scholarly journals Modern spandrels: The roles of genetic drift, gene flow and natural selection in the formation of parallel clines

2018 ◽  
Author(s):  
James S. Santangelo ◽  
Marc T. J. Johnson ◽  
Rob W. Ness
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Genetic Architecture ◽  
Natural Populations ◽  
Urban Environments ◽  
Phenotypic Change ◽  
Phenotypic Traits ◽  
Evolutionary Processes ◽  
Urbanization Gradients

AbstractUrban environments offer the opportunity to study the role of adaptive and non-adaptive evolutionary processes on an unprecedented scale. While the presence of parallel clines in heritable phenotypic traits is often considered strong evidence for the role of natural selection, non-adaptive evolutionary processes can also generate clines, and this may be more likely when traits have a non-additive genetic basis due to epistasis. In this paper, we use spatially-explicit simulations modelled according to the cyanogenesis (HCN) polymorphism in white clover (Trifolium repens) to examine the formation of phenotypic clines along urbanization gradients under varying levels of drift, gene flow and selection. HCN results from an epistatic interaction between two Mendelian-inherited loci. Our results demonstrate that the genetic architecture of this trait makes natural populations susceptible to decreases in HCN frequencies via drift. Gradients in the strength of drift across a landscape resulted in phenotypic clines with lower frequencies of HCN in strongly drifting populations, giving the misleading appearance of deterministic adaptive changes in the phenotype. Studies of heritable phenotypic change in urban populations should generate null models of phenotypic evolution based on the genetic architecture underlying focal traits prior to invoking selection’s role in generating adaptive differentiation.

scholarly journals Modern spandrels: the roles of genetic drift, gene flow and natural selection in the evolution of parallel clines

2018 ◽  
Vol 285 (1878) ◽  
pp. 20180230 ◽  
Author(s):  
James S. Santangelo ◽  
Marc T. J. Johnson ◽  
Rob W. Ness
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Genetic Architecture ◽  
Natural Populations ◽  
Urban Environments ◽  
Phenotypic Change ◽  
Phenotypic Traits ◽  
Evolutionary Processes ◽  
Urbanization Gradients

Urban environments offer the opportunity to study the role of adaptive and non-adaptive evolutionary processes on an unprecedented scale. While the presence of parallel clines in heritable phenotypic traits is often considered strong evidence for the role of natural selection, non-adaptive evolutionary processes can also generate clines, and this may be more likely when traits have a non-additive genetic basis due to epistasis. In this paper, we use spatially explicit simulations modelled according to the cyanogenesis (hydrogen cyanide, HCN) polymorphism in white clover ( Trifolium repens ) to examine the formation of phenotypic clines along urbanization gradients under varying levels of drift, gene flow and selection. HCN results from an epistatic interaction between two Mendelian-inherited loci. Our results demonstrate that the genetic architecture of this trait makes natural populations susceptible to decreases in HCN frequencies via drift. Gradients in the strength of drift across a landscape resulted in phenotypic clines with lower frequencies of HCN in strongly drifting populations, giving the misleading appearance of deterministic adaptive changes in the phenotype. Studies of heritable phenotypic change in urban populations should generate null models of phenotypic evolution based on the genetic architecture underlying focal traits prior to invoking selection's role in generating adaptive differentiation.

scholarly journals Heritability of DNA methylation in threespine stickleback (Gasterosteus aculeatus)

Genetics ◽  
2021 ◽  
Vol 217 (1) ◽  
Author(s):  
Juntao Hu ◽  
Sara J S Wuitchik ◽  
Tegan N Barry ◽  
Heather A Jamniczky ◽  
Sean M Rogers ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genetic Architecture ◽  
Gasterosteus Aculeatus ◽  
Additive Genetic Variance ◽  
Natural Populations ◽  
Threespine Stickleback ◽  
Phenotypic Change ◽  
Cpg Sites ◽  
Cis And Trans ◽  
Methylation Variation

Abstract Epigenetic mechanisms underlying phenotypic change are hypothesized to contribute to population persistence and adaptation in the face of environmental change. To date, few studies have explored the heritability of intergenerationally stable methylation levels in natural populations, and little is known about the relative contribution of cis- and trans-regulatory changes to methylation variation. Here, we explore the heritability of DNA methylation, and conduct methylation quantitative trait loci (meQTLs) analysis to investigate the genetic architecture underlying methylation variation between marine and freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We quantitatively measured genome-wide DNA methylation in fin tissue using reduced representation bisulfite sequencing of F1 and F2 crosses, and their marine and freshwater source populations. We identified cytosines (CpG sites) that exhibited stable methylation levels across generations. We found that additive genetic variance explained an average of 24–35% of the methylation variance, with a number of CpG sites possibly autonomous from genetic control. We also detected both cis- and trans-meQTLs, with only trans-meQTLs overlapping with previously identified genomic regions of high differentiation between marine and freshwater ecotypes. Finally, we identified the genetic architecture underlying two key CpG sites that were differentially methylated between ecotypes. These findings demonstrate a potential role for DNA methylation in facilitating adaptation to divergent environments and improve our understanding of the heritable basis of population epigenomic variation.

