scholarly journals Testing the neutral hypothesis of phenotypic evolution

2017 ◽  
Vol 114 (46) ◽  
pp. 12219-12224 ◽  
Author(s):  
Wei-Chin Ho ◽  
Yoshikazu Ohya ◽  
Jianzhi Zhang
Keyword(s):  
Morphological Traits ◽  
Genetic Model ◽  
Morphological Evolution ◽  
Model Organisms ◽  
Functional Genes ◽  
Phenotypic Traits ◽  
Phenotypic Evolution ◽  
Important Principle ◽  
Phenotypic Variations ◽  
Evolution By Natural Selection

Although evolution by natural selection is widely regarded as the most important principle of biology, it is unknown whether phenotypic variations within and between species are mostly adaptive or neutral due to the lack of relevant studies of large, unbiased samples of phenotypic traits. Here, we examine 210 yeast morphological traits chosen because of experimental feasibility irrespective of their potential adaptive values. Our analysis is based on the premise that, under neutrality, the rate of phenotypic evolution measured in the unit of mutational size declines as the trait becomes more important to fitness, analogous to the neutral paradigm that functional genes evolve more slowly than functionless pseudogenes. However, we find faster evolution of more important morphological traits within and between species, rejecting the neutral hypothesis. By contrast, an analysis of 3,466 gene expression traits fails to refute neutrality. Thus, at least in yeast, morphological evolution appears largely adaptive, but the same may not apply to other classes of phenotypes. Our neutrality test is applicable to other species, especially genetic model organisms, for which estimations of mutational size and trait importance are relatively straightforward.

scholarly journals Testing the neutral hypothesis of phenotypic evolution

2016 ◽  
Author(s):  
Wei-Chin Ho ◽  
Yoshikazu Ohya ◽  
Jianzhi Zhang
Keyword(s):  
Morphological Traits ◽  
Genomic Sequence ◽  
Morphological Evolution ◽  
Large Fraction ◽  
Neutral Theory ◽  
Phenotypic Evolution ◽  
Sequence Variations ◽  
Genomic Studies ◽  
The One ◽  
Multiple Strains

It is generally accepted that a large fraction of genomic sequence variations within and between species are neutral or nearly so1. Whether the same is true for phenotypic variations is a central question in biology2-7. On the one hand, numerous phenotypic adaptations have been documented2,8,9 and even Kimura, the champion of the neutral theory of molecular evolution, believed in widespread adaptive phenotypic evolution1. On the other hand, phenotypic studies are strongly biased toward traits that are likely to be adaptive9, contrasting genomic studies that are typically unbiased. It is thus desirable to test the neutral hypothesis of phenotypic evolution using traits irrespective of their potential involvement in adaptation. Here we present such a test for 210 morphological traits measured in multiple strains of the yeast Saccharomyces cerevisiae and two related species. Our test is based on the premise that, under neutrality, the rate of phenotypic evolution declines as the trait becomes more important to fitness, analogous to the neutral paradigm that functional genes evolve more slowly than functionless pseudogenes10. Neutrality is rejected in favor of adaptation if important traits evolve faster than less important ones, parallel to the demonstration of molecular adaptation when a functional gene evolves faster than pseudogenes. After controlling for the mutational size, we find faster evolution of more important morphological traits within and between species. By contrast, an analysis of 3466 yeast gene expression traits fails to reject neutrality. Thus, yeast morphological evolution is largely adaptive, but the same may not apply to other classes of phenotypes.

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 Insights into mammalian biology from the wild house mouse Mus musculus

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Megan Phifer-Rixey ◽  
Michael W Nachman
Keyword(s):  
House Mouse ◽  
Mus Musculus ◽  
Genetic Model ◽  
Inbred Strains ◽  
Mendelian Inheritance ◽  
Model Organisms ◽  
House Mice ◽  
Small Subset ◽  
Wild Mice ◽  
Wide Range

The house mouse, Mus musculus, was established in the early 1900s as one of the first genetic model organisms owing to its short generation time, comparatively large litters, ease of husbandry, and visible phenotypic variants. For these reasons and because they are mammals, house mice are well suited to serve as models for human phenotypes and disease. House mice in the wild consist of at least three distinct subspecies and harbor extensive genetic and phenotypic variation both within and between these subspecies. Wild mice have been used to study a wide range of biological processes, including immunity, cancer, male sterility, adaptive evolution, and non-Mendelian inheritance. Despite the extensive variation that exists among wild mice, classical laboratory strains are derived from a limited set of founders and thus contain only a small subset of this variation. Continued efforts to study wild house mice and to create new inbred strains from wild populations have the potential to strengthen house mice as a model system.

scholarly journals Biomechanical trade-offs bias rates of evolution in the feeding apparatus of fishes

