scholarly journals Decoupling the variances of heterosis and inbreeding effects is evidenced in yeast’s life-history and proteomic traits

2018 ◽  
Author(s):  
M. Petrizzelli ◽  
D. de Vienne ◽  
C. Dillmann
Keyword(s):  
Life History ◽  
Alcoholic Fermentation ◽  
Real Data ◽  
Diallel Cross ◽  
Hybrid Vigor ◽  
Phenotypic Traits ◽  
Phenotypic Differences ◽  
Clear Cut ◽  
Specific Effects ◽  
Common Parent

ABSTRACTHeterosis (hybrid vigor) and inbreeding depression, commonly considered as corollary phenomena, could nevertheless be decoupled under certain assumptions according to theoretical population genetics works. In order to explore this issue on real data, we analyzed the components of genetic variation in a population derived from a half-diallel cross between strains fromSaccharomyces cerevisiaeandS. uvarum, two related yeast species involved in alcoholic fermentation. A large number of phenotypic traits, either molecular (coming from quantitative proteomics) or related to fermentation and life-history, were measured during alcoholic fermentation. Because the parental strains were included in the design, we were able to distinguish between inbreeding effects, which measures phenotypic differences between inbred and hybrids, and heterosis, which measures phenotypic differences between a specific hybrid and the other hybrids sharing a common parent. The sources of phenotypic variation differed depending on the temperature, indicating the predominance of genotype by environment interactions. Decomposing the total genetic variance into variances of additive (intra- and inter-specific) effects, of inbreeding effects and of heterosis (intra- and inter-specific) effects, we showed that the distribution of variance components defined clear-cut groups of proteins and traits. Moreover, it was possible to cluster fermentation and life-history traits into most proteomic groups. Within groups, we observed positive, negative or null correlations between the variances of heterosis and inbreeding effects. To our knowledge, such a decoupling had never been experimentally demonstrated. This result suggests that, despite a common evolutionary history of individuals within a species, the different types of traits have been subject to different selective pressures.

scholarly journals A latent unknown clustering integrating multi-omics data (LUCID) with phenotypic traits

2019 ◽  
Vol 36 (3) ◽  
pp. 842-850 ◽  
Author(s):  
Cheng Peng ◽  
Jun Wang ◽  
Isaac Asante ◽  
Stan Louie ◽  
Ran Jin ◽  
...  
Keyword(s):  
Real Data ◽  
R Package ◽  
Integrative Model ◽  
Supplementary Information ◽  
Phenotypic Traits ◽  
Omics Data ◽  
Data Types ◽  
Specific Effects ◽  
Metabolomic Data ◽  
Future Prediction

Abstract Motivation Epidemiologic, clinical and translational studies are increasingly generating multiplatform omics data. Methods that can integrate across multiple high-dimensional data types while accounting for differential patterns are critical for uncovering novel associations and underlying relevant subgroups. Results We propose an integrative model to estimate latent unknown clusters (LUCID) aiming to both distinguish unique genomic, exposure and informative biomarkers/omic effects while jointly estimating subgroups relevant to the outcome of interest. Simulation studies indicate that we can obtain consistent estimates reflective of the true simulated values, accurately estimate subgroups and recapitulate subgroup-specific effects. We also demonstrate the use of the integrated model for future prediction of risk subgroups and phenotypes. We apply this approach to two real data applications to highlight the integration of genomic, exposure and metabolomic data. Availability and Implementation The LUCID method is implemented through the LUCIDus R package available on CRAN (https://CRAN.R-project.org/package=LUCIDus). Supplementary information Supplementary materials are available at Bioinformatics online.

Hormones and Behavior

2019 ◽  
pp. 11-26
Author(s):  
Maren N. Vitousek ◽  
Laura A. Schoenle
Keyword(s):  
Life History ◽  
Life Histories ◽  
Life History Traits ◽  
Developmental Plasticity ◽  
Endocrine System ◽  
Phenotypic Traits ◽  
Social Environments ◽  
Trade Offs ◽  
And Behavior

Hormones mediate the expression of life history traits—phenotypic traits that contribute to lifetime fitness (i.e., reproductive timing, growth rate, number and size of offspring). The endocrine system shapes phenotype by organizing tissues during developmental periods and by activating changes in behavior, physiology, and morphology in response to varying physical and social environments. Because hormones can simultaneously regulate many traits (hormonal pleiotropy), they are important mediators of life history trade-offs among growth, reproduction, and survival. This chapter reviews the role of hormones in shaping life histories with an emphasis on developmental plasticity and reversible flexibility in endocrine and life history traits. It also discusses the advantages of studying hormone–behavior interactions from an evolutionary perspective. Recent research in evolutionary endocrinology has provided insight into the heritability of endocrine traits, how selection on hormone systems may influence the evolution of life histories, and the role of hormonal pleiotropy in driving or constraining evolution.