scholarly journals Evolutionary rates for multivariate traits: the role of selection and genetic variation

2014 ◽  
Vol 369 (1649) ◽  
pp. 20130252 ◽  
Author(s):  
William Pitchers ◽  
Jason B. Wolf ◽  
Tom Tregenza ◽  
John Hunt ◽  
Ian Dworkin
Keyword(s):  
Evolutionary Biology ◽  
Genetic Architecture ◽  
Genetic Variance ◽  
Evolutionary Rates ◽  
Phenotypic Traits ◽  
Sexually Selected Traits ◽  
Rates Of Evolution ◽  
Selected Traits ◽  
Multivariate Traits

A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders' equation ( ), which predicts evolutionary change for a suite of phenotypic traits ( ) as a product of directional selection acting on them ( β ) and the genetic variance–covariance matrix for those traits ( G ). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are, in part, due to genetic architecture. We find some evidence that sexually selected traits exhibit faster rates of evolution compared with life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G , we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates.

scholarly journals Two-locus identity probabilities and identity disequilibrium in a partially selfing subdivided population

2001 ◽  
Vol 77 (1) ◽  
pp. 67-81 ◽  
Author(s):  
RENAUD VITALIS ◽  
DENIS COUVET
Keyword(s):  
Gene Flow ◽  
Natural Populations ◽  
Population Data ◽  
Selfing Rate ◽  
Measures Of Association ◽  
Mutation Model ◽  
Subdivided Population ◽  
Selection For ◽  
The Difference

Measures of association of genes at different loci (linkage disequilibrium) are widely used to determine whether the structure of natural populations is clonal or not, to map genes from population data, or to test for the homogeneity of response of molecular markers to background selection, for example. However, the usual definitions of parameters for gametic associations may not be suitable for all these purposes. In this paper, we derive the recursion equations for one- and two-locus identity probabilities in an infinite island model. We study the role of drift, gene flow, partial selfing and mutation model on the expected association of genes across loci. We define the ‘within-subpopulation identity disequilibrium’ as the difference between the joint two-locus probability of identity in state and the expected product of one-locus identity probabilities. We evaluate this parameter as a function of recombination rate, effective size, gene flow and selfing rate. Within-subpopulation identity disequilibrium attains maximum values for intermediate immigration rates, whatever the selfing rate. Moreover, identity disequilibrium may be very small, even for high selfing rates. We discuss the implications of these findings for the analysis of data from natural populations.

scholarly journals Variations of Secondary Metabolites among Natural Populations of Sub-Antarctic Ranunculus Species Suggest Functional Redundancy and Versatility

Plants ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 234 ◽  
Author(s):  
Bastien Labarrere ◽  
Andreas Prinzing ◽  
Thomas Dorey ◽  
Emeline Chesneau ◽  
Françoise Hennion
Keyword(s):  
High Performance Liquid Chromatography ◽  
Liquid Chromatography ◽  
High Performance ◽  
Environmental Changes ◽  
Environmental Gradients ◽  
Natural Populations ◽  
Phenotypic Traits ◽  
Geographical Regions ◽  
The Relationship

Plants produce a high diversity of metabolites which help them sustain environmental stresses and are involved in local adaptation. However, shaped by both the genome and the environment, the patterns of variation of the metabolome in nature are difficult to decipher. Few studies have explored the relative parts of geographical region versus environment or phenotype in metabolomic variability within species and none have discussed a possible effect of the region on the correlations between metabolites and environments or phenotypes. In three sub-Antarctic Ranunculus species, we examined the role of region in metabolite differences and in the relationship between individual compounds and environmental conditions or phenotypic traits. Populations of three Ranunculus species were sampled across similar environmental gradients in two distinct geographical regions in îles Kerguelen. Two metabolite classes were studied, amines (quantified by high-performance liquid chromatography and fluorescence spectrophotometry) and flavonols (quantified by ultra-high-performance liquid chromatography with triple quadrupole mass spectrometry). Depending on regions, the same environment or the same trait may be related to different metabolites, suggesting metabolite redundancy within species. In several cases, a given metabolite showed different or even opposite relations with the same environmental condition or the same trait across the two regions, suggesting metabolite versatility within species. Our results suggest that metabolites may be functionally redundant and versatile within species, both in their response to environments and in their relation with the phenotype. These findings open new perspectives for understanding evolutionary responses of plants to environmental changes.

scholarly journals Exploring the potential of gametic reconstruction of parental genotypes by F1 hybrids as a bridge for rapid introgression

