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 Do LINEs Have a Role in X-Chromosome Inactivation?

2006 ◽  
Vol 2006 ◽  
pp. 1-6 ◽  
Author(s):  
Mary F. Lyon
Keyword(s):  
X Chromosome ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Current Evidence ◽  
X Chromosomes ◽  
Repeat Elements ◽  
Sequencing Project ◽  
Human Genome Sequencing ◽  
Human And Mouse

There is longstanding evidence that X-chromosome inactivation (XCI) travels less successfully in autosomal than in X-chromosomal chromatin. The interspersed repeat elements LINE1s (L1s) have been suggested as candidates for “boosters” which promote the spread of XCI in the X-chromosome. The present paper reviews the current evidence concerning the possible role of L1s in XCI. Recent evidence, accruing from the human genome sequencing project and other sources, confirms that mammalian X-chromosomes are indeed rich in L1s, except in regions where there are many genes escaping XCI. The density of L1s is the highest in the evolutionarily oldest regions. Recent work on X; autosome translocations in human and mouse suggested failure of stabilization of XCI in autosomal material, so that genes are reactivated, but resistance of autosomal genes to the original silencing is not excluded. The accumulation of L1s on the X-chromosome may have resulted from reduced recombination or late replication. Whether L1s are part of the mechanism of XCI or a result of it remains enigmatic.

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 ANALYSIS OF THE AUTOSOMAL MUTATION abo AND ITS INTERACTION WITH THE RIBOSOMAL DNA OF DROSOPHILA MELANOGASTER: THE ROLE OF X-CHROMOSOME HETEROCHROMATIN

Genetics ◽  
1980 ◽  
Vol 95 (3) ◽  
pp. 661-672
Author(s):  
Barry Yedvobnick ◽  
Hallie M Krider ◽  
Bryan I Levine
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
Autosomal Recessive ◽  
Wild Type ◽  
X Chromosomes ◽  
Cr Functions ◽  
Chromosome Inversions ◽  
Ratio Distortion ◽  
Sex Ratio Distortion

ABSTRACT The autosomal recessive, maternal-effect mutation abnormal oocyte (abo: 2-38) preferentially lowers the viability of XO progeny. The severity of the sex-ratio distortion is reduced by duplications of maternal or zygotic heterochromatin chromatin (SANDLER 1970, 1977; PARRY and SANDLER 1974). Utilizing X-chromosome inversions that contain modifications in the quantity and arrangement of the heterochromatic functions, Xhabo and cr  +, we have extended our investigations of nbo's influence on XO male recovery and rDNA redundancy (KRIDER,YEDVOBNICK and LEVINE 1979).——XO males bearing In(1)scs1Lsc4R or In(1)wm4Lsc4R are recovered twice as frequently as X chromosomes containing a single Xh region, implying that these inversions possess a duplication of Xhabo. abo mutant females heterozygous for In(1)scs1Lsc4R and wild-type X chromosomes generate XO progeny that do not contain elevated rDNA redundancies. XO males containing In(1)wm4 exhibit male recoveries and rDNA elevations similar to those of males bearing a wild-type X chromosome, when both derive from a common abo/abo mother. Reciprocal crosses between In(1)wm4 and Canton-S males to attached-X abo females show significant, though reduced, sex ratios in the absence of an rDNA effect. The observation that abo can elevate the rDNA redundancy of In(1)wm4, a chromosome that does not compensate, suggests that abo and cr+ functions are not directly related.

scholarly journals Conversion of random X-inactivation to imprinted X-inactivation by maternal PRC2

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Clair Harris ◽  
Marissa Cloutier ◽  
Megan Trotter ◽  
Michael Hinten ◽  
Srimonta Gayen ◽  
...  
Keyword(s):  
X Chromosome ◽  
Epigenetic Inheritance ◽  
X Inactivation ◽  
Human Embryos ◽  
Xist Expression ◽  
X Chromosomes ◽  
Polycomb Repressive Complex 2 ◽  
Early Embryos ◽  
Early Human

Imprinted X-inactivation silences genes exclusively on the paternally-inherited X-chromosome and is a paradigm of transgenerational epigenetic inheritance in mammals. Here, we test the role of maternal vs. zygotic Polycomb repressive complex 2 (PRC2) protein EED in orchestrating imprinted X-inactivation in mouse embryos. In maternal-null (Eedm-/-) but not zygotic-null (Eed-/-) early embryos, the maternal X-chromosome ectopically induced Xist and underwent inactivation. Eedm-/- females subsequently stochastically silenced Xist from one of the two X-chromosomes and displayed random X-inactivation. This effect was exacerbated in embryos lacking both maternal and zygotic EED (Eedmz-/-), suggesting that zygotic EED can also contribute to the onset of imprinted X-inactivation. Xist expression dynamics in Eedm-/- embryos resemble that of early human embryos, which lack oocyte-derived maternal PRC2 and only undergo random X-inactivation. Thus, expression of PRC2 in the oocyte and transmission of the gene products to the embryo may dictate the occurrence of imprinted X-inactivation in mammals.

