scholarly journals Uplift and erosion of genomic islands with standing genetic variation

2016 ◽  
Author(s):  
Tyler D. Hether
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Biological Diversity ◽  
Empirical Studies ◽  
Theoretical Models ◽  
Divergent Selection ◽  
Genomic Islands ◽  
Island Formation ◽  
Standing Variation ◽  
Uplift And Erosion

AbstractDetails of the processes that generate biological diversity have long been of interest to evolutionary biologists. A common theme in nature is diversification via divergent selection with gene flow. Empirical studies on this topic find variable genetic differentiation throughout the genome, that genetic differentiation is non-randomly distributed, and that loci of adaptive significance are often found clustered together within “genomic islands of divergence”. Theoretical models based on new mutations show how these genomic islands can arise and grow as a result of a complex interaction of various evolutionary and genic processes. In the current study, I ask if such genomic islands can alternatively arise from divergent selection from standing genetic variation and I tested this using a simple two locus model of selection. There are numerous ways in which standing genetic variation can be partitioned (e.g., between alleles, between loci, and between populations) and I tested which of these scenarios can give rise to an island pattern compared to no genomic differentiation or complete genomic differentiation. I found that divergent selection, even without reciprocal gene exchange between populations, following a bout of admixture can relatively quickly produce an island pattern. Moreover, I found two pathways in which islands can form from divergence from standing variation: 1) through the build up of islands and 2) through the breakdown of larger, genome-wide differentiation. Lastly, similar to new mutation theory, I found that the frequency of recombination is an important determinant of island formation from standing genetic variation such that mating behavior of a species (e.g., facultative or obligate sexual) can impact the likelihood of island formation.

scholarly journals Theoretical models of selection and mutation on quantitative traits

2005 ◽  
Vol 360 (1459) ◽  
pp. 1411-1425 ◽  
Author(s):  
Toby Johnson ◽  
Nick Barton
Keyword(s):  
Genetic Variation ◽  
Quantitative Traits ◽  
Balancing Selection ◽  
Empirical Studies ◽  
Theoretical Models ◽  
Selection Models ◽  
Quantitative Genetic ◽  
Major Class

Empirical studies of quantitative genetic variation have revealed robust patterns that are observed both across traits and across species. However, these patterns have no compelling explanation, and some of the observations even appear to be mutually incompatible. We review and extend a major class of theoretical models, ‘mutation–selection models’, that have been proposed to explain quantitative genetic variation. We also briefly review an alternative class of ‘balancing selection models’. We consider to what extent the models are compatible with the general observations, and argue that a key issue is understanding and modelling pleiotropy. We discuss some of the thorny issues that arise when formulating models that describe many traits simultaneously.

scholarly journals Theoretical Expression for the Evolution of Genomic Island of Speciation: From Its Birth to Preservation

2019 ◽  
Author(s):  
T. Sakamoto ◽  
H. Innan
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Divergence ◽  
Genomic Island ◽  
Evolutionary Process ◽  
Ecological Speciation ◽  
Divergent Selection ◽  
Genomic Islands ◽  
Theoretical Expression ◽  
Locally Adaptive

AbstractEcological speciation could be driven by divergent selection that works to maintain phenotypes that are adaptive to each niche. In its early stages, genetic divergence (or FST) can be maintained around the target sites of divergent selection, while in other regions, genetic variation can be mixed by gene flow or migration. Such regions of elevated genetic divergence are called genomic islands of speciation. In this work, we theoretically consider the evolutionary process of a genomic island of speciation, from its birth to stable preservation. Under a simple two-population model, we use a diffusion approach to obtain analytical expressions for the probability of initial establishment of a locally adaptive allele, the reduction of genetic variation due to the spread of the adaptive allele, and the process to the development of a sharp peak of divergence. Our result would be useful to understand how genomes evolve through ecological speciation with gene flow.

