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Adaptive Molecular Evolution
- In Balding,D., Bishop,M. and Cannings,C. (eds), Handbook of Statistical Genetics
, 2001
"... INTRODUCTION While Darwin's theory of evolution by natural selection is accepted by biologists for morphological traits, the importance of selection in molecular evolution has been much debated. The neutral theory (Kimura, 1983) maintains that most observed molecular vari- ation (both diversit ..."
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INTRODUCTION While Darwin's theory of evolution by natural selection is accepted by biologists for morphological traits, the importance of selection in molecular evolution has been much debated. The neutral theory (Kimura, 1983) maintains that most observed molecular vari- ation (both diversity within species and divergence between species) is due to random fixation of mutations with fitness effects so small that random drift rather than natural selection dominates their fate. Population geneticists have developed a number of tests of neutrality (see Wayne and Simonsen, 1998, for a review). Those tests often easily reject the strictly neutral model when applied to real data. However, they are often unable to distinguish different forms of natural selection, or to demonstrate molecular adaptation. Up to now, the most convincing evidence of adaptive molecular evolution appears to have come from comparison of synonymous (silent) and non-synonymous (aminoacid -changing) substitution rate
The sequence and de novo assembly of the giant panda genome.
- Nature
, 2010
"... Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific re ..."
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Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes. The giant panda, Ailuropoda melanoleura, is at high risk of extinction because of human population expansion and destruction of its habitat. The latest molecular census of its population size, using faecal samples and nine microsatellite loci, provided an estimate of only 2,500-3,000 individuals, which were confined to several small mountain habitats in Western China 1 . The giant panda has several unusual biological and behavioural traits, including a famously restricted diet, primarily made up of bamboo, and a very low fecundity rate. Moreover, the panda holds a unique place in evolution, and there has been continuing controversy about its phylogenetic position 2 . At present, there is very little genetic information for the panda, which is an essential tool for detailed understanding of the biology of this organism. A major limitation in obtaining extensive genetic data is the prohibitive costs associated with sequencing and assembling large eukaryotic *These authors contributed equally to this work.
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion
- PLoS Biol
, 2004
"... Primary microcephaly (MCPH) is a neurodevelopmental disorder characterized by global reduction in cerebral cortical volume. The microcephalic brain has a volume comparable to that of early hominids, raising the possibility that some MCPH genes may have been evolutionary targets in the expansion of t ..."
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Primary microcephaly (MCPH) is a neurodevelopmental disorder characterized by global reduction in cerebral cortical volume. The microcephalic brain has a volume comparable to that of early hominids, raising the possibility that some MCPH genes may have been evolutionary targets in the expansion of the cerebral cortex in mammals and especially primates. Mutations in ASPM, which encodes the human homologue of a fly protein essential for spindle function, are the most common known cause of MCPH. Here we have isolated large genomic clones containing the complete ASPM gene, including promoter regions and introns, from chimpanzee, gorilla, orangutan, and rhesus macaque by transformation-associated recombination cloning in yeast. We have sequenced these clones and show that whereas much of the sequence of ASPM is substantially conserved among primates, specific segments are subject to high Ka/Ks ratios (nonsynonymous/synonymous DNA changes) consistent with strong positive selection for evolutionary change. The ASPM gene sequence shows accelerated evolution in the African hominoid clade, and this precedes hominid brain expansion by several million years. Gorilla and human lineages show particularly accelerated evolution in the IQ domain of ASPM. Moreover, ASPM regions under positive selection in primates are also the most highly diverged regions between primates and nonprimate mammals. We report the first direct application of TAR cloning technology
Rapid evolution of primate antiviral enzyme APOBEC3G
- Hum. Mol. Genet
, 2004
"... Human cytidine deaminase APOBEC3G and the virion infectivity factor (vif) of the human immunodeficiency virus (HIV) are a pair of antagonistic molecules. In the absence of vif, APOBEC3G induces a high rate of dC to dU mutations in the nascent reverse transcripts of HIV that leads to the degradation ..."
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Human cytidine deaminase APOBEC3G and the virion infectivity factor (vif) of the human immunodeficiency virus (HIV) are a pair of antagonistic molecules. In the absence of vif, APOBEC3G induces a high rate of dC to dU mutations in the nascent reverse transcripts of HIV that leads to the degradation of the HIV genome. HIV vif, on the other hand, can suppress the translation and trigger the degradation of human APOBEC3G. Here, we studied the rate of APOBEC3G gene evolution from five hominoids and two Old World monkeys. Averaged across the entire coding region, the rate of non-synonymous nucleotide substitutions is 1.4 times the rate of synonymous substitutions, strongly suggesting that APOBEC3G has been under positive Darwinian selec-tion. A comparison between the nucleotide polymorphisms within humans and the substitutions among the seven primates reveals a significant excess of non-synonymous substitutions. Furthermore, the rate of charge-altering non-synonymous substitution is 1.8 times that of charge-conserving substitution, indicat-ing that the selection is promoting the diversity of the protein charge profile. However, no difference in selec-tive pressure on APOBEC3G is detected between hosts and non-hosts of HIV or simian immunodeficiency virus (SIV). These results, together with recent findings that the antiviral activity of APOBEC3G is not limited to HIV/SIV, suggest that the selective pressure on APOBEC3G is not solely from HIV/SIV and that APOBEC3G is a broad antiviral enzyme. The identification of pervasive positive selection for charge-altering amino acid substitutions supports the hypothesis of electrostatic interactions between APOBEC3G and vif or its func-tional equivalents.
The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection
"... The detection of positive Darwinian selection affecting protein-coding genes remains a topic of great interest and importance. The ‘‘branch-site’ ’ test is designed to detect localized episodic bouts of positive selection that affect only a few amino acid residues on particular lineages and has been ..."
