scholarly journals Variable Autosomal and X Divergence Near and Far from Genes Affects Estimates of Male Mutation Bias in Great Apes

2016 ◽  
Vol 8 (11) ◽  
pp. 3393-3405 ◽  
Author(s):  
Pooja Narang ◽  
Melissa A. Wilson Sayres
Keyword(s):  
Great Apes ◽  
Mutation Bias ◽  
Male Mutation Bias

scholarly journals Long-term natural selection affects patterns of neutral divergence on the X chromosome more than the autosomes.

2015 ◽  
Author(s):  
Melissa Ann Wilson Sayres ◽  
Pooja Narang
Keyword(s):  
Natural Selection ◽  
X Chromosome ◽  
Great Apes ◽  
Regulatory Elements ◽  
Mutation Bias ◽  
Term Selection ◽  
Coding Regions ◽  
Male Mutation Bias ◽  
Genomic Regions

Natural selection reduces neutral population genetic diversity near coding regions of the genome because recombination has not had time to unlink selected alleles from nearby neutral regions. For ten sub-species of great apes, including human, we show that long-term selection affects estimates of divergence on the X differently from the autosomes. Divergence increases with increasing distance from genes on both the X chromosome and autosomes, but increases faster on the X chromosome than autosomes, resulting in increasing ratios of X/A divergence in putatively neutral regions. Similarly, divergence is reduced more on the X chromosome in neutral regions near conserved regulatory elements than on the autosomes. Consequently estimates of male mutation bias, which rely on comparing neutral divergence between the X and autosomes, are twice as high in neutral regions near genes versus far from genes. Our results suggest filters for putatively neutral genomic regions differ between the X and autosomes.

scholarly journals Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals

2017 ◽  
Vol 9 (9) ◽  
pp. 2198-2210 ◽  
Author(s):  
Vivian Link ◽  
Diana Aguilar-Gómez ◽  
Ciro Ramírez-Suástegui ◽  
Laurence D. Hurst ◽  
Diego Cortez
Keyword(s):  
Mutation Bias ◽  
Substitution Rates ◽  
Male Mutation Bias

Substitution Rate Heterogeneity and the Male Mutation Bias

2006 ◽  
Vol 62 (2) ◽  
pp. 226-233 ◽  
Author(s):  
Sofia Berlin ◽  
Mikael Brandström ◽  
Niclas Backström ◽  
Erik Axelsson ◽  
Nick G.C. Smith ◽  
...  
Keyword(s):  
Substitution Rate ◽  
Rate Heterogeneity ◽  
Mutation Bias ◽  
Male Mutation Bias

scholarly journals Changes in life history and population size can explain the relative neutral diversity levels on X and autosomes in extant human populations

2020 ◽  
Vol 117 (33) ◽  
pp. 20063-20069
Author(s):  
Guy Amster ◽  
David A. Murphy ◽  
William R. Milligan ◽  
Guy Sella
Keyword(s):  
Life History ◽  
Population Size ◽  
Mutation Rates ◽  
Human Populations ◽  
Effective Population ◽  
Mutation Bias ◽  
Female Ratio ◽  
Generation Times ◽  
Population Sizes ◽  
Male Mutation Bias

In human populations, the relative levels of neutral diversity on the X and autosomes differ markedly from each other and from the naïve theoretical expectation of 3/4. Here we propose an explanation for these differences based on new theory about the effects of sex-specific life history and given pedigree-based estimates of the dependence of human mutation rates on sex and age. We demonstrate that life history effects, particularly longer generation times in males than in females, are expected to have had multiple effects on human X-to-autosome (X:A) diversity ratios, as a result of male-biased mutation rates, the equilibrium X:A ratio of effective population sizes, and the differential responses to changes in population size. We also show that the standard approach of using divergence between species to correct for male mutation bias results in biased estimates of X:A effective population size ratios. We obtain alternative estimates using pedigree-based estimates of the male mutation bias, which reveal that X:A ratios of effective population sizes are considerably greater than previously appreciated. Finally, we find that the joint effects of historical changes in life history and population size can explain the observed X:A diversity ratios in extant human populations. Our results suggest that ancestral human populations were highly polygynous, that non-African populations experienced a substantial reduction in polygyny and/or increase in the male-to-female ratio of generation times around the Out-of-Africa bottleneck, and that current diversity levels were affected by fairly recent changes in sex-specific life history.

