scholarly journals A Microsatellite Variability Screen for Positive Selection Associated With the “Out of Africa” Habitat Expansion of Drosophila melanogaster

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1137-1148
Author(s):  
M O Kauer ◽  
D Dieringer ◽  
C Schlötterer
Keyword(s):  
X Chromosome ◽  
Theoretical Work ◽  
Selective Sweeps ◽  
Mapping Study ◽  
X Chromosomes ◽  
The Third ◽  
African Populations ◽  
Average Loss ◽  
Out Of Africa ◽  
Genomic Regions

Abstract We report a “hitchhiking mapping” study in D. melanogaster, which searches for genomic regions with reduced variability. The study's aim was to identify selective sweeps associated with the “out of Africa” habitat expansion. We scanned 103 microsatellites on chromosome 3 and 102 microsatellites on the X chromosome for reduced variability in non-African populations. When the chromosomes were analyzed separately, the number of loci with a significant reduction in variability only slightly exceeded the expectation under neutrality—six loci on the third chromosome and four loci on the X chromosome. However, non-African populations also have a more pronounced average loss in variability on the X chromosomes as compared to the third chromosome, which suggests the action of selection. Therefore, comparing the X chromosome to the autosome yields a higher number of significantly reduced loci. However, a more pronounced loss of variability on the X chromosome may be caused by demographic events rather than by natural selection. We therefore explored a range of demographic scenarios and found that some of these captured most, but not all aspects of our data. More theoretical work is needed to evaluate how demographic events might differentially affect X chromosomes and autosomes and to estimate the most likely scenario associated with the out of Africa expansion of D. melanogaster.

scholarly journals Strong selective sweeps before 45,000BP displaced archaic admixture across the human X chromosome

2018 ◽  
Author(s):  
L. Skov ◽  
M.C. Macià ◽  
E. Lucotte ◽  
M.I.A. Cavassim ◽  
D. Castellano ◽  
...  
Keyword(s):  
Natural Selection ◽  
X Chromosome ◽  
Selective Sweeps ◽  
High Frequencies ◽  
African Populations ◽  
Neanderthal Admixture ◽  
Archaic Admixture ◽  
Out Of Africa ◽  
Expected Proportion

AbstractThe X chromosome in non-African populations has less diversity and less Neanderthal introgression than expected. We analyzed X chromosome diversity across the globe and discovered seventeen chromosomal regions, where haplotypes of several hundred kilobases have recently reached high frequencies in non-African populations only. The selective sweeps must have occurred more than 45,000 years ago because the ancient Ust’-Ishim male also carries its expected proportion of these haplotypes. Surprisingly, the swept haplotypes are entirely devoid of Neanderthal introgression, which implies that a population without Neanderthal admixture contributed the swept haplotypes. It also implies that the sweeps must have happened after the main interbreeding event with Neanderthals about 55,000 BP. These swept haplotypes may thus be the only genetic remnants of an earlier out-of-Africa event.One Sentence SummaryAfter humans expanded out of Africa, the X chromosome experienced a burst of extreme natural selection that removed Neanderthal admixture.

Chromosomal Patterns of Microsatellite Variability Contrast Sharply in African and Non-African Populations of Drosophila melanogaster

Genetics ◽  
2002 ◽  
Vol 160 (1) ◽  
pp. 247-256
Author(s):  
M Kauer ◽  
B Zangerl ◽  
D Dieringer ◽  
C Schlötterer
Keyword(s):  
Chromosomal Polymorphism ◽  
Background Selection ◽  
Selective Sweeps ◽  
X Chromosomes ◽  
Evolutionary Forces ◽  
Relative Contribution ◽  
African Populations ◽  
Neutral Variation ◽  
Colonization Process ◽  
The Subject

Abstract Levels of neutral variation are influenced by background selection and hitchhiking. The relative contribution of these evolutionary forces to the distribution of neutral variation is still the subject of ongoing debates. Using 133 microsatellites, we determined levels of variability on X chromosomes and autosomes in African and non-African D. melanogaster populations. In the ancestral African populations microsatellite variability was higher on X chromosomes than on autosomes. In non-African populations X-linked polymorphism is significantly more reduced than autosomal variation. In non-African populations we observed a significant positive correlation between X chromosomal polymorphism and recombination rate. These results are consistent with the interpretation that background selection shapes levels of neutral variability in the ancestral populations, while the pattern in derived populations is determined by multiple selective sweeps during the colonization process. Further research, however, is required to investigate the influence of inversion polymorphisms and unequal sex ratios.