In the Eye of the Beholder: A Case for the Visual Hostile Media Phenomenon

2021 ◽  
pp. 009365022110185
Author(s):  
Jörg Matthes ◽  
Desirée Schmuck ◽  
Christian von Sikorski
Keyword(s):  
Visual Communication ◽  
Experimental Studies ◽  
Underlying Mechanism ◽  
Unique Role ◽  
Reasoning Study ◽  
Hostile Media

The hostile media phenomenon (HMP) refers to a process in which supporters and opponents of an issue perceive the identical coverage to be biased against their own views. Despite the relevance of visual communication in our field, scholars have treated hostile media perceptions as a text-based phenomenon ignoring the unique role of visuals. This paper makes the case for a visual hostile media phenomenon (VHMP). The VHMP posits that completely balanced pictures are perceived as biased both by opponents and supporters of an issue. Two experimental studies on the Israel–Palestine conflict provide clear evidence for this reasoning. Study 1 shows that Palestine (Israel) supporters perceived a balanced photo series as biased toward Israel (Palestine) irrespective of the series’ reach. This effect was also visible for clearly slanted pro-Israel and pro-Palestine pictures (i.e., relative VHMP). Study 2 replicates these findings and sheds some first light on the underlying mechanism. Theoretical and methodological implications are discussed.

scholarly journals A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

2019 ◽  
Author(s):  
Andrea M. Quattrini ◽  
Tiana Wu ◽  
Keryea Soong ◽  
Ming-Shiou Jeng ◽  
Yehuda Benayahu ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Species Delimitation ◽  
Incomplete Lineage Sorting ◽  
Dna Barcode ◽  
Species Boundaries ◽  
Future Research ◽  
Species Trees ◽  
Lineage Sorting ◽  
Evolutionary Diversification

AbstractBackgroundOur ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia.ResultsSpecies delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications, likely due to incomplete lineage sorting. In contrast, 12 of the 15 morphospecies examined formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of >6,000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia.ConclusionsA genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating diversity in corals. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.

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 Deciphering the Role of the Barr Body in Malignancy: An insight into head and neck cancer

2018 ◽  
Vol 17 (4) ◽  
pp. 389 ◽  
Author(s):  
Deepti Sharma ◽  
George Koshy ◽  
Shruti Gupta ◽  
Bhushan Sharma ◽  
Sonal Grover
Keyword(s):  
Head And Neck ◽  
X Chromosome ◽  
Expression Patterns ◽  
Barr Body ◽  
X Chromosomes ◽  
Differentiated Cells ◽  
Inactive X Chromosome ◽  
Poorly Differentiated ◽  
Differentiation Status

X chromosome inactivation is the epitome of epigenetic regulation and long non-coding ribonucleic acid function. The differentiation status of cells has been ascribed to X chromosome activity, with two active X chromosomes generally only observed in undifferentiated or poorly differentiated cells. Recently, several studies have indicated that the reactivation of an inactive X chromosome or X chromosome multiplication correlates with the development of malignancy; however, this concept is still controversial. This review sought to shed light on the role of the X chromosome in cancer development. In particular, there is a need for further exploration of the expression patterns of X-linked genes in cancer cells, especially those in head and neck squamous cell carcinoma (HNSCC), in order to identify different prognostic subpopulations with distinct clinical implications. This article proposes a functional relationship between the loss of the Barr body and the disproportional expression of X-linked genes in HNSCC development.

Molecular characterization of the male-specific lethal-3 gene and investigations of the regulation of dosage compensation in Drosophila

Development ◽  
1995 ◽  
Vol 121 (2) ◽  
pp. 463-475 ◽  
Author(s):  
M. Gorman ◽  
A. Franke ◽  
B.S. Baker
Keyword(s):  
X Chromosome ◽  
Dosage Compensation ◽  
The Other ◽  
Single Male ◽  
X Chromosomes ◽  
Male Specific Lethal ◽  
Male Specific ◽  
Chromosome Binding

In Drosophila, dosage compensation occurs by transcribing the single male X chromosome at twice the rate of each of the two female X chromosomes. This hypertranscription requires four autosomal male-specific lethal (msl) genes and is negatively regulated by the Sxl gene in females. Two of the msls, the mle and msl-1 genes, encode proteins that are associated with hundreds of specific sites along the length of the male X chromosome. MLE and MSL-1 X chromosome binding are negatively regulated by Sxl in females and require the functions of the other msls in males. To investigate further the regulation of dosage compensation and the role of the msls in this process, we have cloned and molecularly characterized another msl, the msl-3 gene. We have found that MSL-3 is also associated with the male X chromosome. We have further investigated whether Sxl negatively regulates MSL-3 X-chromosome binding in females and whether MSL-3 X-chromosome binding requires the other msls. Our results suggest that the MLE, MSL-1 and MSL-3 proteins may associate with one another in a male-specific heteromeric complex on the X chromosome to achieve its hypertranscription.

Meiotic CENP-C is a shepherd: bridging the space between the centromere and the kinetochore in time and space

2020 ◽  
Vol 64 (2) ◽  
pp. 251-261
Author(s):  
Jessica E. Fellmeth ◽  
Kim S. McKim
Keyword(s):  
Chromosome Segregation ◽  
New Technologies ◽  
Early Prophase ◽  
Unique Role ◽  
Kinetochore Assembly ◽  
M Phase ◽  
In Vivo Analysis ◽  
Meiosis I

Abstract While many of the proteins involved in the mitotic centromere and kinetochore are conserved in meiosis, they often gain a novel function due to the unique needs of homolog segregation during meiosis I (MI). CENP-C is a critical component of the centromere for kinetochore assembly in mitosis. Recent work, however, has highlighted the unique features of meiotic CENP-C. Centromere establishment and stability require CENP-C loading at the centromere for CENP-A function. Pre-meiotic loading of proteins necessary for homolog recombination as well as cohesion also rely on CENP-C, as do the main scaffolding components of the kinetochore. Much of this work relies on new technologies that enable in vivo analysis of meiosis like never before. Here, we strive to highlight the unique role of this highly conserved centromere protein that loads on to centromeres prior to M-phase onset, but continues to perform critical functions through chromosome segregation. CENP-C is not merely a structural link between the centromere and the kinetochore, but also a functional one joining the processes of early prophase homolog synapsis to late metaphase kinetochore assembly and signaling.

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