scholarly journals A Study of Faster-Z Evolution in the Great Tit (Parus major)

2020 ◽  
Vol 12 (3) ◽  
pp. 210-222 ◽  
Author(s):  
Kai Hayes ◽  
Henry J Barton ◽  
Kai Zeng
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Sex Chromosomes ◽  
Parus Major ◽  
Purifying Selection ◽  
Great Tit ◽  
Z Chromosome ◽  
Male Reproductive Success ◽  
Effective Population ◽  
Major Genome

Abstract Sex chromosomes contribute substantially to key evolutionary processes such as speciation and adaptation. Several theories suggest that evolution could occur more rapidly on sex chromosomes, but currently our understanding of whether and how this occurs is limited. Here, we present an analysis of the great tit (Parus major) genome, aiming to detect signals of faster-Z evolution. We find mixed evidence of faster divergence on the Z chromosome than autosomes, with significantly higher divergence being found in ancestral repeats, but not at 4- or 0-fold degenerate sites. Interestingly, some 4-fold sites appear to be selectively constrained, which may mislead analyses that use these sites as the neutral reference (e.g., dN/dS). Consistent with other studies in birds, the mutation rate is significantly higher in males than females, and the long-term Z-to-autosome effective population size ratio is only 0.5, significantly lower than the expected value of 0.75. These are indicative of male-driven evolution and high variance in male reproductive success, respectively. We find no evidence for an increased efficacy of positive selection on the Z chromosome. In contrast, the Z chromosome in great tits appears to be affected by increased genetic drift, which has led to detectable signals of weakened intensity of purifying selection. These results provide further evidence that the Z chromosome often has a low effective population size, and that this has important consequences for its evolution. They also highlight the importance of considering multiple factors that can affect the rate of evolution and effective population sizes of sex chromosomes.

scholarly journals Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees

2020 ◽  
Author(s):  
Arthur Weyna ◽  
Jonathan Romiguier
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Ecosystem Engineer ◽  
Relative Rate ◽  
Population Decline ◽  
Purifying Selection ◽  
Life History Strategies ◽  
Effective Population ◽  
Social Bees ◽  
Pollinator Species

ABSTRACTWith one of the highest number of parasite, eusocial and pollinator species among all insect orders, Hymenoptera features a great diversity of specific lifestyles. At the population genetic level, such life-history strategies are expected to decrease effective population size and efficiency of purifying selection. In this study, we tested this hypothesis by estimating the relative rate of non-synonymous substitution in 169 species to investigate the variation in natural selection efficiency throughout the hymenopteran tree of life. We found no effect of parasitism or body size, but show that relaxed selection is associated with eusociality, suggesting that the division of reproductive labour decreases effective population size in ants, bees and wasps. Unexpectedly, the effect of eusociality is marginal compared to a striking and widespread relaxation of selection in both social and non social bees, which indicates that these keystone pollinator species generally feature low effective population sizes. This widespread pattern suggests specific constraints in pollinating bees potentially linked to limited resource and high parental investment. The particularly high load of deleterious mutations we report in the genome of these crucial ecosystem engineer species also raises new concerns about their ongoing population decline.

scholarly journals Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds

Heredity ◽  
2015 ◽  
Vol 115 (5) ◽  
pp. 452-459 ◽  
Author(s):  
S J Oyler-McCance ◽  
R S Cornman ◽  
K L Jones ◽  
J A Fike
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Z Chromosome ◽  
Effective Population

scholarly journals The Strength of Selection Against Neanderthal Introgression

2015 ◽  
Author(s):  
Ivan Juric ◽  
Simon Aeschbacher ◽  
Graham Coop
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Human Population ◽  
Genetic Load ◽  
Purifying Selection ◽  
Small Population ◽  
Secondary Contact ◽  
Human Populations ◽  
Effective Population ◽  
Deleterious Alleles

