Gene expression, chromosome heterogeneity and the fast-X effect in mammals

Biology Letters

Volumn 11, Issue 2, 2015, Pages

  Nguyen, Linh Phuong ^a   Galtier, Nicolas ^a   Nabholz, Benoit ^a  

^a INSTITUT DES SCIENCES DE L EVOLUTION   (France)

Author keywords

Fast X; Gene expression; Hemizygosity; Non synonymous substitutions; Synonymous substitutions; X chromosome

Indexed keywords

CHROMOSOME; GENE EXPRESSION; GENETIC VARIATION; HETEROGENEITY; MAMMAL;

MAMMALIA;

ANIMAL; GENE EXPRESSION; GENETIC POLYMORPHISM; GENETICS; HEMIZYGOTE; HUMAN; MAMMAL; MOLECULAR EVOLUTION; MULTIVARIATE ANALYSIS; X CHROMOSOME;

ANIMALS; EVOLUTION, MOLECULAR; GENE EXPRESSION; HEMIZYGOTE; HUMANS; MAMMALS; MULTIVARIATE ANALYSIS; POLYMORPHISM, GENETIC; X CHROMOSOME;

EID: 84929103274     PISSN: 17449561     EISSN: 1744957X     Source Type: Journal    
DOI: 10.1098/rsbl.2015.0010     Document Type: Article

References (16)

1. Lu J, Wu C-I. 2005 Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proc. Natl Acad. Sci. USA 102, 4063-4067. (doi:10.1073/pnas.0500436102)
2. Vicoso B, Charlesworth B. 2006 Evolution on the X chromosome: unusual patterns and processes. Nat. Rev. Genet. 7, 645-653. (doi:10.1038/nrg1914)
3. Charlesworth B, Coyne JA, Barton NH. 1987 The relative rates of evolution of sex chromosomes and autosomes. Am. Nat. 130, 113. (doi:10.1086/284701)
4. Julien P et al. 2012 Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol. 10, e1001328. (doi:10. 1371/journal.pbio.1001328)
5. Drummond DA, Wilke CO. 2008 Mistranslationinduced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134, 341-352. (doi:10.1016/j.cell.2008.05.042)
6. Duret L, Mouchiroud D. 2000 Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol. Biol. Evol. 17, 68-74. (doi:10.1093/oxfordjournals.molbev.a026239)
7. Brawand D et al. 2011 The evolution of gene expression levels in mammalian organs. Nature 478, 343-348. (doi:10.1038/nature10532)
8. Douzery EJP, Scornavacca C, Romiguier J, Belkhir K, Galtier N, Delsuc F, Ranwez V. 2014 OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals. Mol. Biol. Evol. 31, 1923-1928. (doi:10.1093/molbev/msu132)
9. Talavera G, Castresana J. 2007 Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564-577. (doi:10.1080/10635150701472164)
10. Romiguier J, Figuet E, Galtier N, Douzery EJP, Boussau B, Dutheil JY, Ranwez V. 2012 Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping. PLoS ONE 7, e33852. (doi:10.1371/journal.pone.0033852)
11. Frazer KA et al. 2007 A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861. (doi:10.1038/nature06258)
12. Stoletzki N, Eyre-Walker A. 2011 Estimation of the neutrality index. Mol. Biol. Evol. 28, 63-70. (doi:10. 1093/molbev/msq249)
13. Calcagno V, de Mazancourt C. 2010 glmulti: an R package for easy automated model selection with (generalized) linear models. J. Stat. Softw. 34, 1-29.
14. Duret L, Galtier N. 2009 Biased gene conversion and the evolution of mammalian genomic landscapes. Annu. Rev. Genomics Hum. Genet. 10, 285-311. (doi:10.1146/annurev-genom-082908-150001)
15. Hvilsom C et al. 2012 Extensive X-linked adaptive evolution in central chimpanzees. Proc. Natl Acad. Sci. USA 109, 2054-2059. (doi:10.1073/pnas. 1106877109)
16. Kayserili MA, Gerrard DT, Tomancak P, Kalinka AT. 2012 An excess of gene expression divergence on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis. PLoS Genet. 8, e1003200. (doi:10.1371/journal.pgen.1003200)