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

2014 ◽  
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 (Δz = Gβ), which predicts evolutionary change for a suite of phenotypic traits (Δz) 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 ofGandβto 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 evidence that sexually selected traits exhibit faster rates of evolution compared to 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 ofGwe 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 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.

The causes and consequences of ornament variation in a natural population

2019 ◽  
Author(s):  
Annabel Ralph ◽  
Terry Burke ◽  
Shinichi Nakagawa ◽  
Alfredo Sánchez-Tójar ◽  
Julia Schroeder
Keyword(s):  
Sexual Selection ◽  
Evolutionary Biology ◽  
Natural Populations ◽  
Size Variation ◽  
Evolutionary Potential ◽  
House Sparrows ◽  
Sexually Selected Traits ◽  
Evolutionary Response ◽  
Significant Heritability ◽  
Selected Traits

The role of sexual selection in natural populations has long been the subject of debate in evolutionary biology. Ornaments are sexually selected traits, which means they should vary within a population, have a genetic basis, and be associated with fitness. Despite evidence of ornaments meeting these criteria, evolutionary responses to sexual selection are rare in nature. This study focuses on two ornaments in a population of house sparrows; the plumage badge has been well-studied but remains poorly understood and the mask has been largely neglected in the literature. Using quantitative genetic techniques, we estimate the heritability of both traits and test for age-dependency of the heritability estimates. We also estimate the strength and direction of any selection acting upon the traits. We found that both ornaments have low, significant heritability, which does not vary with age. Selection only occurs in a small number of years, although when it does it is positive in both ornaments. We also found that early social environment plays a role in badge size variation. The results of this study suggest that an evolutionary response in the ornaments of this population is unlikely, but we highlight the importance of long-term research to improve our understanding of evolution in natural populations. Studies like these will add to our understanding of sexual selection, the causes of trait variation and the evolutionary potential of traits, which could help us to predict how populations will evolve.

scholarly journals Genetic architecture influences when and how hybridization contributes to colonization

2019 ◽  
Author(s):  
Bryan Reatini ◽  
Todd J. Vision
Keyword(s):  
Environmental Conditions ◽  
Genetic Architecture ◽  
Genetic Variance ◽  
De Novo ◽  
Dispersal Rate ◽  
Intraspecific Hybridization ◽  
Source Populations ◽  
Second Category ◽  
Do So

AbstractThe role of genetic architecture in adaptation to novel environments has received considerable attention when the source of adaptation variation is de novo mutation. Relatively less is known when the source of adaptive variation is inter- or intraspecific hybridization. We model hybridization between divergent source populations and subsequent colonization of an unoccupied novel environment using individual-based simulations in order to understand the influence of genetic architecture on the timing of colonization and the mode of adaptation. We find that two distinct categories of genetic architecture facilitate rapid colonization but that they do so in qualitatively different ways. For few and/or tightly linked loci, the mode of adaptation is via the recovery of adaptive parental genotypes. With many unlinked loci, the mode of adaptation is via the generation of novel hybrid genotypes. The first category results in the shortest colonization lag phases across the widest range of parameter space, but further adaptation is mutation limited. The second category takes longer and is more sensitive to genetic variance and dispersal rate, but can facilitate adaptation to environmental conditions which exceed the tolerance of parental populations. These findings have implications for understanding the origins of biological invasions and the success of hybrid populations.

scholarly journals Genetic architecture of four smoking behaviors using partitioned h2SNP

2020 ◽  
Author(s):  
Luke M. Evans ◽  
Seonkyeong Jang ◽  
Marissa A. Ehringer ◽  
Jacqueline M. Otto ◽  
Scott I. Vrieze ◽  
...  
Keyword(s):  
Smoking Cessation ◽  
Genetic Architecture ◽  
Genetic Variance ◽  
Rare Variants ◽  
Low Frequency ◽  
Smoking Initiation ◽  
Uk Biobank ◽  
Genome Wide ◽  
Smoking Behaviors

AbstractBackground and AimsSmoking is a leading cause of premature death. Although genome-wide association studies have identified many loci that influence smoking behaviors, much of the genetic variance in these traits remains unexplained. We sought to characterize the genetic architecture of four smoking behaviors through SNP-based heritability (h2SNP) analyses.DesignWe applied recently-developed partitioned h2SNP approaches to smoking behavior traits assessed in the UK Biobank.SettingUK Biobank.ParticipantsUK Biobank participants of European ancestry. The number of participants varied depending on the trait, from 54,792 to 323,068.MeasurementsSmoking initiation, age of initiation, cigarettes per day (CPD; count, log-transformed, binned, and dichotomized into heavy versus light), and smoking cessation. Imputed genome-wide SNPs.FindingsWe estimated h2SNP(SE)=0.18(0.01) for smoking initiation and 0.12(0.02) for smoking cessation, which were more than twice the previously reported estimates. Estimated age of initiation h2SNP=0.05(0.01) and binned CPD h2SNP=0.1(0.01) were similar to previous reports. These estimates remained substantially below published twin-based h2 of roughly 50%. CPD encoding strongly influenced estimates, with dichotomized CPD h2SNP=0.28. We found significant contributions of low-frequency variants and variants in low linkage-disequilibrium (LD) with surrounding genomic regions. Functional annotations related to LD, allele frequency, sequence conservation, and selective constraint also contributed significantly to the partitioned heritability. We found no evidence of dominance genetic variance for any trait.Conclusionh2SNP of these four specific smoking behaviors is modest overall. The patterns of partitioned h2SNP for these highly polygenic traits is consistent with negative selection. We found a predominant contribution of common variants, and our results suggest a role of low-frequency or rare variants, poorly tagged by surrounding regions. Deep sequencing of large samples and/or improved imputation will be required to fully assess the role of rare variants.