AbstractHybridization between humans and Neanderthals has resulted in a low level of Neanderthal ancestry scattered across the genomes of many modern-day humans. After hybridization, on average, selection appears to have removed Neanderthal alleles from the human population. Quantifying the strength and causes of this selection against Neanderthal ancestry is key to understanding our relationship to Neanderthals and, more broadly, how populations remain distinct after secondary contact. Here, we develop a novel method for estimating the genome-wide average strength of selection and the density of selected sites using estimates of Neanderthal allele frequency along the genomes of modern-day humans. We confirm that East Asians had somewhat higher initial levels of Neanderthal ancestry than Europeans even after accounting for selection. We find that the bulk of purifying selection against Neanderthal ancestry is best understood as acting on many weakly deleterious alleles. We propose that the majority of these alleles were effectively neutral—and segregating at high frequency—in Neanderthals, but became selected against after entering human populations of much larger effective size. While individually of small effect, these alleles potentially imposed a heavy genetic load on the early-generation human–Neanderthal hybrids. This work suggests that differences in effective population size may play a far more important role in shaping levels of introgression than previously thought.Author SummaryA small percentage of Neanderthal DNA is present in the genomes of many contemporary human populations due to hybridization tens of thousands of years ago. Much of this Neanderthal DNA appears to be deleterious in humans, and natural selection is acting to remove it. One hypothesis is that the underlying alleles were not deleterious in Neanderthals, but rather represent genetic incompatibilities that became deleterious only once they were introduced to the human population. If so, reproductive barriers must have evolved rapidly between Neanderthals and humans after their split. Here, we show that oberved patterns of Neanderthal ancestry in modern humans can be explained simply as a consequence of the difference in effective population size between Neanderthals and humans. Specifically, we find that on average, selection against individual Neanderthal alleles is very weak. This is consistent with the idea that Neanderthals over time accumulated many weakly deleterious alleles that in their small population were effectively neutral. However, after introgressing into larger human populations, those alleles became exposed to purifying selection. Thus, rather than being the result of hybrid incompatibilities, differences between human and Neanderthal effective population sizes appear to have played a key role in shaping our present-day shared ancestry.

scholarly journals Novel insights into joint estimations of demography, mutation rate, and selection using UV sex chromosomes

2021 ◽  
Author(s):  
Sarah B. Carey ◽  
James H. Peniston ◽  
Adam C. Payton ◽  
Min Kim ◽  
Anna Lipzen ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Sex Chromosomes ◽  
Natural Populations ◽  
Effective Population ◽  
Determination System ◽  
Suppressed Recombination ◽  
Whole Genome Resequencing ◽  
Sex Determination System

A central goal in evolutionary genomics is to understand the processes that shape genetic variation in natural populations. In anisogamous species, these processes may generate asymmetries between genes transmitted through sperm or eggs. The unique inheritance of sex chromosomes facilitates studying such asymmetries, but in many systems sex-biased mutation, demography, and selection are confounded with suppressed recombination in only one sex (the W in females, or the Y in males). However, in a UV sex-determination system, both sex chromosomes are sex-specific and experience suppressed recombination. Here we built a spatially-structured simulation to examine the effects of population density and sex-ratio on female and male effective population size in haploids and compare the results to polymorphism data from whole-genome resequencing of the moss Ceratodon purpureus. In the parameter space we simulated, males nearly always had a lower effective population size than females. Using the C. purpureus resequencing data, we found the U and V have lower nucleotide diversity than the autosomal mean, and the V is much lower than the U, however, we found no parameter set in the model that explained both the U/V and U/autosome ratios we observed. We next used standard molecular evolutionary analyses to test for sex-biased mutation and selection. We found that males had a higher mutation rate but that natural selection shapes variation on the UV sex chromosomes. All together the moss system highlights how anisogamy alone can exert a profound influence on genome-wide patterns of molecular evolution.

Sign in / Sign up

Export Citation Format

Share Document