scholarly journals Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Jaewon Lim ◽  
Hong-Tae Park ◽  
Seyoung Ko ◽  
Hyun-Eui Park ◽  
Gyumin Lee ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Phenotypic Diversity ◽  
Control Strategies ◽  
Genomic Diversity ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genomic Features ◽  
Phenotypic Differences ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Type Strains

AbstractMycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.

Comparing Mutational Variabilities

Genetics ◽  
1996 ◽  
Vol 143 (3) ◽  
pp. 1467-1483 ◽  
Author(s):  
David Houle ◽  
Bob Morikawa ◽  
Michael Lynch
Keyword(s):  
Life History ◽  
Morphological Traits ◽  
Life History Traits ◽  
Genetic Variance ◽  
Balance Model ◽  
Phenotypic Traits ◽  
Infinite Population ◽  
Persistence Time ◽  
Coefficients Of Variation ◽  
Balance Hypothesis

Abstract We have reviewed the available data on VM, the amount of genetic variation in phenotypic traits produced each generation by mutation. We use these data to make several qualitative tests of the mutation-selection balance hypothesis for the maintenance of genetic variance (MSB). To compare VM values, we use three dimensionless quantities: mutational heritability, the mutational coefficient of variation, CVM; and the ratio of the standing genetic variance to VM, VG/VM. Since genetic coefficients of variation for life history traits are larger than those for morphological traits, we predict that under MSB, life history traits should also have larger CVM. This is confirmed; life history traits have a median CVM value more than six times higher than that for morphological traits. VG/VM approximates the persistence time of mutations under MSB in an infinite population. In order for MSB to hold, VG/VM must be small, substantially less than 1000, and life history traits should have smaller values than morphological traits. VG/VM averages about 50 generations for life history traits and 100 generations for morphological traits. These observations are all consistent with the predictions of a mutation-selection balance model.

scholarly journals Time spent in distinct life history stages has sex‐specific effects on reproductive fitness in wild Atlantic salmon

2020 ◽  
Vol 29 (6) ◽  
pp. 1173-1184 ◽  
Author(s):  
Kenyon B. Mobley ◽  
Hanna Granroth‐Wilding ◽  
Mikko Ellmén ◽  
Panu Orell ◽  
Jaakko Erkinaro ◽  
...  
Keyword(s):  
Life History ◽  
Atlantic Salmon ◽  
Reproductive Fitness ◽  
Life History Stages ◽  
Specific Effects

scholarly journals Ontogenetic and life history trait changes associated with convergent ecological specializations in extinct ungulate mammals

2017 ◽  
Vol 114 (5) ◽  
pp. 1069-1074 ◽  
Author(s):  
Helder Gomes Rodrigues ◽  
Anthony Herrel ◽  
Guillaume Billet
Keyword(s):  
Life History ◽  
Body Mass ◽  
Life Histories ◽  
Life History Trait ◽  
Phenotypic Traits ◽  
Structural Constraints ◽  
Dental Eruption ◽  
Accelerated Life ◽  
Environmental Variations ◽  
Adaptive Nature

Investigating life history traits in mammals is crucial to understand their survival in changing environments. However, these parameters are hard to estimate in a macroevolutionary context. Here we show that the use of dental ontogenetic parameters can provide clues to better understand the adaptive nature of phenotypic traits in extinct species such as South American notoungulates. This recently extinct order of mammals evolved in a context of important geological, climatic, and environmental variations. Interestingly, notoungulates were mostly herbivorous and acquired high-crowned teeth very early in their evolutionary history. We focused on the variations in crown height, dental eruption pattern, and associated body mass of 69 notoungulate taxa, placed in their phylogenetic and geological contexts. We showed that notoungulates evolved higher crowns several times between 45 and 20 Ma, independently of the variation in body mass. Interestingly, the independent acquisitions of ever-growing teeth were systematically accompanied by eruption of molars faster than permanent premolars. These repeated associations of dental innovations have never been documented for other mammals and raise questions on their significance and causal relationships. We suggest that these correlated changes could originate from ontogenetic adjustments favored by structural constraints, and may indicate accelerated life histories. Complementarily, these more durable and efficient dentitions could be selected to cope with important ingestions of abrasive particles in the context of intensified volcanism and increasing aridity. This study demonstrates that assessing both life history and ecological traits allows a better knowledge of the specializations of extinct mammals that evolved under strong environmental constraints.