Emerging Syndromes

2017 ◽  
Author(s):  
Kelly C. Allison ◽  
Jennifer D. Lundgren
Keyword(s):  
Empirical Studies ◽  
Theoretical Models ◽  
Future Research ◽  
Night Eating Syndrome ◽  
Statistical Manual ◽  
Night Eating ◽  
Diagnostic And Statistical Manual ◽  
Impairment In Functioning ◽  
Atypical Anorexia Nervosa ◽  
Comorbid Psychopathology

The Diagnostic and Statistical Manual, fifth edition, of the American Psychiatric Association (2013) has designated several disorders under the diagnosis of otherwise specified feeding and eating disorder (OSFED). This chapter evaluates three of these, night eating syndrome (NES), purging disorder (PD), and atypical anorexia nervosa (atypical AN). It also reviews orthorexia nervosa, which has been discussed in the clinical realm as well as the popular press. The history and definition for each is reviewed, relevant theoretical models are presented and compared, and evidence for the usefulness of the models is described. Empirical studies examining the disorders’ independence from other disorders, comorbid psychopathology, and, when available, medical comorbidities, are discussed. Distress and impairment in functioning seem comparable between at least three of these emerging disorders and threshold eating disorders. Finally, remaining questions for future research are summarized.

scholarly journals Population genetic variation analysis of bitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae in China using inter simple sequence repeats (ISSR) molecular markers

2021 ◽  
Author(s):  
Rui Zang ◽  
Ying Zhao ◽  
Kangdi Guo ◽  
Kunqi Hong ◽  
Huijun Xi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Fusarium Oxysporum ◽  
Diversity Index ◽  
Gene Diversity ◽  
Pcr Amplification ◽  
Bitter Gourd ◽  
Diseased Plant ◽  
Variation Analysis ◽  
Group I

AbstractBitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae (FOM) is a devastating crop disease in China. A total of 173 isolates characteristic of typical Fusarium oxysporum with abundant microconidia and macroconidia on white or ruby colonies were obtained from diseased plant tissues. BLASTn analysis of the rDNA-ITS of the isolates showed 99% identity with F. oxysporum species. Among the tested isolates, three were infectious toward tower gourd and five were pathogenic to bottle gourd. However, all of the isolates were pathogenic to bitter gourd. For genetic differences analysis, 40 ISSR primers were screened and 11 primers were used for ISSR-PCR amplification. In total, 127 loci were detected, of which 76 were polymorphic at a rate of 59.84%. POPGENE analysis showed that Nei’s gene diversity index (H) and Shannon’s information index (I) were 0.09 and 0.15, respectively, which indicated that the genetic diversity of the 173 isolates was low. The coefficient of gene differentiation (Gst = 0.33 > 0.15) indicated that genetic differentiation was mainly among populations. The strength of gene flow (Nm = 1.01 > 1.0) was weak, indicating that the population differentiation caused by gene drift was blocked to some degree. The dendrogram based on ISSR markers showed that the nine geographical populations were clustered into two groups at the threshold of genetic similarity coefficient of 0.96. The Shandong and Henan populations were clustered into Group I, while the Guangdong, Hainan, Guangxi, Fujian, Jiangxi, and Hubei populations constituted Group II. Results of the genetic variation analysis showed that the Hunan and Guangxi populations had the highest degree of genetic differentiation, while the Hubei population had the lowest genetic differentiation. Our findings enrich the knowledge of the genetic variation characteristics of FOM populations with the goal of developing effective disease-management programs and resistance breeding programs.

scholarly journals The Molecular Basis of Quantitative Genetic Variation in Central and Secondary Metabolism in Arabidopsis

Genetics ◽  
1998 ◽  
Vol 149 (2) ◽  
pp. 739-747 ◽  
Author(s):  
Thomas Mitchell-Olds ◽  
Deana Pedersen
Keyword(s):  
Enzyme Activity ◽  
Genetic Variation ◽  
Secondary Metabolism ◽  
Genetic Correlations ◽  
Theoretical Models ◽  
Model Systems ◽  
Activity Levels ◽  
Significant Qtls ◽  
Cis Acting ◽  
Quantitative Genetic