Genome ◽  
2017 ◽  
Vol 60 (9) ◽  
pp. 713-719 ◽  
Author(s):  
Charles H. Cannon ◽  
C. Lane Scher
Keyword(s):  
Gene Flow ◽  
Genomic Structure ◽  
Natural Populations ◽  
Genomic Analysis ◽  
F1 Hybrids ◽  
Phenotypic Traits ◽  
Crossing Over ◽  
Genetic Introgression ◽  
Apparent Paradox ◽  
Interspecific Gene Flow

Interspecific hybridization and genetic introgression are commonly observed in natural populations of many species, especially trees. Among oaks, gene flow between closely related species has been well documented. And yet, hybridization does not lead to a “melting pot”, i.e., the homogenization of phenotypic traits. Here, we explore how the combination of several common reproductive and genomic traits could create an avenue for interspecific gene flow that partially explains this apparent paradox. During meiosis, F1 hybrids will produce approximately (½)n “reconstructed” parental gametes, where n equals the number of chromosomes. Crossing over would introduce a small amount of introgressive material. The resulting parental-type gametophytes would probably possess a similar fertilization advantage as conspecific pollen. The resulting “backcross” would actually be the genetic equivalent of a conspecific out-cross, with a small amount of heterospecific DNA captured through crossing over. Even with detailed genomic analysis, the resulting offspring would not appear to be a backcross. This avenue for rapid introgression between species through the F1 hybrid will be viable for organisms that meet certain conditions: low base chromosome number, conserved genomic structure and size, production of billions of gametes/gametophytes during each reproductive event, and conspecific fertilization advantage.

Selection

2016 ◽  
Author(s):  
Andrew P. Hendry
Keyword(s):  
Sexual Selection ◽  
Life History ◽  
Gene Flow ◽  
Natural Selection ◽  
Mating Success ◽  
Natural Populations ◽  
Meta Analyses

This chapter begins with a description of how natural selection works and how it is studied in natural populations. It draws on recent meta-analyses to answer fundamental questions about selection in nature, such as how strong and consistent it is, how often it is stabilizing (disfavoring extreme individuals) or disruptive (favoring extreme individuals), what types of traits (e.g., life history or morphology) are under the strongest selection, and how selection differs when fitness is indexed as mating success (sexual selection) or survival/fecundity (natural selection). The chapter also examines selection within “populations,” which are considered to be conspecific groups of individuals within which interbreeding is common (close to panmixia) but among which interbreeding (and therefore gene flow) is restricted.

Population structure and evolutionary progress

Genome ◽  
1989 ◽  
Vol 31 (1) ◽  
pp. 196-202 ◽  
Author(s):  
Montgomery Slatkin
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Genetic Drift ◽  
Natural Populations ◽  
New Combination ◽  
Balance Theory ◽  
Reasonable Time ◽  
Shifting Balance Theory ◽  
Shifting Balance ◽  
Demographic Processes

Wright's shifting-balance theory is discussed as an example of a process that can cause species to evolve combinations of characters that could not evolve under natural selection alone. A review of the existing theory of peak shifts indicates that the conditions of extreme isolation that are necessary to permit genetic drift to alter the outcome of natural selection in local populations would make gene flow too weak to spread a new combination of genes to other populations in a reasonable time. Instead, it seems likely that major demographic changes must occur in a species for the shifting-balance process to work. A discussion of direct and indirect studies of gene flow in natural populations suggests that the current genetic structure of many species is likely to reflect past demographic events rather than ongoing gene flow. It is possible then that demographic processes could be responsible for spreading new traits in a species, but that would be true whether those new traits evolved only owing to natural selection or owing in addition to genetic drift and other forces.Key words: shifting-balance theory, gene flow.

scholarly journals The Role of Adaptation in Archaeological Explanation

1992 ◽  
Vol 57 (1) ◽  
pp. 36-59 ◽  
Author(s):  
Michael J. O'Brien ◽  
Thomas D. Holland
Keyword(s):  
Natural Selection ◽  
Clear Understanding ◽  
Archaeological Record ◽  
Evolutionary Processes ◽  
Ex Post ◽  
Ex Post Facto ◽  
Two Stages ◽  
Prevailing View

Adaptation, a venerable icon in archaeology, often is afforded the vacuous role of being an ex-post-facto argument used to "explain" the appearance and persistence of traits among prehistoric groups—a position that has seriously impeded development of a selectionist perspective in archaeology. Biological and philosophical definitions of adaptation—and by extension, definitions of adaptedness—vary considerably, but all are far removed from those usually employed in archaeology. The prevailing view in biology is that adaptations are features that were shaped by natural selection and that increase the adaptedness of an organism. Thus adaptations are separated from other features that may contribute to adaptedness but are products of other evolutionary processes. Analysis of adaptation comprises two stages: showing that a feature was under selection and how the feature functioned relative to the potential adaptedness of its bearers. The archaeological record contains a wealth of information pertinent to examining the adaptedness of prehistoric groups, but attempts to use it will prove successful only if a clear understanding exists of what adaptation is and is not.

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