Despite evolutionary biology’s obsession with natural selection, few studies have evaluated multigenerational series of patterns of selection on a genome-wide scale in natural populations. Here, we report on a 10-y population-genomic survey of the microcrustacean Daphnia pulex. The genome sequences of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" overflow="scroll"> <mml:mo>></mml:mo> </mml:math> 800 isolates provide insights into patterns of selection that cannot be obtained from long-term molecular-evolution studies, including the following: the pervasiveness of near quasi-neutrality across the genome (mean net selection coefficients near zero, but with significant temporal variance about the mean, and little evidence of positive covariance of selection across time intervals); the preponderance of weak positive selection operating on minor alleles; and a genome-wide distribution of numerous small linkage islands of observable selection influencing levels of nucleotide diversity. These results suggest that interannual fluctuating selection is a major determinant of standing levels of variation in natural populations, challenge the conventional paradigm for interpreting patterns of nucleotide diversity and divergence, and motivate the need for the further development of theoretical expressions for the interpretation of population-genomic data.
Abstract Although the human germline mutation rate is higher than that in any other well-studied species, the rate is not exceptional once the effective genome size and effective population size are taken into consideration. Human somatic mutation rates are substantially elevated above those in the germline, but this is also seen in other species. What is exceptional about humans is the recent detachment from the challenges of the natural environment and the ability to modify phenotypic traits in ways that mitigate the fitness effects of mutations, e.g., precision and personalized medicine. This results in a relaxation of selection against mildly deleterious mutations, including those magnifying the mutation rate itself. The long-term consequence of such effects is an expected genetic deterioration in the baseline human condition, potentially measurable on the timescale of a few generations in westernized societies, and because the brain is a particularly large mutational target, this is of particular concern. Ultimately, the price will have to be covered by further investment in various forms of medical intervention. Resolving the uncertainties of the magnitude and timescale of these effects will require the establishment of stable, standardized, multigenerational measurement procedures for various human traits.
Despite substantial attention from theoreticians, the evolutionary mechanisms that drive intra- and interspecific variation in the mutation rate remain unclear. It has often been argued that mutation rates associated with the major replicative polymerases have been driven down to their physiological limits, defined as the point at which further enhancement in replication fidelity incurs a cost in terms of reproductive output, but no evidence in support of this argument has emerged for cellular organisms. Here, it is suggested that the lower barrier to mutation rate evolution may ultimately be defined not by molecular limitations but by the power of random genetic drift. As the mutation rate is reduced to a very low level, a point will eventually be reached at which the small advantage of any further reduction is overwhelmed by the power of drift. This hypothesis is consistent with a number of observations, including the inverse relationship between the per-site mutation rate and genome size in microbes, the negative scaling between the per-site mutation rate and effective population size in eukaryotes, and the elevated error rates associated with less frequently deployed polymerases and repair pathways.
Although pooled-population sequencing has become a widely used approach for estimating allele frequencies, most work has proceeded in the absence of a proper statistical framework. We introduce a self-sufficient, closed-form, maximum-likelihood estimator for allele frequencies that accounts for errors associated with sequencing, and a likelihood-ratio test statistic that provides a simple means for evaluating the null hypothesis of monomorphism. Unbiased estimates of allele frequencies [Formula: see text] (where N is the number of individuals sampled) appear to be unachievable, and near-certain identification of a polymorphism requires a minor-allele frequency [Formula: see text]. A framework is provided for testing for significant differences in allele frequencies between populations, taking into account sampling at the levels of individuals within populations and sequences within pooled samples. Analyses that fail to account for the two tiers of sampling suffer from very large false-positive rates and can become increasingly misleading with increasing depths of sequence coverage. The power to detect significant allele-frequency differences between two populations is very limited unless both the number of sampled individuals and depth of sequencing coverage exceed 100.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProcessing, Publishing, Storing, Correlating, and Retrieving Biochemical Information at Chemical Abstracts Service.Kenneth H. Zabriskie and Michael F. LynchCite this: J. Chem. Doc. 1966, 6, 1, 30–33Publication Date (Print):February 1, 1966Publication History Published online1 May 2002Published inissue 1 February 1966https://pubs.acs.org/doi/10.1021/c160020a007https://doi.org/10.1021/c160020a007research-articleACS PublicationsRequest reuse permissionsArticle Views14Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Significance Many cellular functions depend on highly specific intermolecular interactions, with mutational changes in each component of the interaction imposing coevolutionary pressure on the remaining members (e.g., a transcription factor and its DNA binding sites). The conflict between mutation pressure toward reduced affinity and selective pressure for greater interaction results in an evolutionary equilibrium distribution for the affinity between interacting partners. Nevertheless, conditional on the maintenance of a critical level of molecular recognition, the sites containing the key residues of binding interfaces are free to evolve. The theory developed suggests that most such evolution is a simple consequence of random genetic drift and not an outcome of adaptive fine tuning.