Clues from other animals and theoretical considerations

Development ◽  
1987 ◽  
Vol 101 (Supplement) ◽  
pp. 3-4
Author(s):  
Anne McLaren
Keyword(s):  
Sex Determination ◽  
Genetic Control ◽  
Y Chromosome ◽  
X Chromosome ◽  
X Chromosomes ◽  
The Third ◽  
Mouse Species ◽  
Primary Male ◽  
Theoretical Considerations ◽  
State Of Activity

In the first two papers of this volume, the genetic control of sex determination in Caenorhabditis and Drosophila is reviewed by Hodgkin and by Nöthiger & Steinmarin-Zwicky, respectively. Sex determination in both cases depends on the ratio of X chromosomes to autosomes, which acts as a signal to a cascade of règulatory genes located either on autosomes or on the X chromosome. The state of activity of the last gene in the sequence determines phenotypic sex. In the third paper, Erickson & Tres describe the structure of the mouse Y chromosome and the polymorphisms that have been detected in different mouse species and strains. As in all mammals, the Y carries the primary male-determining locus; autosomal genes may also be involved in sex determination, but they must act down-stream from the Y-linked locus.

scholarly journals Fine-mapping the Favored Mutation in a Positive Selective Sweep

2017 ◽  
Author(s):  
Ali Akbari ◽  
Joseph J. Vitti ◽  
Arya Iranmehr ◽  
Mehrdad Bakhtiari ◽  
Pardis C. Sabeti ◽  
...  
Keyword(s):  
Selective Sweep ◽  
Population Genomics ◽  
Simulated Data ◽  
Human Populations ◽  
Selective Sweeps ◽  
1000 Genomes ◽  
Candidate Mutation ◽  
African Populations ◽  
Signature Of Selection ◽  
Out Of Africa

AbstractMethods to identify signatures of selective sweeps in population genomics data have been actively developed, but mostly do not identify the specific mutation favored by the selective sweep. We present a method, iSAFE, that uses a statistic derived solely from population genetics signals to pinpoint the favored mutation even when the signature of selection extends to 5Mbp. iSAFE was tested extensively on simulated data and in human populations from the 1000 Genomes Project, at 22 loci with previously characterized selective sweeps. For 14 of the 22 loci, iSAFE ranked the previously characterized candidate mutation among the 13 highest scoring (out of ∼ 21, 000 variants). Three loci did not show a strong signal. For the remaining loci, iSAFE identified previously unreported mutations as being favored. In these regions, all of which involve pigmentation related genes, iSAFE identified identical selected mutations in multiple non-African populations suggesting an out-of-Africa onset of selection. The iSAFE software can be downloaded from https://github.com/alek0991/iSAFE.

scholarly journals Delayed DNA replication in haploid human embryonic stem cells

2021 ◽  
Author(s):  
Matthew Micheal Edwards ◽  
Michael V. Zuccaro ◽  
Ido Sagi ◽  
Qiliang Ding ◽  
Dan Vershkov ◽  
...  
Keyword(s):  
Stem Cells ◽  
Dna Replication ◽  
Embryonic Stem Cells ◽  
X Chromosome ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Replication Timing ◽  
Genetic System ◽  
X Chromosomes ◽  
Genomic Regions

Haploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication. To test this, we profiled DNA replication timing in isogenic haploid and diploid ESCs. The greatest difference was the earlier replication of the X chromosome in haploids, consistent with the lack of X chromosome inactivation. Surprisingly, we also identified 21 autosomal regions that had dramatically delayed replication in haploids, extending beyond the normal S phase and into G2/M. Haploid-delays comprised a unique set of quiescent genomic regions that are also under-replicated in polyploid placental cells. The same delays were observed in female ESCs with two active X chromosomes, suggesting that increased X chromosome dosage may cause delayed autosomal replication. We propose that incomplete replication at the onset of mitosis could prevent cell division and result in re-entry into the cell cycle and whole genome duplication.

scholarly journals Delayed DNA replication in haploid human embryonic stem cells

2021 ◽  
Author(s):  
Matthew M. Edwards ◽  
Michael V. Zuccaro ◽  
Ido Sagi ◽  
Qiliang Ding ◽  
Dan Vershkov ◽  
...  
Keyword(s):  
Stem Cells ◽  
Dna Replication ◽  
Embryonic Stem Cells ◽  
X Chromosome ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Replication Timing ◽  
Genetic System ◽  
X Chromosomes ◽  
Genomic Regions

Haploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication. To test this, we profiled DNA replication timing in isogenic haploid and diploid ESCs. The greatest difference was the earlier replication of the X Chromosome in haploids, consistent with the lack of X-Chromosome inactivation. We also identified 21 autosomal regions that had delayed replication in haploids, extending beyond the normal S phase and into G2/M. Haploid-delays comprised a unique set of quiescent genomic regions that are also underreplicated in polyploid placental cells. The same delays were observed in female ESCs with two active X Chromosomes, suggesting that increased X-Chromosome dosage may cause delayed autosomal replication. We propose that incomplete replication at the onset of mitosis could prevent cell division and result in re-entry into the cell cycle and whole genome duplication.

scholarly journals Strong selective sweeps on the X chromosome in the human-chimpanzee ancestor explain its low divergence

2014 ◽  
Author(s):  
Julien Y Dutheil ◽  
Kasper Munch ◽  
Kiwoong Nam ◽  
Thomas Mailund ◽  
Mikkel Schierup
Keyword(s):  
X Chromosome ◽  
Incomplete Lineage Sorting ◽  
Underlying Mechanism ◽  
Selective Sweeps ◽  
Lineage Sorting ◽  
X Chromosomes ◽  
Unique Role ◽  
Ancestral Species ◽  
Low Diversity

The human and chimpanzee X chromosomes are less divergent than expected based on autosomal divergence. This has led to a controversial hypothesis proposing a unique role of the X chromosome in human-chimpanzee speciation. We study incomplete lineage sorting patterns between humans, chimpanzees and gorillas to show that this low divergence is entirely due to megabase-sized regions comprising one-third of the X chromosome, where polymorphism in the human-chimpanzee ancestral species was severely reduced. Background selection can explain 10% of this reduction at most. Instead, we show that several strong selective sweeps in the ancestral species can explain this reduction of diversity in the ancestor. We also report evidence of population specific sweeps in extant humans that overlap the regions of low diversity in the ancestral species. These regions further correspond to chromosomal sections shown to be devoid of Neanderthal introgression into modern humans. This suggests that the same X-linked regions that undergo selective sweeps are among the first to form reproductive barriers between diverging species. We hypothesize that meiotic drive is the underlying mechanism causing these two observations.

scholarly journals Extreme selective sweeps independently targeted the X chromosomes of the great apes

2015 ◽  
Vol 112 (20) ◽  
pp. 6413-6418 ◽  
Author(s):  
Kiwoong Nam ◽  
Kasper Munch ◽  
Asger Hobolth ◽  
Julien Yann Dutheil ◽  
Krishna R. Veeramah ◽  
...  
Keyword(s):  
X Chromosome ◽  
Synonymous Substitution ◽  
Male Meiosis ◽  
Direct Selection ◽  
Chromosome Polymorphism ◽  
Genomic Feature ◽  
Selective Sweeps ◽  
X Chromosomes ◽  
Intragenomic Conflict ◽  
Accelerated Evolution

