Adaptive evolution of non-coding DNA in Drosophila

By P. Andolfatto. Nature, 2005

668 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/010863a85534aac937f4fd1f42cdab53c3a67650

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Citations in the corpus

A model of substitution trajectories in sequence space and long-term protein evolution. (2015, background): “Thus, the impact of slightly deleterious and beneﬁcial substitutions on molecular evolution cannot be taken into account, even though their contribution may be considerable (Ohta 1998; Andolfatto 2005; Popadin et al. 2007; McCandlish et al. 2013).”
The Evolution and Emergence of RNA Viruses (2009, background): “In eukaryotes, a number of different types of DNA sequence may fall into this category, including introns, inter-genic DNA, pseudogenes, and synonymous sites, although selection in some of these classes has been observed (Eyre-Walker 1999; Chamary and Hurst 2004; Plotkin et al. 2004; Andolfatto 2005”
The relationship between non-protein-coding DNA and eukaryotic complexity. (2007, positive): “Moreover, a recent comparative study of Drosophila genomes indicated that a large fraction of the non-protein-coding sequences are functionally important and subject to both purifying selection and adaptive evolution.((92)) In addition, it seems clear that the extent of promoter-enhancer regions, es”
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm (2008, background): “It has been estimated that over half of the bases in intergenic and intronic DNA have evolved under purifying selection [51,52], compared to roughly 5% in mammals [53].”
Taxonomy and the mediocrity of DNA barcoding - some remarks on Packer et al. 2009: DNA barcoding and the mediocrity of morphology (2010, background): “Darwin arrived at different conclusions than Lamarck; Einstein modifi ed the ‘laws’ formulated by Newton; what few years ago was considered ‘junk DNA’ is now known to play a very important role (ANDOLFATTO 2005; CHECK 2006, 2007); in 2000 one eminent geologist (R.”
THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION (2007, background): “Andolfatto (2005), for example, showed that patterns of nucleotide variation in untranslated regions (UTRs) of the Drosophila genome are consistent with the view that changes in these regions affect fitness.”
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007, background): “Within the ENCODE regions, 55% of RFBRs overlap the high-confidence MK-test 111,112 ) and the Hudson–Kreitman–Aguade (HKA) 113 test (see Supplementary Information section 5.2.1), to examine whether an entire set of sequence elements shows an excess of polymorphisms or an excess of inter-species…”
The Drosophila melanogaster Genetic Reference Panel (2012, neutral): “We used the standard 24 and generalized 13,25,26 McDonald Kreitman tests (MKT) to scan the genome for evidence of selection.”
The Loci of Evolution: How Predictable is Genetic Evolution? (2008, background): “Estimates based on evolutionary comparisons of rates of sequence evolution between closely related Drosophila species reveal that 40–70% of nucleotides in noncoding regions are more conserved than synonymous sites, suggesting that they are under functional constraint (Andolfatto 2005).”