Models of Fluctuating Selection for a Quantitative Trait

Farm animals show individual variation in their behavioural responses to handling and management systems on farms. These behavioural responses are presumed to reflect underlying temperament traits such as fear or aggression. Information about the location of genes that influence temperament traits could be used in selective breeding programmes to improve animal welfare, as selection for desirable behavioural responses would increase the ability of animals to cope with stressors encountered on farms. The aims of this study were to obtain reliable temperament measurements in cattle using behavioural tests, and to use this data to localise the genes (quantitative trait loci) that are involved in such traits.Behavioural data obtained in temperament tests must be shown to reflect underlying traits by demonstrating intra-animal repeatability, inter-animal variability and validity. The objectives of this experiment were i) to carry out four behaviour tests on a group of heifers, and examine the repeatability, variability and validity of the results obtained; ii) to correlate the behavioural data with genotyping data from a large number of heifers to look for associations between behavioural phenotypes and genetic markers. Associations localise quantitative trait loci (QTLs), or regions of the genome, that are involved in these traits.

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Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection

10.1101/729095 ◽

2019 ◽

Author(s):

Caroline B. Turner ◽

Sean W. Buskirk ◽

Katrina B. Harris ◽

Vaughn S. Cooper

Keyword(s):

Evolutionary Dynamics ◽

Burkholderia Cenocepacia ◽

Natural Environments ◽

Fluctuating Selection ◽

Frequency Dependent ◽

Frequency Dependent Selection ◽

Fluctuating Environment ◽

Fluctuating Environments ◽

Negative Frequency Dependent Selection ◽

Selection For

AbstractNatural environments are rarely static; rather selection can fluctuate on time scales ranging from hours to centuries. However, it is unclear how adaptation to fluctuating environments differs from adaptation to constant environments at the genetic level. For bacteria, one key axis of environmental variation is selection for planktonic or biofilm modes of growth. We conducted an evolution experiment with Burkholderia cenocepacia, comparing the evolutionary dynamics of populations evolving under constant selection for either biofilm formation or planktonic growth with populations in which selection fluctuated between the two environments on a weekly basis. Populations evolved in the fluctuating environment shared many of the same genetic targets of selection as those evolved in constant biofilm selection, but were genetically distinct from the constant planktonic populations. In the fluctuating environment, mutations in the biofilm-regulating genes wspA and rpfR rose to high frequency in all replicate populations. A mutation in wspA first rose rapidly and nearly fixed during the initial biofilm phase but was subsequently displaced by a collection of rpfR mutants upon the shift to the planktonic phase. The wspA and rpfR genotypes coexisted via negative frequency-dependent selection around an equilibrium frequency that shifted between the environments. The maintenance of coexisting genotypes in the fluctuating environment was unexpected. Under temporally fluctuating environments coexistence of two genotypes is only predicted under a narrow range of conditions, but the frequency-dependent interactions we observed provide a mechanism that can increase the likelihood of coexistence in fluctuating environments.

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Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)

The ISME Journal ◽

10.1038/s41396-021-01102-w ◽

2021 ◽

Author(s):

Dustin T. Dial ◽

Kathryn M. Weglarz ◽

Akintunde O. Aremu ◽

Nathan P. Havill ◽

Taylor A. Pearson ◽

...

Keyword(s):

Evolutionary History ◽

Life Cycles ◽

Fluctuating Selection ◽

Complex Life Cycles ◽

History Of ◽

Sap Feeding ◽

Selection For ◽

Gains And Losses ◽

Conifer Trees ◽

Plant Sap

AbstractMany plant-sap-feeding insects have maintained a single, obligate, nutritional symbiont over the long history of their lineage. This senior symbiont may be joined by one or more junior symbionts that compensate for gaps in function incurred through genome-degradative forces. Adelgids are sap-sucking insects that feed solely on conifer trees and follow complex life cycles in which the diet fluctuates in nutrient levels. Adelgids are unusual in that both senior and junior symbionts appear to have been replaced repeatedly over their evolutionary history. Genomes can provide clues to understanding symbiont replacements, but only the dual symbionts of hemlock adelgids have been examined thus far. Here, we sequence and compare genomes of four additional dual-symbiont pairs in adelgids. We show that these symbionts are nutritional partners originating from diverse bacterial lineages and exhibiting wide variation in general genome characteristics. Although dual symbionts cooperate to produce nutrients, the balance of contributions varies widely across pairs, and total genome contents reflect a range of ages and degrees of degradation. Most symbionts appear to be in transitional states of genome reduction. Our findings support a hypothesis of periodic symbiont turnover driven by fluctuating selection for nutritional provisioning related to gains and losses of complex life cycles in their hosts.

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Optimal Multiple Trait Selection for Multiple Linked Quantitative Trait Loci

Acta Genetica Sinica ◽

10.1016/s0379-4172(06)60043-7 ◽

2006 ◽

Vol 33 (3) ◽

pp. 220-228 ◽

Cited By ~ 1

Author(s):

Guo-Qing TANG ◽

Xue-Wei LI

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Multiple Trait ◽

Trait Loci ◽

Selection For

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Building reusable phage and antibiotic treatments via exploitation of bacteria-phage coevolutionary dynamics.

