Inferring the Frequency Spectrum of Derived Variants to Quantify Adaptive Molecular Evolution in Protein-Coding Genes of Drosophila melanogaster

Many approaches for inferring adaptive molecular evolution analyze the unfolded site frequency spectrum (SFS), a vector of counts of sites with different numbers of copies of derived alleles in a sample of alleles from a population. Accurate inference of the high copy number elements of the SFS is difficult, however, because of misassignment of alleles as derived versus ancestral. This is a known problem with parsimony using outgroup species. Here, we show that the problem is particularly serious if there is variation in the substitution rate among sites brought about by variation in selective constraint levels. We present a new method for inferring the SFS using one or two outgroups, which attempts to overcome the problem of misassignment. We show that two outgroups are required for accurate estimation of the SFS if there is substantial variation in selective constraints, which is expected to be the case for nonsynonymous sites of protein-coding genes. We apply the method to estimate unfolded SFSs for synonymous and nonsynonymous sites from Phase 2 of the Drosophila Population Genomics Project. We use the unfolded spectra to estimate the frequency and strength of advantageous and deleterious mutations, and estimate that ~50% of amino acid substitutions are positively selected, but that less than 0.5% of new amino acid mutations are beneficial, with a scaled selection strength of Nes ≈ 12.

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An Exploration of the Sequence of a 2.9-Mb Region of the Genome of Drosophila melanogaster: The Adh Region

Genetics ◽

10.1093/genetics/153.1.179 ◽

1999 ◽

Vol 153 (1) ◽

pp. 179-219 ◽

Cited By ~ 15

Author(s):

M Ashburner ◽

S Misra ◽

J Roote ◽

S E Lewis ◽

R Blazej ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Transposable Element ◽

Large Scale ◽

Chromosome Region ◽

Complete Sequence ◽

Test Methods ◽

P Element ◽

Cdna Libraries ◽

Protein Coding ◽

Protein Coding Genes

Abstract A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized “Adh region.” A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and 17 transposable element sequences. At least 38 of the protein-coding genes are arranged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 kb; the transposable element density is one element every 171 kb. Of 73 genes in this region identified by genetic analysis, 49 have been located on the sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66%) have clear similarities to proteins in other organisms. Genes known to have mutant phenotypes are more likely to be represented in cDNA libraries, and far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberration breakpoints map to this chromosome region, and their nonrandom distribution on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis has allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species.

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Unbiasing in the Genome Analysis of Iconic Shark Species

10.20944/preprints201911.0214.v1 ◽

2019 ◽

Author(s):

Kazuaki Yamaguchi ◽

Shigehiro Kuraku

Keyword(s):

Molecular Evolution ◽

Genome Stability ◽

White Shark ◽

Shark Species ◽

Whole Genome ◽

Potential Bias ◽

Short Article ◽

Protein Coding ◽

Protein Coding Genes ◽

Selection Of

A previous study involving whole genome sequencing of the white shark suggested unique molecular evolution accounting for gigantism and the enhanced longevity of sharks including positive selection of dozens of protein-coding genes potentially involved in genome stability. We performed a reanalysis on some of the genes and identified serious flaws in their results. In this short article, we scrutinize one of the serious problems we identified, report other concerns, and point out a potential bias in analyzing iconic shark species in general.

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Comparative Molecular Evolution of Primary (Buchnera) and Secondary Symbionts of Aphids Based on Two Protein-Coding Genes

Journal of Molecular Evolution ◽

10.1007/s00239-001-2307-8 ◽

2002 ◽

Vol 55 (2) ◽

pp. 127-137 ◽

Cited By ~ 18

Author(s):

Andrés Moya ◽

Amparo Latorre ◽

Beatriz Sabater-Muñoz ◽

Francisco J. Silva

Keyword(s):

Molecular Evolution ◽

Protein Coding ◽

Protein Coding Genes

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Comparing Molecular Evolution in Two Mitochondrial Protein Coding Genes (Cytochromeband ND2) in the Dabbling Ducks (Tribe: Anatini)