2011 ◽  
Vol 279 (1732) ◽  
pp. 1287-1292 ◽  
Author(s):  
Roi Holzman ◽  
David C. Collar ◽  
Samantha A. Price ◽  
C. Darrin Hulsey ◽  
Robert C. Thomson ◽  
...  
Keyword(s):  
Genetic Factors ◽  
Morphological Evolution ◽  
The Body ◽  
Body Parts ◽  
Phenotypic Evolution ◽  
Genetic Constraints ◽  
Functional Systems ◽  
Rates Of Evolution ◽  
Trade Offs

Morphological diversification does not proceed evenly across the organism. Some body parts tend to evolve at higher rates than others, and these rate biases are often attributed to sexual and natural selection or to genetic constraints. We hypothesized that variation in the rates of morphological evolution among body parts could also be related to the performance consequences of the functional systems that make up the body. Specifically, we tested the widely held expectation that the rate of evolution for a trait is negatively correlated with the strength of biomechanical trade-offs to which it is exposed. We quantified the magnitude of trade-offs acting on the morphological components of three feeding-related functional systems in four radiations of teleost fishes. After accounting for differences in the rates of morphological evolution between radiations, we found that traits that contribute more to performance trade-offs tend to evolve more rapidly, contrary to the prediction. While ecological and genetic factors are known to have strong effects on rates of phenotypic evolution, this study highlights the role of the biomechanical architecture of functional systems in biasing the rates and direction of trait evolution.

scholarly journals A circadian clock in Saccharomyces cerevisiae

2010 ◽  
Vol 107 (5) ◽  
pp. 2043-2047 ◽  
Author(s):  
Zheng Eelderink-Chen ◽  
Gabriella Mazzotta ◽  
Marcel Sturre ◽  
Jasper Bosman ◽  
Till Roenneberg ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Model ◽  
Circadian Clocks ◽  
Model Systems ◽  
Model Organisms ◽  
Biological Clocks ◽  
Experimental Systems ◽  
Fundamental Biological Process ◽  
Free Running ◽  
And Behavior

Circadian timing is a fundamental biological process, underlying cellular physiology in animals, plants, fungi, and cyanobacteria. Circadian clocks organize gene expression, metabolism, and behavior such that they occur at specific times of day. The biological clocks that orchestrate these daily changes confer a survival advantage and dominate daily behavior, for example, waking us in the morning and helping us to sleep at night. The molecular mechanism of circadian clocks has been sketched out in genetic model systems from prokaryotes to humans, revealing a combination of transcriptional and posttranscriptional pathways, but the clock mechanism is far from solved. Although Saccharomyces cerevisiae is among the most powerful genetic experimental systems and, as such, could greatly contribute to our understanding of cellular timing, it still remains absent from the repertoire of circadian model organisms. Here, we use continuous cultures of yeast, establishing conditions that reveal characteristic clock properties similar to those described in other species. Our results show that metabolism in yeast shows systematic circadian entrainment, responding to cycle length and zeitgeber (stimulus) strength, and a (heavily damped) free running rhythm. Furthermore, the clock is obvious in a standard, haploid, auxotrophic strain, opening the door for rapid progress into cellular clock mechanisms.

scholarly journals Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows

2020 ◽  
Author(s):  
Dan Sun ◽  
Thomas S. Layman ◽  
Hyeonsoo Jeong ◽  
Paramita Chatterjee ◽  
Kathleen Grogan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Chromosome Pair ◽  
Dna Methyltransferases ◽  
Model Organisms ◽  
Phenotypic Traits ◽  
Zonotrichia Albicollis ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Nucleotide Resolution

ABSTRACTDNA methylation is known to play critical roles in key biological processes. Most of our knowledge on regulatory impacts of DNA methylation has come from laboratory-bred model organisms, which may not exhibit the full extent of variation found in wild populations. Here, we investigated naturally-occurring variation in DNA methylation in a wild avian species, the white-throated sparrow (Zonotrichia albicollis). This species offers exceptional opportunities for studying the link between genetic differentiation and phenotypic traits because of a non-recombining chromosome pair linked to both plumage and behavioral phenotypes. Using novel single-nucleotide resolution methylation maps and gene expression data, we show that DNA methylation and the expression of DNA methyltransferases are significantly higher in adults than in nestlings. Genes for which DNA methylation varied between nestlings and adults were implicated in development and cell differentiation and were located throughout the genome. In contrast, differential methylation between plumage morphs was localized to the non-recombining chromosome pair. One subset of CpGs on the non-recombining chromosome was extremely hypomethylated and localized to transposable elements. Changes in methylation predicted changes in gene expression for both chromosomes. In summary, we demonstrate changes in genome-wide DNA methylation that are associated with development and with specific functional categories of genes in white-throated sparrows. Moreover, we observe substantial DNA methylation reprogramming associated with the suppression of recombination, with implications for genome integrity and gene expression divergence. These results offer an unprecedented view of ongoing epigenetic reprogramming in a wild population.

