scholarly journals Adaptive Molecular Evolution of HINTW, a Female-Specific Gene in Birds

2003 ◽  
Vol 21 (2) ◽  
pp. 249-254 ◽  
Author(s):  
H. Ceplitis
Keyword(s):  
Molecular Evolution ◽  
Specific Gene ◽  
Adaptive Molecular Evolution ◽  
Female Specific

scholarly journals The Effect of Variation in the Effective Population Size on the Rate of Adaptive Molecular Evolution in Eukaryotes

2012 ◽  
Vol 4 (5) ◽  
pp. 658-667 ◽  
Author(s):  
Toni I. Gossmann ◽  
Peter D. Keightley ◽  
Adam Eyre-Walker
Keyword(s):  
Molecular Evolution ◽  
Population Size ◽  
Effective Population Size ◽  
Effective Population ◽  
Adaptive Molecular Evolution

scholarly journals Inferring the frequency spectrum of derived variants to quantify adaptive molecular evolution in protein-coding genes of Drosophila melanogaster

2016 ◽  
Author(s):  
Peter D. Keightley ◽  
Jose Campos ◽  
Tom Booker ◽  
Brian Charlesworth
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Frequency Spectrum ◽  
Population Genomics ◽  
Selective Constraint ◽  
Accurate Estimation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Adaptive Molecular Evolution ◽  
Amino Acid Mutations

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.

scholarly journals Adaptive Molecular Evolution of PHYE in Primulina, a Karst Cave Plant

PLoS ONE ◽  
2015 ◽  
Vol 10 (6) ◽  
pp. e0127821 ◽  
Author(s):  
Junjie Tao ◽  
Qingwen Qi ◽  
Ming Kang ◽  
Hongwen Huang
Keyword(s):  
Molecular Evolution ◽  
Karst Cave ◽  
Adaptive Molecular Evolution

scholarly journals Separating Spandrels from Phenotypic Targets of Selection in Adaptive Molecular Evolution

2016 ◽  
pp. 309-325 ◽  
Author(s):  
Stevan A. Springer ◽  
Michael Manhart ◽  
Alexandre V. Morozov
Keyword(s):  
Molecular Evolution ◽  
Adaptive Molecular Evolution

scholarly journals Adaptive Molecular Evolution

2019 ◽  
pp. 369-396
Author(s):  
Ziheng Yang
Keyword(s):  
Molecular Evolution ◽  
Adaptive Molecular Evolution

scholarly journals Sexually dimorphic gene expression and transcriptome evolution provides mixed evidence for a fast-Z effect in Heliconius

2018 ◽  
Author(s):  
A Pinharanda ◽  
M Rousselle ◽  
SH Martin ◽  
JJ Hanly ◽  
JW Davey ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Evolution ◽  
Adaptive Evolution ◽  
Sex Chromosomes ◽  
Expression Profiles ◽  
Sequence Divergence ◽  
Gene Expression Profiles ◽  
Purifying Selection ◽  
Specific Gene ◽  
Sex Determination System

AbstractSex chromosomes have different evolutionary properties as compared to the autosomes due to their hemizygous nature. In particular, recessive mutations are more readily exposed to selection, which can lead to faster rates of molecular evolution. Here, we report patterns of gene expression and molecular evolution in the sex chromosomes of a group of tropical butterflies. We first improved the completeness of the Heliconius melpomene reference annotation, a neotropical butterfly with a ZW sex determination system. Then we sequenced RNA from male and female whole abdomens and female ovary and gut tissue to identify sex and tissue specific gene expression profiles in H. melpomene. Using these expression profiles we compare sequence divergence and polymorphism, the strength of positive and negative selection and rates of adaptive evolution for Z and autosomal genes between two species of Heliconius butterflies, H. melpomene and H. erato.We show that the rate of adaptive substitutions is higher for Z as compared to autosomal genes, but contrary to expectation it is also higher for male as compared to female biased genes. There is therefore mixed evidence that hemizygosity influences the rate of adaptive substitutions. Additionally, we find no significant increase in the rate of adaptive evolution or purifying selection on genes expressed in ovary tissue, a heterogametic specific tissue. Together our results provide limited support for fast-Z evolution. This contributes to a growing body of literature from other ZW systems that also provide mixed evidence for a fast-Z effect.

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