scholarly journals Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis.

2015 ◽  
Author(s):  
Nicolas Galtier
Keyword(s):  
Amino Acid ◽  
Population Size ◽  
Effective Population Size ◽  
Adaptive Evolution ◽  
Protein Evolution ◽  
Amino Acid Substitution ◽  
Animal Species ◽  
Effective Population ◽  
Large Populations ◽  
Adaptive Processes

The rate at which genomes adapt to environmental changes and the prevalence of adaptive processes in molecular evolution are two controversial issues in current evolutionary genetics. Previous attempts to quantify the genome-wide rate of adaptation through amino-acid substitution have revealed a surprising diversity of patterns, with some species (e.g. Drosophila) experiencing a very high adaptive rate, while other (e.g. humans) are dominated by nearly-neutral processes. It has been suggested that this discrepancy reflects between-species differences in effective population size. Published studies, however, were mainly focused on model organisms, and relied on disparate data sets and methodologies, so that an overview of the prevalence of adaptive protein evolution in nature is currently lacking. Here we extend existing estimators of the amino-acid adaptive rate by explicitly modelling the effect of favourable mutations on non-synonymous polymorphism patterns, and we apply these methods to a newly-built, homogeneous data set of 44 non-model animal species pairs. Data analysis uncovers a major contribution of adaptive evolution to the amino-acid substitution process across all major metazoan phyla - with the notable exception of humans and primates. The proportion of adaptive amino-acid substitution is found to be positively correlated to species effective population size. This relationship, however, appears to be primarily driven by a decreased rate of nearly-neutral amino-acid substitution due to more efficient purifying selection in large populations. Our results reveal that adaptive processes dominate the evolution of proteins in most animal species, but do not corroborate the hypothesis that adaptive substitutions accumulate at a faster rate in large populations. Implications regarding the factors influencing the rate of adaptive evolution and positive selection detection in humans vs. other organisms are discussed.

Changing Effective Population Size and the McDonald-Kreitman Test

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 2017-2024 ◽  
Author(s):  
Adam Eyre-Walker
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Population Size ◽  
Effective Population Size ◽  
Adaptive Evolution ◽  
Synonymous Codon ◽  
Low Frequency ◽  
Effective Population ◽  
Amino Acid Mutations ◽  
Codon Use

Abstract Artifactual evidence of adaptive amino acid substitution can be generated within a McDonald-Kreitman test if some amino acid mutations are slightly deleterious and there has been an increase in effective population size. Here I investigate the conditions under which this occurs. I show that fairly small increases in effective population size can generate artifactual evidence of positive selection if there is no selection upon synonymous codon use. This problem is exacerbated by the removal of low-frequency polymorphisms. However, selection on synonymous codon use restricts the conditions under which artifactual evidence of adaptive evolution is produced.

scholarly journals Adaptive Evolution and Effective Population Size in Wild House Mice

2012 ◽  
Vol 29 (10) ◽  
pp. 2949-2955 ◽  
Author(s):  
M. Phifer-Rixey ◽  
F. Bonhomme ◽  
P. Boursot ◽  
G. A. Churchill ◽  
J. Pialek ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Adaptive Evolution ◽  
House Mice ◽  
Effective Population ◽  
Wild House Mice

scholarly journals Population size influences the type of nucleotide variations in humans

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
High Frequency ◽  
Genetic Diseases ◽  
Large Population ◽  
Low Frequency ◽  
Small Population ◽  
Effective Population ◽  
Genome Data ◽  
Large Populations

Abstract Background It is well known that the effective size of a population (Ne) is one of the major determinants of the amount of genetic variation within the population. However, it is unclear whether the types of genetic variations are also dictated by the effective population size. To examine this, we obtained whole genome data from over 100 populations of the world and investigated the patterns of mutational changes. Results Our results revealed that for low frequency variants, the ratio of AT→GC to GC→AT variants (β) was similar across populations, suggesting the similarity of the pattern of mutation in various populations. However, for high frequency variants, β showed a positive correlation with the effective population size of the populations. This suggests a much higher proportion of high frequency AT→GC variants in large populations (e.g. Africans) compared to those with small population sizes (e.g. Asians). These results imply that the substitution patterns vary significantly between populations. These findings could be explained by the effect of GC-biased gene conversion (gBGC), which favors the fixation of G/C over A/T variants in populations. In large population, gBGC causes high β. However, in small populations, genetic drift reduces the effect of gBGC resulting in reduced β. This was further confirmed by a positive relationship between Ne and β for homozygous variants. Conclusions Our results highlight the huge variation in the types of homozygous and high frequency polymorphisms between world populations. We observed the same pattern for deleterious variants, implying that the homozygous polymorphisms associated with recessive genetic diseases will be more enriched with G or C in populations with large Ne (e.g. Africans) than in populations with small Ne (e.g. Europeans).