Abstract To find the genes controlling quantitative variation, we need model systems where functional information on physiology, development, and gene regulation can guide evolutionary inferences. We mapped quantitative trait loci (QTLs) influencing quantitative levels of enzyme activity in primary and secondary metabolism in Arabidopsis. All 10 enzymes showed highly significant quantitative genetic variation. Strong positive genetic correlations were found among activity levels of 5 glycolytic enzymes, PGI, PGM, GPD, FBP, and G6P, suggesting that enzymes with closely related metabolic functions are coregulated. Significant QTLs were found influencing activity of most enzymes. Some enzyme activity QTLs mapped very close to known enzyme-encoding loci (e.g., hexokinase, PGI, and PGM). A hexokinase QTL is attributable to cis-acting regulatory variation at the AtHXK1 locus or a closely linked regulatory locus, rather than polypeptide sequence differences. We also found a QTL on chromosome IV that may be a joint regulator of GPD, PGI, and G6P activity. In addition, a QTL affecting PGM activity maps within 700 kb of the PGM-encoding locus. This QTL is predicted to alter starch biosynthesis by 3.4%, corresponding with theoretical models, suggesting that QTLs reflect pleiotropic effects of mutant alleles.

scholarly journals Ecological Divergence and the Origins of Intrinsic Postmating Isolation with Gene Flow

2011 ◽  
Vol 2011 ◽  
pp. 1-15 ◽  
Author(s):  
Aneil F. Agrawal ◽  
Jeffrey L. Feder ◽  
Patrik Nosil
Keyword(s):  
Linkage Disequilibrium ◽  
Gene Flow ◽  
Natural Selection ◽  
Theoretical Models ◽  
Ecological Speciation ◽  
Divergent Selection ◽  
Postmating Isolation ◽  
Divergent Natural Selection ◽  
Mathematical Exploration ◽  
Neutral Gene

The evolution of intrinsic postmating isolation has received much attention, both historically and in recent studies of speciation genes. Intrinsic isolation often stems from between-locus genetic incompatibilities, where alleles that function well within species are incompatible with one another when brought together in the genome of a hybrid. It can be difficult for such incompatibilities to originate when populations diverge with gene flow, because deleterious genotypic combinations will be created and then purged by selection. However, it has been argued that if genes underlying incompatibilities are themselves subject to divergent selection, then they might overcome gene flow to diverge between populations, resulting in the origin of incompatibilities. Nonetheless, there has been little explicit mathematical exploration of such scenarios for the origin of intrinsic incompatibilities during ecological speciation with gene flow. Here we explore theoretical models for the origin of intrinsic isolation where genes subject to divergent natural selection also affect intrinsic isolation, either directly or via linkage disequilibrium with other loci. Such genes indeed overcome gene flow, diverge between populations, and thus result in the evolution of intrinsic isolation. We also examine barriers to neutral gene flow. Surprisingly, we find that intrinsic isolation sometimes weakens this barrier, by impeding differentiation via ecologically based divergent selection.

scholarly journals A Systematic Review on Attachment and Sleep at Preschool Age

Children ◽  
2021 ◽  
Vol 8 (10) ◽  
pp. 895
Author(s):  
Catarina Perpétuo ◽  
Eva Diniz ◽  
Manuela Veríssimo
Keyword(s):  
Systematic Review ◽  
Attachment Security ◽  
Biological Process ◽  
Sleep Problems ◽  
Empirical Studies ◽  
Theoretical Models ◽  
Preschool Age ◽  
Future Research ◽  
Parent Child Relationships ◽  
Present Systematic Review

Sleep is a biological process that impacts nearly every domain of a child’s life. Sleep-wake regulation influences and it is highly influenced by developmental variables related to parent-child relationships, such as attachment. The main goal of the present systematic review is to analyze and integrate the findings of empirical studies investigating the relations between attachment and sleep in preschool age, a period marked by important developmental changes that challenge both attachment system and sleep-wake regulation. A database search was performed using a combination of relevant keywords, leading to the identification of 524 articles, with 19 manuscripts assessed for eligibility; finally, seven studies (2344 children) were included. Overall, the findings were not consistent, with some studies reporting significant associations between attachment security and sleep quality, as well as between attachment insecurity and sleep problems, whereas others did not find significant associations. The results are discussed in light of the available theoretical models and integrated in the context of measurement approaches to attachment and sleep heterogeneity, aiming to guide future research on the topic.

