scholarly journals Codon usage bias in animals: disentangling the effects of natural selection, effective population size and GC-biased gene conversion

2017 ◽  
Author(s):  
N. Galtier ◽  
C. Roux ◽  
M. Rousselle ◽  
J. Romiguier ◽  
E. Figuet ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Population Size ◽  
Gene Conversion ◽  
Effective Population Size ◽  
Codon Usage Bias ◽  
Effective Population ◽  
Translational Selection ◽  
Wide Range ◽  
Biased Gene Conversion

AbstractSelection on codon usage bias is well documented in a number of microorganisms. Whether codon usage is also generally shaped by natural selection in large organisms, despite their relatively small effective population size (Ne), is unclear. Codon usage bias in animals has only been studied in a handful of model organisms so far, and can be affected by confounding, non-adaptive processes such as GC-biased gene conversion and experimental artefacts. Using population transcriptomics data we analysed the relationship between codon usage, gene expression, allele frequency distribution and recombination rate in 31 non-model species of animals, each from a different family, covering a wide range of effective population sizes. We disentangled the effects of translational selection and GC-biased gene conversion on codon usage by separately analysing GC-conservative and GC-changing mutations. We report evidence for effective translational selection on codon usage in large-Ne species of animals, but not in small-Ne ones, in agreement with the nearly neutral theory of molecular evolution. C- and T-ending codons are generally preferred over synonymous G- and A-ending ones, for reasons that remain to be determined. In contrast, we uncovered a conspicuous effect of GC-biased gene conversion, which is widespread in animals and the main force determining the fate of AT↔GC mutations. Intriguingly, the strength of its effect was uncorrelated with Ne.

scholarly journals Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

2018 ◽  
Vol 35 (5) ◽  
pp. 1092-1103 ◽  
Author(s):  
Nicolas Galtier ◽  
Camille Roux ◽  
Marjolaine Rousselle ◽  
Jonathan Romiguier ◽  
Emeric Figuet ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Population Size ◽  
Gene Conversion ◽  
Effective Population Size ◽  
Codon Usage Bias ◽  
Effective Population ◽  
Biased Gene Conversion

scholarly journals The effective population size modulates the strength of GC biased gene conversion in two passerines

2021 ◽  
Author(s):  
Henry J Barton ◽  
Kai Zeng
Keyword(s):  
Population Size ◽  
Gene Conversion ◽  
Effective Population Size ◽  
Zebra Finch ◽  
Nucleotide Diversity ◽  
Gc Content ◽  
Effective Population ◽  
Coding Regions ◽  
Crossover Rate ◽  
Biased Gene Conversion

Understanding the determinants of genomic base composition is fundamental to understanding genome evolution. GC biased gene conversion (gBGC) is a key driving force behind genomic GC content, through the preferential incorporation of GC alleles over AT alleles during recombination, driving them towards fixation. The majority of work on gBGC has focussed on its role in coding regions, largely to address how it confounds estimates of selection. Non-coding regions have received less attention, particularly in regard to the interaction of gBGC and the effective population size (Ne) within and between species. To address this, we investigate how the strength of gBGC (B = 4Neb, where b is the conversion bias) varies within the non-coding genome of two wild passerines. We use a dataset of published high coverage genomes (10 great tits and 10 zebra finches) to estimate B, nucleotide diversity, changes in Ne, and crossover rates from linkage maps, in 1Mb homologous windows in each species. We demonstrate remarkable conservation of both B and crossover rate between species. We show that the mean strength of gBGC in the zebra finch is more than double that in the great tit, consistent with its twofold greater effective population size. B also correlates with both crossover rate and nucleotide diversity in each species. Finally, we estimate equilibrium GC content from both divergence and polymorphism data, which indicates that B has been increasing in both species, and provide support for population expansion explaining a large proportion of this increase in the zebra finch.

scholarly journals Selection in a growing bacterial/yeast colony biases results of mutation accumulation experiments

2021 ◽  
Author(s):  
Anjali Mahilkar ◽  
Sharvari Kemkar ◽  
Supreet Saini
Keyword(s):  
Natural Selection ◽  
Population Size ◽  
Effective Population Size ◽  
Colony Growth ◽  
Mutation Accumulation ◽  
Rate Of Change ◽  
Raw Material ◽  
Effective Population ◽  
The Face ◽  
Mean Fitness

AbstractMutations provide the raw material for natural selection to act. Therefore, understanding the variety and relative frequency of different type of mutations is critical to understanding the nature of genetic diversity in a population. Mutation accumulation (MA) experiments have been used in this context to estimate parameters defining mutation rates, distribution of fitness effects (DFE), and spectrum of mutations. MA experiments performed with organisms such asDrosophilahave an effective population size of one. However, in MA experiments with bacteria and yeast, a single founder is allowed to grow to a size of a colony (~108). The effective population size in these experiments is of the order of 10. In this scenario, while it is assumed that natural selection plays a minimal role in dictating the dynamics of colony growth and therefore, the MA experiment; this effect has not been tested explicitly. In this work, we simulate colony growth and perform an MA experiment, and demonstrate that selection ensures that, in an MA experiment, fraction of all mutations that are beneficial is over represented by a factor greater than two. The DFE of beneficial and deleterious mutations are accurately captured in an MA experiment. We show that the effect of selection in a growing colony varies non-monotonically and that, in the face of natural selection dictating an MA experiment, estimates of mutation rate of an organism is not trivial. We perform experiments with 160 MA lines ofE. coli, and demonstrate that rate of change of mean fitness is a non-monotonic function of the colony size, and that selection acts differently in different sectors of a growing colony. Overall, we demonstrate that the results of MA experiments need to be revisited taking into account the action of selection in a growing colony.

