Estimating the intensity of male-driven evolution in rodents by using X-linked and Y-linked Ube 1 genes and pseudogenes

Chang, Benny Hung-Junn; Li, Wen-Hsiung

doi:10.1007/bf00166597

Cited by 37 publications

(2 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Most studies of male-biased mutation so far reported using the evolutionary approach have analysed either mammals (Shimmin et al 1993a(Shimmin et al , 1994Chang et al 1994;Chang & Li 1995;Agulnik et al 1997;Huang et al 1997;McVean & Hurst 1997;Bohossian et al 2000;Lawson & Hewitt 2002;Malcom et al 2003;Tucker et al 2003;Sandstedt & Tucker 2005) or birds (Ellegren & Fridolfsson 1997;Kahn & Quinn 1999;Carmichael et al 2000;Garcia-Moreno & Mindell 2000;Bartosch-Härlid et al 2003;Axelsson et al 2004;Berlin et al 2006), so the correlates with life history are mainly restricted to these groups of species. A study of salmonid fishes revealed an a m estimate of 6 (Ellegren & Fridolfsson 2003) and in dioecious plants there are also evidence for higher rate of mutation on the Y than the X chromosome (Filatov & Charlesworth 2002;Whittle & Johnston 2002); indeed, there are more cell divisions in pollen than in ovule production.…”

Section: Life History and The Male Mutation Biasmentioning

confidence: 99%

Characteristics, causes and evolutionary consequences of male-biased mutation

2006

View full text Add to dashboard Cite

Mutation has traditionally been considered a random process, but this paradigm is challenged by recent evidence of divergence rate heterogeneity in different genomic regions. One facet of mutation rate variation is the propensity for genetic change to correlate with the number of germ cell divisions, reflecting the replication-dependent origin of many mutations. Haldane was the first to connect this association of replication and mutation to the difference in the number of cell divisions in oogenesis (low) and spermatogenesis (usually high), and the resulting sex difference in the rate of mutation. The concept of male-biased mutation has been thoroughly analysed in recent years using an evolutionary approach, in which sequence divergence of autosomes and/or sex chromosomes are compared to allow inference about the relative contribution of mothers and fathers in the accumulation of mutations. For instance, assuming that a neutral sequence is analysed, that rate heterogeneity owing to other factors is cancelled out by the investigation of many loci and that the effect of ancestral polymorphism is properly taken into account, the male-to-female mutation rate ratio, alpham, can be solved from the observed difference in rate of X and Y chromosome divergence. The male mutation bias is positively correlated with the relative excess of cell divisions in the male compared to the female germ line, as evidenced by a generation time effect: in mammals, alpham is estimated at approximately 4-6 in primates, approximately 3 in carnivores and approximately 2 in small rodents. Another life-history correlate is sexual selection: when there is intense sperm competition among males, increased sperm production will be associated with a larger number of mitotic cell divisions in spermatogenesis and hence an increase in alpham. Male-biased mutation has implications for important aspects of evolutionary biology such as mate choice in relation to mutation load, sexual selection and the maintenance of genetic diversity despite strong directional selection, the tendency for a disproportionate large role of the X (Z) chromosome in post-zygotic isolation, and the evolution of sex.

show abstract

Section: Life History and The Male Mutation Biasmentioning

confidence: 99%

Characteristics, causes and evolutionary consequences of male-biased mutation

2006

View full text Add to dashboard Cite

show abstract

“…Spontaneous mutation rate traditionally was measured in mutation accumulation experiments which are tedious and, for practical reasons, have been done mainly on viruses and a few rapidly replicating bacterial species [241, 242]. Dating the origin of pseudogenes and then comparing their divergence against their functional counterparts [243-246] allow for an estimation of spontaneous mutation rate (approximated by the neutral substitution rate) and mutation spectrum. High mutation rate and large population size increase the chance of parasites developing drug resistance.…”

Section: Bioinformatics and Drug Resistancementioning

confidence: 99%

Bioinformatics and Drug Discovery

Xia

2017

CTMC

158

View full text Add to dashboard Cite

Bioinformatic analysis can not only accelerate drug target identification and drug candidate screening and refinement, but also facilitate characterization of side effects and predict drug resistance. High-throughput data such as genomic, epigenetic, genome architecture, cistromic, transcriptomic, proteomic, and ribosome profiling data have all made significant contribution to mechanism-based drug discovery and drug repurposing. Accumulation of protein and RNA structures, as well as development of homology modeling and protein structure simulation, coupled with large structure databases of small molecules and metabolites, paved the way for more realistic protein-ligand docking experiments and more informative virtual screening. I present the conceptual framework that drives the collection of these high-throughput data, summarize the utility and potential of mining these data in drug discovery, outline a few inherent limitations in data and software mining these data, point out news ways to refine analysis of these diverse types of data, and highlight commonly used software and databases relevant to drug discovery.

show abstract

Male-Driven Evolution Among Eoaves? A Test of the Replicative Division Hypothesis in a Heterogametic Female (ZW) System

Kahn

Quinn

1999

J Mol Evol

View full text Add to dashboard Cite

Because avian females are heterogametic, the reverse of mammals, avian sex chromosomes undergo significantly different patterns and numbers of DNA replications than do those in mammals. This makes the W (female-specific) and the Z chromosomes an excellent model system for the study of the replicative division hypothesis, which purports that DNA substitution rate is determined by the number of germline replications. The sex-specific chromosome in birds (the W) is predicted to change at the slowest rate of all avian chromosomes because it undergoes the fewest rounds of replication per unit of evolutionary time. Using published data on gametogenesis from a variety of sources, we estimated the ratio of male-to-female germline replications (c) in galliforms and anseriforms to be approximately 4.4. The value of c should predict the value of the ratio of male-to-female mutation rates (alpha(m)) if the replicative division hypothesis is true. Homologous DNA sequences including an intron and parts of two exons of the CHD gene were obtained from the W and the Z chromosomes in ostrich, sage grouse, canvasback duck, tundra swan, and snow goose. The exons show significantly different nucleotide composition from the introns, and the W-linked exons show evidence of relaxed constraint. The Z-linked intron is diverging approximately 3.1 times faster than the W-linked intron. From this, alpha(m) was calculated to be approximately 4.1, with a confidence interval of 3.1 to 5.1. The data support the idea that the number of replicative divisions is a major determinant of substitution rate in the Eoavian genome.

show abstract

Estimating the intensity of male-driven evolution in rodents by using X-linked and Y-linked Ube 1 genes and pseudogenes

Cited by 37 publications

References 20 publications

Characteristics, causes and evolutionary consequences of male-biased mutation

Characteristics, causes and evolutionary consequences of male-biased mutation

Bioinformatics and Drug Discovery

Male-Driven Evolution Among Eoaves? A Test of the Replicative Division Hypothesis in a Heterogametic Female (ZW) System

Contact Info

Product

Resources

About