10.1101/2021.03.31.437900 ◽

2021 ◽

Author(s):

James Gurney ◽

Sam P Brown

Keyword(s):

Phage Therapy ◽

Treatment Options ◽

Arms Race ◽

Evolutionary Dynamic ◽

Fluctuating Selection ◽

Dynamic Selection ◽

Selection Dynamics ◽

Genomic Characterization ◽

Selection For

People with chronic (long-lasting) infections face the problem that treatment options diminish in time as the pathogen evolves increasing resistance. To address this challenge, we exploit phage and bacterial co-evolution, producing dynamic selection pressures that can return the pathogen to a state of susceptibility to the initial (regulator-approved) therapy. We show that phage OMKO1 alone triggers Arms Race Dynamic (ARD) co-evolution with the pathogen Pseudomonas aeruginosa, leading to generalized phage resistance and crucially - failure at reuse. In contrast, co-administration of the phage with antibiotics triggers Fluctuating Selection Dynamics (FSD) co-evolution, allowing for effective reuse after 20 days of treatment. We pursue medical relevance in our experiments with the use of clinically important pathogens, antibiotics, phage, and a benchmarked synthetic sputum medium. Phenotypic and genomic characterization of evolved isolates demonstrates that efflux-targeting phage OMKO1 exerts continued selection for antibiotic susceptibility regardless of co-evolutionary dynamic or antibiotic co-treatment, opening the door for evolutionary robust phage therapy.

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Optimal Sibship Selection for Genotyping in Quantitative Trait Locus Linkage Analysis

Human Heredity ◽

10.1159/000053350 ◽

2001 ◽

Vol 52 (1) ◽

pp. 1-13 ◽

Cited By ~ 23

Author(s):

S. Purcell ◽

S.S. Cherny ◽

J.K. Hewitt ◽

P.C. Sham

Keyword(s):

Quantitative Trait Locus ◽

Linkage Analysis ◽

Quantitative Trait ◽

Selection For ◽

Trait Locus

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Model selection for quantitative trait locus analysis in polyploids

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.97.14.7951 ◽

2000 ◽

Vol 97 (14) ◽

pp. 7951-7956 ◽

Cited By ~ 26

Author(s):

R. W. Doerge ◽

B. A. Craig

Keyword(s):

Quantitative Trait Locus ◽

Model Selection ◽

Quantitative Trait Locus Analysis ◽

Quantitative Trait ◽

Selection For ◽

Trait Locus

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SNP selection for predicting a quantitative trait

Journal of Applied Statistics ◽

10.1080/02664763.2012.750282 ◽

2013 ◽

Vol 40 (3) ◽

pp. 600-613

Author(s):

S. Subedi ◽

Z. Feng ◽

R. Deardon ◽

F. S. Schenkel

Keyword(s):

Quantitative Trait ◽

Selection For

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Quantitative trait loci controlling kernel discoloration in barley (Hordeum vulgare L.)

Australian Journal of Agricultural Research ◽

10.1071/ar03002 ◽

2003 ◽

Vol 54 (12) ◽

pp. 1251 ◽

Cited By ~ 15

Author(s):

C. D. Li ◽

R. C. M. Lance ◽

H. M. Collins ◽

A. Tarr ◽

S. Roumeliotis ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Phenotypic Variation ◽

Quantitative Trait ◽

Marker Assisted Selection ◽

Major Gene ◽

Heading Date ◽

Major Qtls ◽

Trait Loci ◽

Selection For ◽

Kernel Discoloration

Barley kernel discoloration (KD) leads to substantial annual loss in value through downgrading and discounting of malting barley. KD is a difficult trait to introgress into elite varieties as it is controlled by multiple genes and strongly influenced by environment and maturity. As the first step towards marker assisted selection for KD tolerance, we mapped quantitative trait loci (QTLs) controlling KD measured by grain brightness [Minolta L; (Min L)], redness (Min a), and yellowness (Min b) in 7 barley populations. One to 3 QTLs were detected for grain brightness in various populations, and one QTL could account for 5–31% of the phenotypic variation. The QTL located around the centromere region of chromosome 2H was consistently detected in 6 of the 7 populations, explaining up to 28% of the phenotypic variation. In addition, QTLs for grain brightness were most frequently identified on chromosomes 3H and 7H in various populations. Australian varieties Galleon, Chebec, and Sloop contribute an allele to increase grain brightness on chromosome 7H in 3 different populations. A major gene effect was detected for grain redness. One QTL on chromosome 4H explained 54% of the phenotypic variation in the Sloop/Halcyon population, and was associated with the blue aleurone trait. A second QTL was detected on the long arm of chromosome 2H in 3 populations, accounting for 23–47% of the phenotypic variation. The major QTLs for grain yellowness were mapped on chromosomes 2H and 5H. There were strong associations between the QTLs for heading date, grain brightness, and yellowness. The molecular markers linked with the major QTLs should be useful for marker assisted selection for KD.

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