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The detection of positive Darwinian selection affecting protein-coding genes remains a topic of great interest and importance. The ‘‘branch-site’ ’ test is designed to detect localized episodic bouts of positive selection that affect only a few amino acid residues on particular lineages and has been shown to have reasonable power and low false-positive rates for a wide range of selection schemes. Previous simulations examining the performance of the test, however, were conducted under idealized conditions without insertions, deletions, or alignment errors. As the test is sometimes used to analyze divergent sequences, the impact of indels and alignment errors is a major concern. Here, we used a recently developed indelsimulation program to examine the false-positive rate and power of the branch-site test. We find that insertions and deletions do not cause excessive false positives if the alignment is correct, but alignment errors can lead to unacceptably high false positives. Of the alignment methods evaluated, PRANK consistently outperformed MUSCLE, MAFFT, and ClustalW, mostly because the latter programs tend to place nonhomologous codons (or amino acids) into the same column, producing shorter and less accurate alignments and giving the false impression that many amino acid substitutions have occurred at those sites. Our examination of two previous studies suggests that alignment errors may impact the analysis of mammalian and vertebrate genes by the branch-site test, and it is important to use reliable alignment methods.
Positive selection on the human genome
- Hum. Mol. Genet
, 2004
"... Positive selection has undoubtedly played a critical role in the evolution of Homo sapiens. Of the many phenotypic traits that define our species—notably the enormous brain, advanced cognitive abilities, complex vocal organs, bipedalism and opposable thumbs—most (if not all) are likely the product o ..."
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Cited by 37 (0 self)
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Positive selection has undoubtedly played a critical role in the evolution of Homo sapiens. Of the many phenotypic traits that define our species—notably the enormous brain, advanced cognitive abilities, complex vocal organs, bipedalism and opposable thumbs—most (if not all) are likely the product of strong positive selection. Many other aspects of human biology not necessarily related to the ‘branding ’ of our species, such as host–pathogen interactions, reproduction, dietary adaptation and physical appearance, have also been the substrate of varying levels of positive selection. Comparative genetics/genomics studies in recent years have uncovered a growing list of genes that might have experienced positive selection during the evolution of human and/or primates. These genes offer valuable inroads into understanding the biological processes specific to humans, and the evolutionary forces that gave rise to them. Here, we present a comprehensive review of these genes, and their implications for human evolution. Traditionally, studies of human biology have operated under the assumption, either explicitly or implicitly, that much of the molecular processes in humans (and the genes that underlie them) are conserved in other species. The pervasive-ness of this sentiment is perhaps best reflected in the wide
Hotspots of biased nucleotide substitutions in human genes
- PLoS Biol
, 2009
"... Genes that have experienced accelerated evolutionary rates on the human lineage during recent evolution are candidates for involvement in human-specific adaptations. To determine the forces that cause increased evolutionary rates in certain genes, we analyzed alignments of 10,238 human genes to thei ..."
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Cited by 32 (0 self)
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Genes that have experienced accelerated evolutionary rates on the human lineage during recent evolution are candidates for involvement in human-specific adaptations. To determine the forces that cause increased evolutionary rates in certain genes, we analyzed alignments of 10,238 human genes to their orthologues in chimpanzee and macaque. Using a likelihood ratio test, we identified protein-coding sequences with an accelerated rate of base substitutions along the human lineage. Exons evolving at a fast rate in humans have a significant tendency to contain clusters of AT-to-GC (weak-to-strong) biased substitutions. This pattern is also observed in noncoding sequence flanking rapidly evolving exons. Accelerated exons occur in regions with elevated male recombination rates and exhibit an excess of nonsynonymous substitutions relative to the genomic average. We next analyzed genes with significantly elevated ratios of nonsynonymous to synonymous rates of base substitution (dN/dS) along the human lineage, and those with an excess of amino acid replacement substitutions relative to human polymorphism. These genes also show evidence of clusters of weak-to-strong biased substitutions. These findings indicate that a recombination-associated process, such as biased gene conversion (BGC), is driving fixation of GC alleles in the human genome. This process can lead to accelerated evolution in coding sequences and excess amino acid replacement substitutions, thereby generating significant results for tests of positive selection.
Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection
, 1999
"... Parallel or convergent evolution at the molecular level has been difficult to demonstrate especially when rigorous statistical criteria are applied. We present sequence data from the protease gene from eight patients infected with the human immunodeficiency virus (HIV-1). These patients have been o ..."
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Cited by 22 (1 self)
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Parallel or convergent evolution at the molecular level has been difficult to demonstrate especially when rigorous statistical criteria are applied. We present sequence data from the protease gene from eight patients infected with the human immunodeficiency virus (HIV-1). These patients have been on multiple drug therapies for at least 2 years. We present sequence data from two timepoints: time zero-the initiation of drug therapy-and a subsequent timepoint between 59 and 104 weeks after the initiation of drug therapy. In addition to the sequence data, we present viral load data from both initial and final timepoints. Our phylogenetic analyses indicate significant evolution of virus from initial to final time points, even in three of eight patients who show low viral loads. Of the five patients who escaped drug therapy, identical amino acid replacements were seen in all five patients at two different codon positions, an indication of parallel evolution. We also measured genetic diversity for these patients and found no correlation between genetic diversity and viral load. Finally, we calculated the nonsynonymous and synonymous substitution rates and showed that the ratio of nonsynonymous to synonymous substitution compared to the value of one may be a poor indicator of natural selection.
Genome networks root the tree of life between prokaryotic domains
- Genome Biology and Evolution
, 2010
"... 2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ..."
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2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
