The Evolution of Mammalian Gene Families

Demuth, Jeffery P.; Bie, Tijl De; Stajich, Jason E.; Cristianini, Nello; Hahn, Matthew W.

doi:10.1371/journal.pone.0000085

Cited by 300 publications

(274 citation statements)

References 57 publications

(84 reference statements)

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“…Human-specific patterns of alternative splicing have been found to be particularly widespread within the brain (50). Also, it has been estimated that humans and chimpanzees differ by at least 6% in their complement of genes (51). The trichromatic visual system is one of the dramatic specializations present in the human lineage compared with other mammals.…”

Section: Discussionmentioning

confidence: 99%

Alternative Splicing Governs Cone Cyclic Nucleotide-gated (CNG) Channel Sensitivity to Regulation by Phosphoinositides

Dai

Lama-Sherpa

Varnum

2014

Journal of Biological Chemistry

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Background: Variants of photoreceptor CNG channels are produced by alternative splicing of precursor mRNA. Results: Inclusion of an optional exon in human CNGA3 transcripts produces channel isoforms with enhanced sensitivity to phosphoinositides via an allosteric mechanism. Conclusion: Alternative splicing of CNGA3 transcripts controls phosphoinositide regulation of cone CNG channels. Significance: These findings reveal the functional importance of CNGA3 alternative splicing.

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Section: Discussionmentioning

confidence: 99%

Alternative Splicing Governs Cone Cyclic Nucleotide-gated (CNG) Channel Sensitivity to Regulation by Phosphoinositides

Dai

Lama-Sherpa

Varnum

2014

Journal of Biological Chemistry

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“…A model for the evolution of the HBA genes in the European rabbit Recent studies have highlighted the fast rate of gene gain and loss in the multigene families of many mammalian species (Demuth et al, 2006;Hahn et al, 2007;Hoffmann et al, 2010). The pattern of gene turnover has been especially well characterized in the a-globin gene cluster of mammals (Zimmer et al, 1980;Hoffmann et al, 2008a;Storz et al, 2008).…”

Section: Copy Number Polymorphism and Hybridization R Campos Et Almentioning

confidence: 99%

Copy number polymorphism in the α-globin gene cluster of European rabbit (Oryctolagus cuniculus)

2011

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Comparative genomic studies have revealed that mammals typically possess two or more tandemly duplicated copies of the a-globin (HBA) gene. The domestic rabbit represents an exception to this general rule, as this species was found to possess a single HBA gene. Previous electrophoretic surveys of HBA polymorphism in natural populations of the European rabbit (Oryctolagus cuniculus) revealed extensive geographic variation in the frequencies of three main electromorphs. The variation in frequency of two electromorphs is mainly partitioned between two distinct subspecies of European rabbit, and a third is restricted to the hybrid zone between the two rabbit subspecies in Iberia. Here we report the results of a survey of nucleotide polymorphism, which revealed HBA copy number polymorphism in Iberian populations of the European rabbit. By characterizing patterns of HBA polymorphism in populations from the native range of the European rabbit, we were able to identify the specific amino-acid substitutions that distinguish the previously characterized electromorphs. Within the hybrid zone, we observed the existence of a second HBA gene duplicate, named HBA2, that mostly represents a novel sequence haplotype, which occurs in higher frequency within the hybrid zone, and thus appears to have arisen in hybrids of the two distinct subspecies. Although this novel gene is also present in other wild Iberian populations, it is almost absent from French populations, which suggest a recent ancestry, associated with the establishment of the post-Pleistocene contact zone between the two European rabbit subspecies.

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“…Recent studies have found that such large-scale mutations can have dramatic evolutionary and phenotypic consequences. Comparative genomic studies have revealed that changes in gene copy number caused by duplication and deletion events are often adaptive (Demuth et al 2006) and suggest that gene duplication events can result in the evolution of new gene functions [e.g., the excess of d N /d S ratios .1 in young gene duplicates observed in Kondrashov et al (2002) and Zhang et al (2003)]. In addition, large duplications and deletions segregating within populations, often referred to as copy-number variants (CNVs), have been shown to be both beneficial (Perry et al 2007;Turner et al 2008;Kolaczkowski et al 2011) and deleterious (McCarroll and Altshuler 2007;Stankiewicz and Lupski 2010;Girirajan et al 2011); these polymorphisms are widespread in Drosophila (Emerson et al 2008;Langley et al 2012).…”

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confidence: 99%

Rates and Genomic Consequences of Spontaneous Mutational Events inDrosophila melanogaster

et al. 2013

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Because spontaneous mutation is the source of all genetic diversity, measuring mutation rates can reveal how natural selection drives patterns of variation within and between species. We sequenced eight genomes produced by a mutation-accumulation experiment in Drosophila melanogaster. Our analysis reveals that point mutation and small indel rates vary significantly between the two different genetic backgrounds examined. We also find evidence that 2% of mutational events affect multiple closely spaced nucleotides. Unlike previous similar experiments, we were able to estimate genome-wide rates of large deletions and tandem duplications. These results suggest that, at least in inbred lines like those examined here, mutational pressures may result in net growth rather than contraction of the Drosophila genome. By comparing our mutation rate estimates to polymorphism data, we are able to estimate the fraction of new mutations that are eliminated by purifying selection. These results suggest that 99% of duplications and deletions are deleterious-making them 10 times more likely to be removed by selection than nonsynonymous mutations. Our results illuminate not only the rates of new small-and large-scale mutations, but also the selective forces that they encounter once they arise.B ECAUSE all genetic variation on which natural selection acts originates via spontaneous mutation, the rate at which various types of mutations appear in natural populations has important consequences for the manner in which organisms evolve. Once we determine the rate at which adaptive and deleterious alleles arise, we can understand how natural selection shapes the spectrum of variation within and between species (Lynch et al. 2008). Mutationaccumulation (MA) experiments are the most widely used method for directly measuring spontaneous mutation rates (Halligan and Keightley 2009). In these experiments genetically identical individuals are subdivided into initially homogeneous sublines, and these sublines are maintained over many generations. At each generation a minimum number of individuals are randomly selected to reproduce and propagate the MA subline, thereby limiting the ability of natural selection to purge new deleterious mutations or to favor new adaptive alleles. Because the MA sublines are initially identical (barring any contamination or residual heterozygosity), any genetic differences among lines must arise via mutations occurring during the course of the experiment.Mutation-accumulation experiments were initially used to assess the phenotypic impacts of mutation (e.g., Mukai et al. 1972). More recently, mutation-accumulation has been used to assess the rate of spontaneous mutation on the genome at specific loci (Mukai and Cockerham 1977), selected genomic regions (Haag-Liautard et al. 2007), or, with the advent of next-generation sequencing technology, genome-wide. Mutation accumulation is now used to estimate genome-wide estimates of per-site mutation rates in a variety of eukaryotes, including Saccharomyces cerevis...

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The Evolution of Mammalian Gene Families

Cited by 300 publications

References 57 publications

Alternative Splicing Governs Cone Cyclic Nucleotide-gated (CNG) Channel Sensitivity to Regulation by Phosphoinositides

Alternative Splicing Governs Cone Cyclic Nucleotide-gated (CNG) Channel Sensitivity to Regulation by Phosphoinositides

Copy number polymorphism in the α-globin gene cluster of European rabbit (Oryctolagus cuniculus)

Rates and Genomic Consequences of Spontaneous Mutational Events inDrosophila melanogaster

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