scholarly journals Demography and natural selection have shaped genome-wide variation in the widely distributed conifer Norway Spruce (Picea abies)

2019 ◽  
Author(s):  
Xi Wang ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Picea Abies ◽  
Population Size ◽  
Effective Population Size ◽  
Norway Spruce ◽  
Demographic History ◽  
Sequencing Data ◽  
Effective Population ◽  
Genome Wide

AbstractUnder the neutral theory, species with larger effective population sizes are expected to harbour higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere and it consequently plays a major role in European forestry. Here, we use whole-genome re-sequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an enormous current population size, our analyses find that genetic diversity of P.abies is low across a number of populations (p=0.005-0.006). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterised by several re-occurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

Why Ecology and Evolution Occupy Distinct Epistemic Niches

2019 ◽  
Vol 47 (1) ◽  
pp. 143-165
Author(s):  
Stefan Linquist ◽  
Keyword(s):  
Natural Selection ◽  
Population Size ◽  
Effective Population Size ◽  
Rapid Evolution ◽  
Directional Selection ◽  
Effective Population ◽  
Trait Variation ◽  
Ecological Relationships ◽  
Generally True ◽  
Evolutionary Explanations

Recent examples of rapid evolution under natural selection seem to require that the disciplines of ecology and evolution become better integrated. This inference makes sense only if one’s understanding of these disciplines is based on Hutchinson’s two-speed model of the ecological theater and the evolutionary play. Instead, these disciplines are more accurately viewed as occupying distinct “epistemic niches.” When so understood, we see that rapid evolution under selection, even if it is generally true, does not imply that evolutionary explanations are improved by the inclusion of ecological details. Nor are ecological explanations necessarily improved by the inclusion of information about trait variation, heritability, effective population size, or other standard evolutionary factors. To illustrate, I develop a version of Kitcher’s (1984) “gory details” argument to show that, even for some trait that is under strong directional selection, a dynamically sufficient explanation of its ecological relationships should ignore most of the information explaining why that trait is evolving. The wholesale integration of ecology and evolution looks even less appealing when empirical sufficiency, a purely practical requirement, is taken into account. As a way forward, I propose an eco-evo partitioning framework. This strategy enables researchers to estimate the empirical sufficiency of a purely ecological, a purely evolutionary, or a combined eco-evo approach.

scholarly journals Stabilizing the dynamics of laboratory populations ofDrosophila melanogasterthrough upper and lower limiter controls

2015 ◽  
Author(s):  
Sudipta Tung ◽  
Abhishek Mishra ◽  
Sutirth Dey
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Real Life ◽  
Extinction Probability ◽  
Population Fluctuations ◽  
Control Methods ◽  
Effective Population ◽  
Population Dynamics Model ◽  
Wide Range ◽  
Laboratory Populations

Although a large number of methods exist to control the dynamics of populations to a desired state, few of them have been empirically validated. This limits the scope of using these methods in real-life scenarios. To address this issue, we tested the efficacy of two well-known control methods in enhancing different kinds of stability in highly fluctuating, extinction-prone populations ofDrosophila melanogaster. The Upper Limiter Control (ULC) method was able to reduce the fluctuations in population sizes as well as the extinction probability of the populations. On the negative side, it had no effect on the effective population size and required a large amount of effort. On the other hand, Lower Limiter Control (LLC) enhanced effective population size and reduced extinction probability at a relatively low amount of effort. However, its effects on population fluctuations were equivocal. We examined the population size distributions with and without the control methods, to derive biologically intuitive explanations for how these control methods work. We also show that biologically-realistic simulations, using a very general population dynamics model, are able to capture most of the trends of our data. This suggests that our results are likely to be generalizable to a wide range of scenarios.

scholarly journals Inferring population size history from large samples of genome wide molecular data - an approximate Bayesian computation approach

2016 ◽  
Author(s):  
Simon Boitard ◽  
Willy Rodriguez ◽  
Flora Jay ◽  
Stefano Mona ◽  
Frederic Austeritz
Keyword(s):  
Population Genetics ◽  
Population Size ◽  
Effective Population Size ◽  
Approximate Bayesian Computation ◽  
Recent Common Ancestor ◽  
Bayesian Computation ◽  
Effective Population ◽  
Wide Range ◽  
Complete Genomes ◽  
Approximate Bayesian

Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles.

scholarly journals The genetic structure of populations of orchids and its evolutionary importance: understanding processes from patterns

Lankesteriana ◽  
2016 ◽  
Vol 3 (2) ◽  
Author(s):  
Raymond L. Tremblay
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Genetic Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Mating Systems ◽  
Mutation Rates ◽  
Effective Population ◽  
Genetic Structure Of Populations

<div class="page" title="Page 1"><div class="layoutArea"><div class="column"><p><span>Evolution through either natural selection or genetic drift is dependent on variation at the genetic and mor- phological levels. Processes that influence the genetic structure of populations include mating systems, effective population size, mutation rates and gene flow among populations. </span></p></div></div></div>

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