Molecular evolution of genes in avian genomes

Nam, Kiwoong; Mugal, Carina F.; Nabholz, Benoît; Schielzeth, Holger; Wolf, Jochen B. W.; Backström, Niclas; Künstner, Axel; Balakrishnan, Christopher N.; Heger, Andreas; Ponting, Chris P.; Clayton, David F.; Ellegren, Hans

doi:10.1186/gb-2010-11-6-r68

Cited by 138 publications

(146 citation statements)

References 123 publications

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“…This is very similar to a point estimate based on divergence at fourfold degenerate sites in the lineage leading to zebra finch (2.2 × 10 −9 per site per year) (Nam et al 2010), which like flycatchers belongs to the order Passeriformes. It is somewhat higher than point estimates obtained for Galliformes, including chicken and turkey, based on intronic divergence (1.3 × 10 −9 ) (Axelsson et al 2004) and divergence at fourfold degenerate sites Figure 2.…”

Section: Discussionsupporting

confidence: 86%

Direct estimate of the rate of germline mutation in a bird

2016

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The fidelity of DNA replication together with repair mechanisms ensure that the genetic material is properly copied from one generation to another. However, on extremely rare occasions when damages to DNA or replication errors are not repaired, germline mutations can be transmitted to the next generation. Because of the rarity of these events, studying the rate at which new mutations arise across organisms has been a great challenge, especially in multicellular nonmodel organisms with large genomes. We sequenced the genomes of 11 birds from a three-generation pedigree of the collared flycatcher (Ficedula albicollis) and used highly stringent bioinformatic criteria for mutation detection and used several procedures to validate mutations, including following the stable inheritance of new mutations to subsequent generations. We identified 55 de novo mutations with a 10-fold enrichment of mutations at CpG sites and with only a modest male mutation bias. The estimated rate of mutation per site per generation was 4.6 × 10−9, which corresponds to 2.3 × 10−9 mutations per site per year. Compared to mammals, this is similar to mouse but about half of that reported for humans, which may be due to the higher frequency of male mutations in humans. We confirm that mutation rate scales positively with genome size and that there is a strong negative relationship between mutation rate and effective population size, in line with the drift-barrier hypothesis. Our study illustrates that it should be feasible to obtain direct estimates of the rate of mutation in essentially any organism from which family material can be obtained.

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Section: Discussionsupporting

confidence: 86%

Direct estimate of the rate of germline mutation in a bird

2016

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“…The CYP2A-like enzymes vary among birds; zebra finches, unlike chickens, turkeys, ducks, and quails, do not metabolize coumarin to 7-hydroxycoumarin in vitro (Murcia et al, 2011). This variation is consistent with the divergence over 100 million years ago between the Galloanserae, which includes fowl, ducks, and geese, and the Neoaves, which includes the songbirds (Nam et al, 2010). It remains to be seen whether in the Galloanserae, the formation of cotinine from nicotine is mediated by a CYP2A-like enzyme, similar to humans, monkeys, and mice.…”

supporting

confidence: 55%

“…The CYP2 family in birds is less diverse than in mammals, and orthologs of CYP2A and CYP2B have not been identified in zebra finches or other birds (the evolutionary ancestors of mammals and birds diverged more than 300 million years ago) (Nam et al, 2010;Kubota et al, 2011). Sequence comparisons suggest that mammalian CYP2A and CYP2B isozymes are most similar to zebra finch CYP2C45 and CYP2H1, with the isozymes sharing approximately 50% amino acid sequence identity.…”

mentioning

confidence: 98%

Nicotine Kinetics in Zebra Finches In Vivo and In Vitro

Miksys

Cappendijk²,

Perry³

et al. 2013

Drug Metab Dispos

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Nicotine enhances cognitive performance, and in the zebra finch (Taeniopygia guttata), which is a well-established model of cognition, the effects of nicotine on song production have been reported. Nicotine and cotinine plasma levels were assessed in vivo after subcutaneous injection of 0.18 mg/kg nicotine, a dose that elicits changes in song production. The half-life of nicotine elimination was 33 minutes, and levels were undetectable by 4 hours. Average plasma nicotine over 2 hours was 32 ng/ml, similar to levels seen in human smokers and rat models of nicotine behavior. Nicotine brain levels were 30 and 14 ng/g 1 and 2 hours after treatment. To understand the potential for drug interactions and the regulation of nicotine metabolism in zebra finches, we characterized in vitro nicotine metabolism and the hepatic enzyme involved. In humans, cytochrome P450 2A6 metabolizes nicotine to cotinine, and CYP2A-like activity and protein have been reported in some birds. Zebra finch liver microsomes metabolized nicotine and bupropion (a CYP2B substrate) but not coumarin (a CYP2A substrate). Nicotine was metabolized to cotinine with a MichaelisMenten constant (K m ) of 96 mM and a V max of 56 pmol/min per milligram. Nicotine and bupropion metabolism was inhibited by C-8-xanthate (a specific CYP2B inhibitor) but not by CYP2A-specific inhibitors, and hepatic levels of CYP2B-like but not CYP2A-like proteins correlated with nicotine (r = 0.52; P = 0.04) and bupropion metabolism (r = 0.81; P < 0.001), suggesting CYP2B-mediation of nicotine metabolism as seen in rats. These results will facilitate further investigation of nicotine's effects in zebra finches.

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“…Since MSMC has a low power to estimate population size at relatively recent times, the effective population sizes for present day RJF and VC populations were taken from elsewhere [68] (1.6 × 10 5 and 4 × 10 5 , respectively). Generation time (g) and mutation rate per year (u) for chicken used here is 1 year and 1.91 × 10 −9 , respectively [69].…”

Section: Demographic History and Coalescent Simulationsmentioning

confidence: 99%

Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication

Wang

Zhang

et al. 2016

Cell Res

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As noted by Darwin, chickens have the greatest phenotypic diversity of all birds, but an interesting evolutionary difference between domestic chickens and their wild ancestor, the Red Junglefowl, is their comparatively weaker vision. Existing theories suggest that diminished visual prowess among domestic chickens reflect changes driven by the relaxation of functional constraints on vision, but the evidence identifying the underlying genetic mechanisms responsible for this change has not been definitively characterized. Here, a genome-wide analysis of the domestic chicken and Red Junglefowl genomes showed significant enrichment for positively selected genes involved in the development of vision. There were significant differences between domestic chickens and their wild ancestors regarding the level of mRNA expression for these genes in the retina. Numerous additional genes involved in the development of vision also showed significant differences in mRNA expression between domestic chickens and their wild ancestors, particularly for genes associated with phototransduction and photoreceptor development, such as RHO (rhodopsin), GUCA1A, PDE6B and NR2E3. Finally, we characterized the potential role of the VIT gene in vision, which experienced positive selection and downregulated expression in the retina of the village chicken. Overall, our results suggest that positive selection, rather than relaxation of purifying selection, contributed to the evolution of vision in domestic chickens. The progenitors of domestic chickens harboring weaker vision may have showed a reduced fear response and vigilance, making them easier to be unconsciously selected and/or domesticated.

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Molecular evolution of genes in avian genomes

Cited by 138 publications

References 123 publications

Direct estimate of the rate of germline mutation in a bird

Direct estimate of the rate of germline mutation in a bird

Nicotine Kinetics in Zebra Finches In Vivo and In Vitro

Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication

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