scholarly journals The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7216 ◽  
Author(s):  
Lucile Vigué ◽  
Adam Eyre-Walker
Keyword(s):  
Population Genetics ◽  
Gene Transfer ◽  
Neisseria Meningitidis ◽  
Population Size ◽  
Effective Population Size ◽  
Adaptive Evolution ◽  
Lateral Gene Transfer ◽  
Pathogenic Bacteria ◽  
Core Genome ◽  
Effective Population

Neisseria meningitidis and N. gonorrhoeae are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 N. meningitidis and 15 N. gonorrhoeae genomes. We find that N. meningitidis is seven-times more diverse than N. gonorrhoeae in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however, we find that N. meningitidis has acquired more of its diversity by recombination than N. gonorrhoeae. We find that linkage disequilibrium (LD) declines rapidly across the genomes of both species. Several observations suggest that N. meningitidis has a higher effective population size than N. gonorrhoeae; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote in N. meningitidis. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome using a McDonald–Kreitman test and by considering the diversity around non-synonymous sites that are fixed for different alleles in the two species. We find some evidence for adaptive evolution using both approaches.

scholarly journals Why are there so many independent origins of artemisinin resistance in malaria parasites?

2016 ◽  
Author(s):  
Timothy J.C. Anderson ◽  
Shalini Nair ◽  
Marina McDew-White ◽  
Ian H. Cheeseman ◽  
Standwell Nkhoma ◽  
...  
Keyword(s):  
Amino Acid ◽  
Population Size ◽  
Effective Population Size ◽  
Clearance Rate ◽  
Retrospective Studies ◽  
Artemisinin Resistance ◽  
Target Size ◽  
Effective Population ◽  
Malaria Parasites ◽  
Multiple Alleles

SummaryMultiple alleles at thekelch13locus conferring artemisinin resistance (ART-R) are currently spreading through malaria parasite populations in Southeast Asia, providing a unique opportunity to directly observe an ongoing soft selective sweep, to investigate why resistance alleles have evolved multiple times and to determine fundamental population genetic parameters for Plasmodium. We sequenced thekelch13gene (n=1,876), genotyped 75 flanking SNPs, and measured clearance rate (n=3,552) in parasite infections from Western Thailand (2001-2014). We describe 32 independent coding mutations: these included common mutations outside thekelch13propeller region associated with significant reductions in clearance rate. Mutations were first observed in 2003 and rose to 90% by 2014, consistent with a selection coefficient of ~0.079. There was no change in diversity in flanking markers, but resistance allele diversity rose until 2012 and then dropped as one allele (C580Y) spread to high frequency. The rapid spread of C580Y suggests that the genomic signature may be considerably harder in the near future, and that retrospective studies may underestimate the complexity of selective sweeps. The frequency with which adaptive alleles arise is determined by the rate of mutation to generate beneficial alleles and the population size. Two factors drive this soft sweep: (1) multiple amino-acid mutations inkelch13can confer resistance providing a large mutational target – we estimate the target size is between 87 and 163bp. (2) The population mutation parameter (Θ=2Neμ) can be estimated from the frequency distribution of resistant alleles and is ~ 5.69, suggesting that short term effective population size is between 88 thousand and 1.2 million. This is 52 to 705-fold greater thanNeestimates based on fluctuation in allele frequencies, suggesting that we have previously underestimated the capacity for adaptive evolution in Plasmodium. Our central conclusions are that retrospective studies may underestimate the complexity of selective events, ART-R evolution is not limited by availability of mutations, and theNerelevant for adaptation for malaria is considerably higher than previously estimated.Significance StatementPrevious work has identified surprisingly few origins of resistance to antimalarial drugs such as chloroquine and pyrimethamine. This has lead to optimism about prospects for minimizing resistance evolution through combination therapy. We studied a longitudinal collection of malaria parasites from the Thai-Myanmar border (2001–14) to examine an ongoing selective event in which ≥32 independent alleles associated with ART-R evolved. Three factors appear to explain the large number of origins observed: the large number of amino acid changes that result in resistance (i.e. large mutational “target size”), the large estimated effective population size (Ne), and the fact that we were able to document this selective event in real time, rather than retrospectively.

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