scholarly journals LIFE HISTORY AND THE MALE MUTATION BIAS

Evolution ◽  
2003 ◽  
Vol 57 (10) ◽  
pp. 2398-2406 ◽  
Author(s):  
Anna Bartosch -Harlid ◽  
Sofia Berlin ◽  
Nick G. C. Smith ◽  
Anders P. Mosller ◽  
Hans Ellegren
Keyword(s):  
Life History ◽  
Mutation Bias ◽  
Male Mutation Bias

scholarly journals Deciphering Ancestral Sex Chromosome Turnovers Based on Analysis of Male Mutation Bias

2019 ◽  
Vol 11 (11) ◽  
pp. 3054-3067 ◽  
Author(s):  
Armando Acosta ◽  
Mónica L Martínez-Pacheco ◽  
Karina Díaz-Barba ◽  
Niccole Porras ◽  
Mariana Gutiérrez-Mariscal ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Same Sex ◽  
Mutation Bias ◽  
Substitution Rates ◽  
Transcriptomic Data ◽  
Phylogenetic Reconstructions ◽  
Sex Chromosome System ◽  
Male Mutation Bias

Abstract The age of sex chromosomes is commonly obtained by comparing the substitution rates of XY gametologs. Coupled with phylogenetic reconstructions, one can refine the origin of a sex chromosome system relative to specific speciation events. However, these approaches are insufficient to determine the presence and duration of ancestral sex chromosome systems that were lost in some species. In this study, we worked with genomic and transcriptomic data from mammals and squamates and analyzed the effect of male mutation bias on X-linked sequences in these groups. We searched for signatures indicating whether monotremes shared the same sex chromosomes with placental mammals or whether pleurodonts and acrodonts had a common ancestral sex chromosome system. Our analyses indicate that platypus did not share the XY chromosomes with placental mammals, in agreement with previous work. In contrast, analyses of agamids showed that this lineage maintained the pleurodont XY chromosomes for several million years. We performed multiple simulations using different strengths of male mutation bias to confirm the results. Overall, our work shows that variations in substitution rates due to male mutation bias could be applied to uncover signatures of ancestral sex chromosome systems.

LIFE HISTORY AND THE MALE MUTATION BIAS

Evolution ◽  
2003 ◽  
Vol 57 (10) ◽  
pp. 2398 ◽  
Author(s):  
Anna Bartosch-Härlid ◽  
Sofia Berlin ◽  
Nick G. C. Smith ◽  
Anders P. Møller ◽  
Hans Ellegren
Keyword(s):  
Life History ◽  
Mutation Bias ◽  
Male Mutation Bias

scholarly journals Male Mutation Bias and Possible Long-Term Effects of Human Activities

2010 ◽  
Vol 24 (5) ◽  
pp. 1190-1197 ◽  
Author(s):  
SAMUEL COTTON ◽  
CLAUS WEDEKIND
Keyword(s):  
Human Activities ◽  
Long Term Effects ◽  
Mutation Bias ◽  
Male Mutation Bias

scholarly journals Strong and Weak Male Mutation Bias at Different Sites in the Primate Genomes: Insights from the Human-Chimpanzee Comparison

2005 ◽  
Vol 23 (3) ◽  
pp. 565-573 ◽  
Author(s):  
James Taylor ◽  
Svitlana Tyekucheva ◽  
Michael Zody ◽  
Francesca Chiaromonte ◽  
Kateryna D. Makova
Keyword(s):  
Mutation Bias ◽  
Male Mutation Bias
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