scholarly journals A High Load of Non-neutral Amino-Acid Polymorphisms Explains High Protein Diversity Despite Moderate Effective Population Size in a Marine Bivalve With Sweepstakes Reproduction

2013 ◽  
Vol 3 (2) ◽  
pp. 333-341 ◽  
Author(s):  
Estelle Harrang ◽  
Sylvie Lapègue ◽  
Benjamin Morga ◽  
Nicolas Bierne
Keyword(s):  
Amino Acid ◽  
Population Size ◽  
Effective Population Size ◽  
High Load ◽  
High Protein ◽  
Neutral Amino Acid ◽  
Marine Bivalve ◽  
Effective Population ◽  
Protein Diversity

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.

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 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.

scholarly journals Myotis rufoniger Genome Sequence and Analyses: M. rufoniger’s Genomic Feature and the Decreasing Effective Population Size of Myotis Bats

2017 ◽  
Author(s):  
Youngjune Bhak ◽  
Yeonsu Jeon ◽  
Sungwon Jeon ◽  
Oksung Chung ◽  
Sungwoong Jho ◽  
...  
Keyword(s):  
Amino Acid ◽  
Population Size ◽  
Effective Population Size ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Demographic History ◽  
Divergence Time ◽  
Functional Enrichment ◽  
Genomic Feature ◽  
Effective Population

AbstractMyotis rufoniger is a vesper bat in the genus Myotis. Here we report the whole genome sequence and analyses of the M. rufoniger. We generated 124 Gb of short-read DNA sequences with an estimated genome size of 1.88 Gb at a sequencing depth of 66× fold. The sequences were aligned to M. brandtii bat reference genome at a mapping rate of 96.50% covering 95.71% coding sequence region at 10× coverage. The divergence time of Myotis bat family is estimated to be 11.5 million years, and the divergence time between M. rufoniger and its closest species M. davidii is estimated to be 10.4 million years. We found 1,239 function-altering M. rufoniger specific amino acid sequences from 929 genes compared to other Myotis bat and mammalian genomes. The functional enrichment test of the 929 genes detected amino acid changes in melanin associated DCT, SLC45A2, TYRP1, and OCA2 genes possibly responsible for the M. rufoniger’s red fur color and a general coloration in Myotis. N6AMT1 gene, associated with arsenic resistance, showed a high degree of function alteration in M. rufoniger. We further confirmed that M. rufoniger also has bat-specific sequences within FSHB, GHR, IGF1R, TP53, MDM2, SLC45A2, RGS7BP, RHO, OPN1SW, and CNGB3 genes that have already been published to be related to bat’s reproduction, lifespan, flight, low vision, and echolocation. Additionally, our demographic history analysis found that the effective population size of Myotis clade has been consistently decreasing since ∼30k years ago. M. rufoniger’s effective population size was the lowest in Myotis bats, confirming its relatively low genetic diversity.

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