Molecular Phylogenetics and Evolution ◽

10.1006/mpev.1997.0481 ◽

1998 ◽

Vol 10 (1) ◽

pp. 82-94 ◽

Cited By ~ 194

Author(s):

Kevin P Johnson ◽

Michael D Sorenson

Keyword(s):

Molecular Evolution ◽

Mitochondrial Protein ◽

Dabbling Ducks ◽

Protein Coding ◽

Protein Coding Genes

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Genomic analysis of the four ecologically distinct cactus host populations ofDrosophila mojavensis

10.1101/530154 ◽

2019 ◽

Cited By ~ 3

Author(s):

Carson W. Allan ◽

Luciano M. Matzkin

Keyword(s):

Molecular Evolution ◽

Genomic Analysis ◽

Drosophila Mojavensis ◽

Shape Variation ◽

Isolated Populations ◽

High Coverage ◽

Protein Coding ◽

Protein Coding Genes ◽

Santa Catalina Island ◽

And Behavior

AbstractBackgroundRelationships between an organism and its environment can be fundamental in the understanding how populations change over time and species arise. Local ecological conditions can shape variation at multiple levels, among these are the evolutionary history and trajectories of coding genes. This study examines the rate of molecular evolution at protein-coding genes throughout the genome in response to host adaptation in the cactophilicDrosophila mojavensis. These insects are intimately associated with cactus necroses, developing as larvae and feeding as adults in these necrotic tissues.Drosophila mojavensisis composed of four isolated populations across the deserts of western North America and each population has adapted to utilize different cacti that are chemically, nutritionally, and structurally distinct.ResultsHigh coverage Illumina sequencing was performed on three previously unsequenced populations ofD. mojavensis. Genomes were assembled using the previously sequenced genome ofD. mojavensisfrom Santa Catalina Island (USA) as a template. Protein coding genes were aligned across all four populations and rates of protein evolution were determined for all loci using a several approaches.ConclusionsLoci that exhibited elevated rates of molecular evolution tended to be shorter, have fewer exons, low expression, be transcriptionally responsive to cactus host use and have fixed expression differences across the four cactus host populations. Fast evolving genes were involved with metabolism, detoxification, chemosensory reception, reproduction and behavior. Results of this study gives insight into the process and the genomic consequences of local ecological adaptation.

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Genomic analysis of the four ecologically distinct cactus host populations of Drosophila mojavensis

BMC Genomics ◽

10.1186/s12864-019-6097-z ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 4

Author(s):

Carson W. Allan ◽

Luciano M. Matzkin

Keyword(s):

Molecular Evolution ◽

Genomic Analysis ◽

Drosophila Mojavensis ◽

Shape Variation ◽

Isolated Populations ◽

High Coverage ◽

Protein Coding ◽

Protein Coding Genes ◽

Santa Catalina Island ◽

And Behavior

Abstract Background Relationships between an organism and its environment can be fundamental in the understanding how populations change over time and species arise. Local ecological conditions can shape variation at multiple levels, among these are the evolutionary history and trajectories of coding genes. This study examines the rate of molecular evolution at protein-coding genes throughout the genome in response to host adaptation in the cactophilic Drosophila mojavensis. These insects are intimately associated with cactus necroses, developing as larvae and feeding as adults in these necrotic tissues. Drosophila mojavensis is composed of four isolated populations across the deserts of western North America and each population has adapted to utilize different cacti that are chemically, nutritionally, and structurally distinct. Results High coverage Illumina sequencing was performed on three previously unsequenced populations of D. mojavensis. Genomes were assembled using the previously sequenced genome of D. mojavensis from Santa Catalina Island (USA) as a template. Protein coding genes were aligned across all four populations and rates of protein evolution were determined for all loci using a several approaches. Conclusions Loci that exhibited elevated rates of molecular evolution tend to be shorter, have fewer exons, low expression, be transcriptionally responsive to cactus host use and have fixed expression differences across the four cactus host populations. Fast evolving genes were involved with metabolism, detoxification, chemosensory reception, reproduction and behavior. Results of this study give insight into the process and the genomic consequences of local ecological adaptation.

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