an AS team at both time points decreased use by 62.2 per 1000 patient days (p=0.0324). Conclusion The findings showed that AS teams reduced inpatient antibiotic use over time. While changes in having feedback on antimicrobial use and clinical pharmacist on wards showed reduced antimicrobial use between 2012–2015, the differences were not statistically significant. These strategies may already be a part of a comprehensive AS program and employed by AS teams. In further development of stewardship programs within healthcare organizations, the association between AS teams and antibiotic use should inform program design and implementation. Disclosures All Authors: No reported disclosures

scholarly journals Association between EFHD2 gene polymorphisms and schizophrenia among the Han population in northern China

2020 ◽  
Vol 48 (6) ◽  
pp. 030006052093280
Author(s):  
Meng Gao ◽  
Kuo Zeng ◽  
Ya Li ◽  
Yong-ping Liu ◽  
Xi Xia ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Neurodevelopmental Disorder ◽  
Haplotype Frequency ◽  
Northern China ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Gene Encoding ◽  
Frequency Distributions ◽  
And Control

Objective Schizophrenia is a severe neurodevelopmental disorder with a complex genetic and environmental etiology. The gene encoding EF-hand domain-containing protein D2 ( EFHD2) may be a genetic risk locus for schizophrenia. Methods We genotyped four EFHD2 single-nucleotide polymorphisms (281 schizophrenia cases [SCZ], 321 controls) from northern Chinese Han individuals using Sanger sequencing and polymerase chain reaction-restriction fragment length polymorphism analysis. Differences existed in genotype, allele, and haplotype frequency distributions between SCZ and control groups. Results The rs2473357 genotype and allele frequency distributions differed between SCZ and controls; however, this difference disappeared after Bonferroni correction. Differences in rs2473357 genotype and allele frequency distributions between SCZ and controls were more pronounced in men than in women. The G allele increased schizophrenia risk (odds ratio = 1.807, 95% confidence interval = 1.164–2.803). Among six haplotypes (G–, A–, G-insC, A-C, G-C, and G-T), the G– haplotype frequency distribution differed between SCZ and controls in women; the A-C and G-C haplotype frequency distributions differed between SCZ and controls in men. Conclusions EFHD2 may be involved in schizophrenia. Sex differences in EFHD2 genotype and allele frequency distributions existed among schizophrenia patients. Further research is needed to determine the role of EFHD2 in schizophrenia.

scholarly journals X-chromosomal STR based genetic polymorphisms and demographic history of Sri Lankan ethnicities and their relationship with global populations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nandika Perera ◽  
Gayani Galhena ◽  
Gaya Ranawaka
Keyword(s):  
Allele Frequency ◽  
Demographic History ◽  
Evolutionary Genetics ◽  
Haplotype Frequency ◽  
Allele Frequency Distribution ◽  
Sri Lankan ◽  
Frequency Distributions ◽  
Autosomal Str ◽  
History Of ◽  
Multiplex System

AbstractA new 16 X-short tandem repeat (STR) multiplex PCR system has recently been developed for Sr Lankans, though its applicability in evolutionary genetics and forensic investigations has not been thoroughly assessed. In this study, 838 unrelated individuals covering all four major ethnic groups (Sinhalese, Sri Lankan Tamils, Indian Tamils and Moors) in Sri Lanka were successfully genotyped using this new multiplex system. The results indicated a high forensic efficiency for the tested loci in all four ethnicities confirming its suitability for forensic applications of Sri Lankans. Allele frequency distribution of Indian Tamils showed subtle but statistically significant differences from those of Sinhalese and Moors, in contrast to frequency distributions previously reported for autosomal STR alleles. This suggest a sex biased demographic history among Sri Lankans requiring a separate X-STR allele frequency database for Indian Tamils. Substantial differences observed in the patterns of LD among the four groups demand the use of a separate haplotype frequency databases for each individual ethnicity. When analysed together with other 14 world populations, all Sri Lankan ethnicities except Indian Tamils clustered closely with populations from Indian Bhil tribe, Bangladesh and Europe reflecting their shared Indo-Aryan ancestry.

FC 068QUALITY OF LIFE OVER TIME IN OLDER MEN AND WOMEN WITH ADVANCED CKD - RESULTS FROM THE EQUAL STUDY

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
Nicholas Chesnaye ◽  
Yvette Meuleman ◽  
Esther De Rooij ◽  
Friedo W Dekker ◽  
Marie Evans ◽  
...  
Keyword(s):  
Harmful Effect ◽  
Patient Characteristics ◽  
P Value ◽  
Joint Models ◽  
Cross Sectional ◽  
Linear Interaction ◽  
Men And Women ◽  
Negative Effect ◽  
The Difference ◽  
Over Time

Abstract Background and Aims Differences between the sexes are apparent in the epidemiology of CKD. Cross-sectional studies show that women consistently report a poorer health-related quality of life (QoL) than men, however, longitudinal studies are lacking. Here we investigate the sex-specific evolution of QoL over time in advanced CKD. As a secondary aim, we explore the sex-specific determinants of QoL. Method EQUAL is an observational prospective cohort study in stages 4 and 5 CKD patients ≥65 years not on dialysis with an incident estimated glomerular filtration rate (eGFR) < 20 ml/min/1.73m². Data on QoL (measured using the RAND-36), clinical and demographic patient characteristics were collected between April 2012 and September 2020. QoL trajectories were modelled by sex using linear mixed models, and joint models were applied to deal with informative censoring. We followed patients until death or dialysis initiation. Results We included 5151 QoL measurements in 1416 patients over a total of 1986 person years of follow-up. Overall, the physical component summary (PCS) declined with 2.0 (95% CI 1.4-2.6) points and the mental component summary (MCS) by 2.4 (95% CI 1.8-3.0) points per year. Although women had overall lower QoL scores, figure 1 demonstrates that PCS and MCS declined more than twice as fast in men (PCS: 2.4 per year, 95% CI 1.7 – 3.1, MCS: 2.9 per year, 95% CI 2.2 – 3.6) compared with women (PCS: 1.1 per year, 95% CI -0.2 – 2.0, MCS: 1.5 per year, 95% CI 0.5 – 2.4). We identified a non-linear interaction effect between sex and eGFR levels on QoL, demonstrating a stronger negative effect of decreased eGFR on both PCS (p=0.02) and MCS (p=0.04) in men compared with women. Subsequent adjustment for renal decline attenuated the difference in rate of QoL decline between men and women (difference after adjustment; PCS: 1.1, 95% CI -0.1 – 2.2, MCS: 1.2, 95% 0.0 – 2.3). In univariable analyses, higher serum haemoglobin was more beneficial to QoL in men compared to women (p-value for interaction; PCS: p=0.03, MCS: p=0.01). Higher serum phosphate had a strong harmful effect on both PCS and MCS in men, but not in women (PCS & MCS: p<0.001). The presence of pre-existing diabetes had a negative effect on PCS and MCS in men, but to a lesser extent in women (PCS: p=0.02, MCS: p=0.01). Conclusion Despite the higher overall QoL reported by men, both their physical and mental QoL declined approximately twice as fast compared with women. The faster decline in men was mediated in part by their lower levels of renal function, which had a stronger impact on their QoL as compared with women. Furthermore, in exploratory analyses we identified that high levels of phosphate, low levels of haemoglobin, and pre-existing diabetes were more detrimental to QoL in men than in women.

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