Abstract SUMMARY: The Genetic Simulation Library (GSL) is a set of C++ programs and classes that can be used in individual-based simulation models of plant and animal populations. The classes in this library build representations of genes for a wide variety of different types of organisms, from asexually reproducing single-cell organisms to chromosome-structured sexually reproducing species. AVAILABILITY: http://www.csi.uoregon.edu/projects/genetics/GSL . Free for non-commercial applications; others should contact the author.
Here is the list of all genes in <em>P. tetraurelia</em>, <em>P. biaurelia</em>, <em>P. sexaurelia</em>, and <em>P. caudatum</em>, for which it is indicated whether they harbor a segregating loss-of-function variant and of which type. <br> These files were generated when performing analyses in the manuscript - "<strong>A population-genetic lens into the process of gene loss following whole-genome duplication"</strong>.
We examined sequence conservation and signatures of selection in Rab7 proteins across 11 <i>Paramecium aurelia</i> species, and determined the localization patterns of two <i>P. tetraurelia</i> Rab7 paralogs when expressed as GFP fusions in live cells. We found that, while there is a variable number of Rab7 paralogs per genome, Rab7 genes are highly conserved in sequence and appear to be under strong purifying selection across <i>aurelias</i>. Additionally, and surprisingly based on earlier studies, we found that two <i>P. tetraurelia</i> Rab7 proteins have virtually identical localization patterns. Consistent with this, when we examined the gene family of a highly conserved Rab binding partner across <i>aurelias</i> (Rab-Interacting Lysosomal Protein, or RILP), we found that residues in key binding sites in RILPs were absolutely conserved in 13 of 21 proteins, representing genes from 9 of the 11 species examined. Of note, RILP gene number appears to be even more constrained than Rab7 gene number per genome. <b>Abbreviation</b>: WGD: Whole genome duplication.
Flagellar-driven motility grants unicellular organisms the ability to gather more food and avoid predators, but the energetic costs of construction and operation of flagella are considerable. Paths of flagellar evolution depend on the deviations between fitness gains and energy costs. Using structural data available for all three major flagellar types (bacterial, archaeal, and eukaryotic), flagellar construction costs were determined for Escherichia coli , Pyrococcus furiosus , and Chlamydomonas reinhardtii . Estimates of cell volumes, flagella numbers, and flagellum lengths from the literature yield flagellar costs for another ~200 species. The benefits of flagellar investment were analysed in terms of swimming speed, nutrient collection, and growth rate; showing, among other things, that the cost-effectiveness of bacterial and eukaryotic flagella follows a common trend. However, a comparison of whole-cell costs and flagellum costs across the Tree of Life reveals that only cells with larger cell volumes than the typical bacterium could evolve the more expensive eukaryotic flagellum. These findings provide insight into the unsolved evolutionary question of why the three domains of life each carry their own type of flagellum.
We examined sequence conservation and signatures of selection in Rab7 proteins across 11 <i>Paramecium aurelia</i> species, and determined the localization patterns of two <i>P. tetraurelia</i> Rab7 paralogs when expressed as GFP fusions in live cells. We found that, while there is a variable number of Rab7 paralogs per genome, Rab7 genes are highly conserved in sequence and appear to be under strong purifying selection across <i>aurelias</i>. Additionally, and surprisingly based on earlier studies, we found that two <i>P. tetraurelia</i> Rab7 proteins have virtually identical localization patterns. Consistent with this, when we examined the gene family of a highly conserved Rab binding partner across <i>aurelias</i> (Rab-Interacting Lysosomal Protein, or RILP), we found that residues in key binding sites in RILPs were absolutely conserved in 13 of 21 proteins, representing genes from 9 of the 11 species examined. Of note, RILP gene number appears to be even more constrained than Rab7 gene number per genome. <b>Abbreviation</b>: WGD: Whole genome duplication
Abstract Flagellar-driven motility grants unicellular organisms the ability to gather more food and avoid predators, but the energetic costs of construction and operation of flagella are considerable. Paths of flagellar evolution depend on the deviations between fitness gains and energy costs. Using structural data available for all three major flagellar types (bacterial, archaeal, and eukaryotic), flagellar construction costs were determined for Escherichia coli, Pyrococcus furiosus , and Chlamydomonas reinhardtii . Estimates of cell volumes, flagella numbers, and flagellum lengths from the literature, yield flagellar costs for another ∼200 species. The benefits of flagellar investment were analysed in terms of swimming speed, nutrient collection, and growth rate; showing, among other things, that the cost-effectiveness of bacterial and eukaryotic flagella follows a common trend. However, a comparison of whole cell costs and flagellum costs across the Tree of Life reveals that only cells with larger cell volumes than the typical bacterium could evolve the more expensive eukaryotic flagellum. These findings provide insight into the unsolved evolutionary question of why the three domains of life each carry their own type of flagellum.