The unique inheritance pattern of the X chromosome exposes it to natural selection in a way that is different from that of the autosomes, potentially resulting in accelerated evolution. We perform a comparative analysis of X chromosome polymorphism in 10 great ape species, including humans. In most species, we identify striking megabase-wide regions, where nucleotide diversity is less than 20% of the chromosomal average. Such regions are found exclusively on the X chromosome. The regions overlap partially among species, suggesting that the underlying targets are partly shared among species. The regions have higher proportions of singleton SNPs, higher levels of population differentiation, and a higher nonsynonymous-to-synonymous substitution ratio than the rest of the X chromosome. We show that the extent to which diversity is reduced is incompatible with direct selection or the action of background selection and soft selective sweeps alone, and therefore, we suggest that very strong selective sweeps have independently targeted these specific regions in several species. The only genomic feature that we can identify as strongly associated with loss of diversity is the location of testis-expressed ampliconic genes, which also have reduced diversity around them. We hypothesize that these genes may be responsible for selective sweeps in the form of meiotic drive caused by an intragenomic conflict in male meiosis.

scholarly journals Bisection of the X chromosome disrupts the initiation of chromosome silencing during meiosis in Caenorhabditis elegans

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yisrael Rappaport ◽  
Hanna Achache ◽  
Roni Falk ◽  
Omer Murik ◽  
Oren Ram ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Rna Polymerase Ii ◽  
X Chromosome ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Transcription Analysis ◽  
X Chromosomes ◽  
Unique Character ◽  
Active Transcription ◽  
Heterogametic Sex

AbstractDuring meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans nematodes with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments are enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome are upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.

scholarly journals DNA methylation and behavioral dysfunction in males with 47,XXY and 49,XXXXY: a pilot study

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Richard S. Lee ◽  
Sophia Q. Song ◽  
Henri M. Garrison-Desany ◽  
Jenny L. Carey ◽  
Patricia Lasutschinkow ◽  
...  
Keyword(s):  
Pilot Study ◽  
X Chromosome ◽  
Child Behavior Checklist ◽  
Epigenetic Modification ◽  
Cpg Methylation ◽  
Monoamine Oxidase A ◽  
Low Fertility ◽  
X Chromosomes ◽  
Behavioral Dysfunction ◽  
Study Results

Abstract Background Equal dosage of X-linked genes between males and females is maintained by the X-inactivation of the second X chromosome in females through epigenetic mechanisms. Boys with aneuploidy of the X chromosome exhibit a host of symptoms such as low fertility, musculoskeletal anomalies, and cognitive and behavioral deficits that are presumed to be caused by the abnormal dosage of these genes. The objective of this pilot study is to assess the relationship between CpG methylation, an epigenetic modification, at several genes on the X chromosome and behavioral dysfunction in boys with supernumerary X chromosomes. Results Two parental questionnaires, the Behavior Rating Inventory of Executive Function (BRIEF) and Child Behavior Checklist (CBCL), were analyzed, and they showed expected differences in both internal and external behaviors between neurotypical (46,XY) boys and boys with 49,XXXXY. There were several CpGs in AR and MAOA of boys with 49,XXXXY whose methylation levels were skewed from levels predicted from having one active (Xa) and three inactive (Xi) X chromosomes. Further, methylation levels of multiple CpGs in MAOA showed nominally significant association with externalizing behavior on the CBCL, and the methylation level of one CpG in AR showed nominally significant association with the BRIEF Regulation Index. Conclusions Boys with 49,XXXXY displayed higher levels of CpG methylation at regulatory intronic regions in X-linked genes encoding the androgen receptor (AR) and monoamine oxidase A (MAOA), compared to that in boys with 47,XXY and neurotypical boys. Our pilot study results suggest a link between CpG methylation levels and behavior in boys with 49,XXXXY.

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