scholarly journals Sexual selection and natural selection in bird speciation

1998 ◽  
Vol 353 (1366) ◽  
pp. 251-260 ◽  
Author(s):  
Trevor Price
Keyword(s):  
Sexual Selection ◽  
Adaptive Radiation ◽  
Species Recognition ◽  
Correlated Response ◽  
Premating Isolation ◽  
Sexual Imprinting ◽  
Sexually Selected Traits ◽  
Isolating Mechanisms ◽  
Selected Traits

The role of sexual selection in speciation is investigated, addressing two main issues. First, how do sexually selected traits become species recognition traits? Theory and empirical evidence suggest that female preferences often do not evolve as a correlated response to evolution of male traits. This implies that, contrary to runaway (Fisherian) models of sexual selection, premating isolation will not arise as an automatic side effect of divergence between populations in sexually selected traits. I evaluate premating isolating mechanisms in one group, the birds. In this group premating isolation is often a consequence of sexual imprinting, whereby young birds learn features of their parents and use these features in mate choice. Song, morphology and plumage are known recognition cues. I conclude that perhaps the main role for sexual selection in speciation is in generating differences between populations in traits. Sexual imprinting then leads to these traits being used as species recognition mechanisms. The second issue addressed in this paper is the role of sexual selection in adaptive radiation, again concentrating on birds. Ecological differences between species include large differences in size, which may in themselves be sufficient for species recognition, and differences in habitat, which seem to evolve frequently and at all stages of an adaptive radiation. Differences in habitat often cause song and plumage patterns to evolve as a result of sexual selection for efficient communication. Therefore sexual selection is likely to have an important role in generating premating isolating mechanisms throughout an adaptive radiation. It is also possible that sexual selection, by creating more allopatric species, creates more opportunity for ecological divergence to occur. The limited available evidence does not support this idea. A role for sexual selection in accelerating ecological diversification has yet to be demonstrated.

scholarly journals Genomic analysis reveals a polygenic architecture of antler morphology in wild red deer (Cervus elaphus)

2021 ◽  
Author(s):  
Lucy Peters ◽  
Jisca Huisman ◽  
Loeske E.B. Kruuk ◽  
Josephine M. Pemberton ◽  
Susan E. Johnston
Keyword(s):  
Genetic Variation ◽  
Cervus Elaphus ◽  
Genetic Architecture ◽  
Empirical Bayes ◽  
Red Deer ◽  
Genetic Correlations ◽  
Rapid Evolution ◽  
Genomic Analysis ◽  
Sexually Selected Traits ◽  
Selected Traits

AbstractSexually-selected traits show large variation and rapid evolution across the animal kingdom, yet genetic variation often persists within populations despite apparent directional selection. A key step in solving this long-standing paradox is to determine the genetic architecture of sexually-selected traits to understand evolutionary drivers and constraints at the genomic level. Antlers are a form of sexual weaponry in male red deer. On the island of Rum, Scotland, males with larger antlers have increased breeding success, yet there has been no response to selection observed at the genetic level. To better understand the underlying mechanisms of this observation, we investigate the genetic architecture of ten antler traits and their principle components using genomic data from >38,000 SNPs. We estimate the heritabilities and genetic correlations of the antler traits using a genomic relatedness approach. We then use genome-wide association and haplotype-based regional heritability to identify regions of the genome underlying antler morphology, and an Empirical Bayes approach to estimate the underlying distributions of allele effect sizes. We show that antler morphology is heritable with a polygenic architecture, highly repeatable over an individual’s lifetime, and that almost all aspects are positively genetically correlated with some loci identified as having pleiotropic effects. Our findings suggest that a large mutational target and pleiotropy with traits sharing similar complex polygenic architectures are likely to contribute to the maintenance of genetic variation in antler morphology in this population.

scholarly journals Robust methods for detecting convergent shifts in evolutionary rates

2018 ◽  
Author(s):  
Raghavendran Partha ◽  
Amanda Kowalczyk ◽  
Nathan Clark ◽  
Maria Chikina
Keyword(s):  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Evolutionary Rates ◽  
Sequence Evolution ◽  
Protein Coding ◽  
Robust Detection ◽  
Genetic Elements ◽  
Rates Of Evolution ◽  
Improved Performance

AbstractIdentifying genomic elements underlying phenotypic adaptations is an important problem in evolutionary biology. Comparative analyses learning from convergent evolution of traits are gaining momentum in accurately detecting such elements. We previously developed a method for predicting phenotypic associations of genetic elements by contrasting patterns of sequence evolution in species showing a phenotype with those that do not. Using this method, we successfully demonstrated convergent evolutionary rate shifts in genetic elements associated with two phenotypic adaptations, namely the independent subterranean and marine transitions of terrestrial mammalian lineages. Our method calculates gene-specific rates of evolution on branches of phylogenetic trees using linear regression. These rates represent the extent of sequence divergence on a branch after removing the expected divergence on the branch due to background factors. The rates calculated using this regression analysis exhibit an important statistical limitation, namely heteroscedasticity. We observe that the rates on branches that are longer on average show higher variance, and describe how this problem adversely affects the confidence with which we can make inferences about rate shifts. Using a combination of data transformation and weighted regression, we have developed an updated method that corrects this heteroscedasticity in the rates. We additionally illustrate the improved performance offered by the updated method at robust detection of convergent rate shifts in phylogenetic trees of protein-coding genes across mammals, as well as using simulated tree datasets. Overall, we present an important extension to our evolutionary-rates-based method that performs more robustly and consistently at detecting convergent shifts in evolutionary rates.

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