The Intellectual Challenge of Morphological Evolution: A Case for Variational Structuralism

2014 ◽  
Author(s):  
Günter P. Wagner
Keyword(s):  
Developmental Biology ◽  
Evolutionary Biology ◽  
Morphological Evolution ◽  
Evolutionary Developmental Biology ◽  
Phenotypic Evolution ◽  
Developmental Variation ◽  
Core Idea ◽  
Intellectual Challenge

This chapter explores variational structuralism, whose core idea is that organisms and their parts play causal roles in shaping the patterns of phenotypic evolution. Drawing on the work of pioneers such as Ron Amundson, it discusses the conceptual incompatibilities between two styles of thinking in evolutionary biology: functionalism and structuralism. It proceeds by explaining the meaning of developmental types and structuralist concepts arising from macromolecular studies. It also examines facts and ideas about bodies, Rupert Riedl's theory of the “immitatory epigenotype,” and Neil Shubin and Pere Alberch's developmental interpretation of tetrapod limbs. Finally, it looks at the emergence of molecular structuralism and the enigma of developmental variation. The chapter argues that typology naturally emerged from the facts of evolutionary developmental biology and that it would be seriously problematic to try to avoid it.

scholarly journals Impact of transition to a subterranean lifestyle on morphological disparity and integration in talpid moles (Mammalia, Talpidae)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Gabriele Sansalone ◽  
Paolo Colangelo ◽  
Anna Loy ◽  
Pasquale Raia ◽  
Stephen Wroe ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Morphological Variability ◽  
Phenotypic Integration ◽  
Phenotypic Traits ◽  
Phenotypic Evolution ◽  
Morphological Disparity ◽  
Morphological Diversification ◽  
Phylogenetic Conservatism ◽  
Selective Forces ◽  
Subterranean Species

Abstract Background Understanding the mechanisms promoting or constraining morphological diversification within clades is a central topic in evolutionary biology. Ecological transitions are of particular interest because of their influence upon the selective forces and factors involved in phenotypic evolution. Here we focused on the humerus and mandibles of talpid moles to test whether the transition to the subterranean lifestyle impacted morphological disparity and phenotypic traits covariation between these two structures. Results Our results indicate non-subterranean species occupy a significantly larger portion of the talpid moles morphospace. However, there is no difference between subterranean and non-subterranean moles in terms of the strength and direction of phenotypic integration. Conclusions Our study shows that the transition to a subterranean lifestyle significantly reduced morphological variability in talpid moles. However, this reduced disparity was not accompanied by changes in the pattern of traits covariation between the humerus and the mandible, suggesting the presence of strong phylogenetic conservatism within this pattern.

scholarly journals Standardized mounting method of (zebrafish) embryos using a 3D-printed stamp for high-content, semi-automated confocal imaging

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
David Simon Kleinhans ◽  
Virginie Lecaudey
Keyword(s):  
Coordinate System ◽  
Light Exposure ◽  
Confocal Imaging ◽  
Model Organisms ◽  
Limiting Factor ◽  
Phenotypic Traits ◽  
Embryo Morphology ◽  
Zebrafish Embryos ◽  
High Content Imaging ◽  
3D Printed

Abstract Background Developmental biology relies to a large extent on the observation and comparison of phenotypic traits through time using high resolution microscopes. In this context, transparent model organisms such as the zebrafish Danio rerio in which developing tissues and organs can be easily observed and imaged using fluorescent proteins have become very popular. One limiting factor however is the acquisition of a sufficient amount of data, in standardized and reproducible conditions, to allow robust quantitative analysis. One way to improve this is by developing mounting methods to increase the number of embryos that can be imaged simultaneously in near-to-identical orientation. Results Here we present an improved mounting method allowing semi-automated and high-content imaging of zebrafish embryos. It is based on a 3D-printed stamp which is used to create a 2D coordinate system of multiple μ-wells in an agarose cast. Each μ-well models a negative of the average zebrafish embryo morphology between 22 and 96 h-post-fertilization. Due to this standardized and reproducible arrangement, it is possible to define a custom well plate in the respective imaging software that allows for a semi-automated imaging process. Furthermore, the improvement in Z-orientation significantly reduces post-processing and improves comparability of volumetric data while reducing light exposure and thus photo-bleaching and photo-toxicity, and improving signal-to-noise ratio (SNR). Conclusions We present here a new method that allows to standardize and improve mounting and imaging of embryos. The 3D-printed stamp creates a 2D coordinate system of μ-wells in an agarose cast thus standardizing specimen mounting and allowing high-content imaging of up to 44 live or mounted zebrafish embryos simultaneously in a semi-automated, well-plate like manner on inverted confocal microscopes. In summary, image data quality and acquisition efficiency (amount of data per time) are significantly improved. The latter might also be crucial when using the services of a microscopy facility.

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