scholarly journals Adaptive molecular evolution of MC 1R gene reveals the evidence for positive diversifying selection in indigenous goat populations

2017 ◽  
Vol 7 (14) ◽  
pp. 5170-5180 ◽  
Author(s):  
Hafiz Ishfaq Ahmad ◽  
Guiqiong Liu ◽  
Xunping Jiang ◽  
Chenhui Liu ◽  
Yuqing Chong ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Diversifying Selection ◽  
Adaptive Molecular Evolution ◽  
Indigenous Goat

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 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 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.

Calreticulin molecular evolution: a strong purifying and episodic diversifying selection result

Biologia ◽  
2014 ◽  
Vol 69 (3) ◽  
Author(s):  
Rigers Bakiu
Keyword(s):  
Molecular Evolution ◽  
Higher Plants ◽  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Amino Acid Sequences ◽  
Over Expression ◽  
Diversifying Selection ◽  
Pathological Conditions ◽  
Weight Protein ◽  
Low Molecular Weight Protein

AbstractCalreticulin (CRT) is a low molecular weight protein present in vertebrates, invertebrates and higher plants. Its multiple functions have been demonstrated. It plays an important role as a chaperone and Ca2+ buffer inside sarcoplasmic/endoplasmic reticulum (SR/ER), and outside the ER in many physiological/pathological processes. Recently it has been observed that CRT over-expression or its absence is linked to various pathological conditions, such as malignant evolution and progression, and these facts really increased its study interests. Using an evolution approach CRT was further characterized. Several Bayesian phylogenetic analyses were performed using coding and amino acid sequences. CRT molecular evolution was investigated for the presence of negative or/and positive selection using HyPhy package. The results indicated that the purifying selection might have operated over the whole CRT primary structure. Although, an episodic diversifying selection was also found on the analyzed CRT sequences.

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
Sign in / Sign up

Export Citation Format

Share Document