scholarly journals Genetic variation in dispersal plasticity in an aquatic host-parasite model system

2020 ◽  
Author(s):  
Giacomo Zilio ◽  
Louise Solveig Noergaard ◽  
Giovanni Petrucci ◽  
Nathalie Zeballos ◽  
Claire Gougat-Barbera ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Internal State ◽  
Theoretical Models ◽  
Infection Prevalence ◽  
Main Role ◽  
Dependent Plasticity ◽  
Evolutionary Forces ◽  
State Dependent ◽  
Context Dependent ◽  
Host Parasite

Dispersal plays a main role in determining spatial dynamics, and both theory and empirical evidence indicate that evolutionary optima exist for constitutive or plastic dispersal behaviour. Plasticity in dispersal can be influenced by factors both internal (state-dependent) or external (context-dependent) to individuals. Parasitism is interesting in this context, as it can influence both types of host dispersal plasticity: individuals can disperse in response to internal infection status but might also respond to the presence of infected individuals around them. We still know little about the driving evolutionary forces of host dispersal plasticity, but a first requirement is the presence of a genetic basis on which natural selection can act. In this study, we used microcosm dispersal mazes to investigate plastic dispersal of 20 strains of the freshwater protist Paramecium caudatum in response to the bacterial parasite Holospora undulata. We additionally quantified the genetic component of the plastic responses, i.e. the heritability of state- and context-depended dispersal. We found that infection by the parasite can either increase or decrease dispersal of individual strains relative to the uninfected (state-dependent plasticity), and this to be heritable. We also found strain-specific change of dispersal of uninfected Paramecium when exposed to variable infection prevalence (context-dependent plasticity) with very low level of heritability. To our knowledge, this is the first explicit empirical demonstration and quantification of genetic variation of plastic dispersal in a host-parasite system, which could have important implications for meta-population and epidemiological dynamics. We discuss some of the underlying mechanisms of this variation and link our results to the existing theoretical models.

scholarly journals The effect of common inversion polymorphisms In(2L)t and In(3R)Mo on patterns of transcriptional variation in Drosophila melanogaster

2017 ◽  
Author(s):  
Erik Lavington ◽  
Andrew D. Kern
Keyword(s):  
Genetic Variation ◽  
Genomic Sequence ◽  
Position Effect ◽  
Transcript Abundance ◽  
Theoretical Models ◽  
Regulatory Elements ◽  
Sterol Uptake ◽  
Genome Wide ◽  
Transcriptional Variation ◽  
Niemann Pick

AbstractChromosomal inversions are an ubiquitous feature of genetic variation. Theoretical models describe several mechanisms by which inversions can drive adaptation and be maintained as polymorphisms. While inversions have been shown previously to be under selection, or contain genetic variation under selection, the specific phenotypic consequences of inversions leading to their maintenance remain unclear. Here we use genomic sequence and expression data from the Drosophila Genetic Reference Panel to explore the effects of two cosmopolitan inversions, In(2L)t and In(3R)Mo, on patterns of transcriptional variation. We demonstrate that each inversion has a significant effect on transcript abundance for hundreds of genes across the genome. Inversion affected loci (IAL) appear both within inversions as well as on unlinked chromosomes. Importantly, IAL do not appear to be influenced by the previously reported genome-wide expression correlation structure. We found that five genes involved with sterol uptake, four of which are Niemann-Pick Type 2 orthologs, are upregulated in flies with In(3R)Mo but do not have SNPs in LD with the inversion. We speculate that this upregulation is driven by genetic variation in mod(mdg4) that is in LD with In(3R)Mo. We find that there is little evidence for regional or position effect of inversions on gene expression at the chromosomal level but do find evidence for the distal breakpoint of In(3R)Mo interrupting one gene and possibly disassociating the two flanking genes from regulatory elements.

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