Geomorphology induces life history changes in invertebrates of sandy beaches: the case of the mole crab Emerita analoga in Chile

2005 ◽  
Vol 85 (1) ◽  
pp. 113-120 ◽  
Author(s):  
Alejandro Brazeiro
Keyword(s):  
Life History ◽  
Environmental Conditions ◽  
Critical Role ◽  
Sandy Beaches ◽  
Central Chile ◽  
Phenotypic Differences ◽  
Emerita Analoga ◽  
Vital Functions ◽  
Environmental Variations ◽  
Life History Patterns

The hypothesis that vital functions of one of the most successful macroinvertebrates of sandy beaches of Chile, the mole crab Emerita analoga are negatively affected by the environmental conditions of reflective beaches was tested. Twelve exposed sandy beaches distributed along 200 km of coast of central Chile, and selected to cover a wide morphodynamic spectrum were sampled every two months from April 1997 to November 1998. Significant phenotypic differences among local populations of the sand crab were detected. Important life history traits of the sand crab, linked to growth pattern, reproductive biology and burrowing capacity, were negatively affected by the environmental conditions of reflective beaches. The present results reinforce the view that environmental variations associated with beach morphodynamics, play a critical role in the life history patterns of sandy beach organisms.

scholarly journals Consistent sex ratio bias of individual female dragon lizards

2006 ◽  
Vol 2 (4) ◽  
pp. 569-572 ◽  
Author(s):  
Tobias Uller ◽  
Beth Mott ◽  
Gaetano Odierna ◽  
Mats Olsson
Keyword(s):  
Genetic Variation ◽  
Sex Ratio ◽  
Incubation Temperature ◽  
Sex Ratios ◽  
Phenotypic Traits ◽  
Female Size ◽  
Offspring Sex Ratio ◽  
Phenotypic Differences ◽  
Sex Ratio Bias ◽  
Offspring Sex

Sex ratio evolution relies on genetic variation in either the phenotypic traits that influence sex ratios or sex-determining mechanisms. However, consistent variation among females in offspring sex ratio is rarely investigated. Here, we show that female painted dragons ( Ctenophorus pictus ) have highly repeatable sex ratios among clutches within years. A consistent effect of female identity could represent stable phenotypic differences among females or genetic variation in sex-determining mechanisms. Sex ratios were not correlated with female size, body condition or coloration. Furthermore, sex ratios were not influenced by incubation temperature. However, the variation among females resulted in female-biased mean population sex ratios at hatching both within and among years.

Winter corticosterone and body condition predict breeding investment in a nonmigratory bird

2019 ◽  
Vol 30 (6) ◽  
pp. 1642-1652 ◽  
Author(s):  
Chloé Montreuil-Spencer ◽  
Kelsey Schoenemann ◽  
Ádám Z Lendvai ◽  
Frances Bonier
Keyword(s):  
Life History ◽  
Breeding Season ◽  
Body Condition ◽  
Reproductive Investment ◽  
Phenotypic Traits ◽  
Residual Body ◽  
Life History Stage ◽  
Nonbreeding Season ◽  
Fat Reserves ◽  
Fat Score

Abstract Reproduction is an energetically demanding life history stage that requires costly physiological and behavioral changes, yet some individuals will invest more into reproduction and breed more successfully than others. To understand variation in reproductive investment, previous studies have evaluated factors during breeding, but conditions outside of this life history stage may also play a role. Using a free-ranging population of black-capped chickadees (Poecile atricapillus), we assessed the repeatability of plastic traits relating to energetic condition (circulating initial corticosterone concentrations and body condition) during the nonbreeding season and evaluated whether these traits predicted reproductive investment in the subsequent breeding season. We found that initial corticosterone concentrations and an index of body condition, but not fat score, were moderately repeatable over a 1-week period in winter. This trait repeatability supports the interpretation that among-individual variation in these phenotypic traits could reflect an intrinsic strategy to cope with challenging conditions across life history stages. We found that females with larger fat reserves during winter laid eggs sooner and tended to spend more time incubating their eggs and feeding their offspring. In contrast, we found that females with higher residual body mass delayed breeding, after controlling for the relationship between fat score and timing of breeding. Additionally, females with higher initial corticosterone in winter laid lighter eggs. Our findings suggest that conditions experienced outside of the breeding season may be important factors explaining variation in reproductive investment.

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