scholarly journals Evolution trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

2016 ◽  
Author(s):  
Wei Yin ◽  
Zong-ji Wang ◽  
Qi-ye Li ◽  
Jin-ming Lian ◽  
Yang Zhou ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Deep Understanding ◽  
Recombination Suppression ◽  
Comparative Analyses ◽  
Lineage Specific Expansion ◽  
Show Evidence ◽  
Specific Expansion ◽  
History Of ◽  
Thermal Sensing ◽  
Deinagkistrodon Acutus

AbstractSnake’s numerous fascinating features distinctive from other tetrapods necessitate a rich history of genome evolution that is still obscure. To address this, we report the first high-quality genome of a viper,Deinagkistrodon acutusand comparative analyses using other species from major snake and lizard lineages. We map the evolution trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion. And in the viper many TEs may have been rewired into the regulatory network of brain genes, as shown by their associated expression with nearby genes in the brain but not in other tissues. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes, and also functional degeneration of genes associated with vision and hearing. ManyHoxandTbxlimb-patterning genes show evidence of relaxed selective constraints, and such genes’ phylogenetic distribution supports fossil evidence for a successive loss of forelimbs then hindlimbs during the snake evolution. Finally, we infer that the Z and W sex chromosomes had undergone at least three recombination suppression events at the ancestor of advanced snakes, with the W chromosomes showing a gradient of degeneration from basal to advanced snakes. These results, together with all the genes identified as undergoing adaptive or degenerative evolution episodes at respective snake lineages forge a framework for our deep understanding into snakes’ molecular evolution history.

scholarly journals Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds

2018 ◽  
Author(s):  
Luo-hao Xu ◽  
Gabriel Auer ◽  
Valentina Peona ◽  
Alexander Suh ◽  
Yuan Deng ◽  
...  
Keyword(s):  
Sexual Selection ◽  
Sex Chromosomes ◽  
Evolutionary History ◽  
Sequence Divergence ◽  
Species Number ◽  
Recombination Suppression ◽  
Chromosome Inversion ◽  
Linked Gene ◽  
Accelerated Evolution ◽  
History Of

AbstractSongbirds have a species number almost equivalent to that of mammals, and are classic models for studying mechanisms of speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. To elucidate that, we characterize female genomes of 11 songbird species having ZW sex chromosomes, with 5 genomes of bird-of-paradise species newly produced in this work. We conclude that songbird sex chromosomes have undergone at least four steps of recombination suppression before their species radiation, producing a gradient pattern of pairwise sequence divergence termed ‘evolutionary strata’. Interestingly, the latest stratum probably emerged due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, or chromosome inversion on the W chromosome. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and GC contents, as well as W-linked gene loss rate that are associated with the age of strata. Over 30 W-linked genes have been preserved for their essential functions, indicated by their higher and broader expression of orthologs in lizard than those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes vs. autosomal genes among different species, potentially reflecting their diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes, and provide novel insights into the mechanisms of recombination suppression.

scholarly journals Differential Gene Expression between Fungal Mating Types Is Associated with Sequence Degeneration

2020 ◽  
Vol 12 (4) ◽  
pp. 243-258 ◽  
Author(s):  
Wen-Juan Ma ◽  
Fantin Carpentier ◽  
Tatiana Giraud ◽  
Michael E Hood
Keyword(s):  
Differential Expression ◽  
Differentially Expressed Genes ◽  
Mating Type ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Gc Content ◽  
Differentially Expressed ◽  
Mating Types ◽  
Sexual Antagonism ◽  
Recombination Suppression

Abstract Degenerative mutations in non-recombining regions, such as in sex chromosomes, may lead to differential expression between alleles if mutations occur stochastically in one or the other allele. Reduced allelic expression due to degeneration has indeed been suggested to occur in various sex-chromosome systems. However, whether an association occurs between specific signatures of degeneration and differential expression between alleles has not been extensively tested, and sexual antagonism can also cause differential expression on sex chromosomes. The anther-smut fungus Microbotryum lychnidis-dioicae is ideal for testing associations between specific degenerative signatures and differential expression because 1) there are multiple evolutionary strata on the mating-type chromosomes, reflecting successive recombination suppression linked to mating-type loci; 2) separate haploid cultures of opposite mating types help identify differential expression between alleles; and 3) there is no sexual antagonism as a confounding factor accounting for differential expression. We found that differentially expressed genes were enriched in the four oldest evolutionary strata compared with other genomic compartments, and that, within compartments, several signatures of sequence degeneration were greater for differentially expressed than non-differentially expressed genes. Two particular degenerative signatures were significantly associated with lower expression levels within differentially expressed allele pairs: upstream insertion of transposable elements and mutations truncating the protein length. Other degenerative mutations associated with differential expression included nonsynonymous substitutions and altered intron or GC content. The association between differential expression and allele degeneration is relevant for a broad range of taxa where mating compatibility or sex is determined by genes located in large regions where recombination is suppressed.

RECENT INVESTIGATIONS AT TULA CHICO, TULA, HIDALGO

2021 ◽  
Vol 32 (1) ◽  
pp. 41-55
Author(s):  
Robert H. Cobean ◽  
Dan M. Healan ◽  
María Elena Suárez
Keyword(s):  
Classic Period ◽  
Cultural Continuity ◽  
Direct Control ◽  
Early Postclassic ◽  
Initial Settlement ◽  
Show Evidence ◽  
History Of

AbstractRecent excavations at Tula Chico, the monumental center for Tula's earliest settlement, revealed a long and complex history of occupation, beginning with its initial settlement in the Middle Classic period by Coyotlatelco peoples, when much of the region was under Teotihuacan's direct control. During the Epiclassic period, a program of monumental construction began that developed the monumental complex seen today over a period of about 200 years. Although Tula Chico was superseded by Tula Grande, the monumental center for the Early Postclassic city, it continued to be occupied and maintained until its destruction by fire. Tula Chico and Tula Grande show evidence of clear cultural continuity in ceramics, architecture, and sculpture, including “Toltec style” sculpture characteristic of Tula Grande that is present in temporally early contexts at Tula Chico.

scholarly journals Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lingzhan Xue ◽  
Yu Gao ◽  
Meiying Wu ◽  
Tian Tian ◽  
Haiping Fan ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Chromosome Pair ◽  
Sex Chromosome ◽  
Structural Variations ◽  
Recombination Suppression ◽  
Chromosome Differentiation ◽  
Y Chromosomes ◽  
Recent Origin ◽  
Mastacembelus Armatus

Abstract Background The origin of sex chromosomes requires the establishment of recombination suppression between the proto-sex chromosomes. In many fish species, the sex chromosome pair is homomorphic with a recent origin, providing species for studying how and why recombination suppression evolved in the initial stages of sex chromosome differentiation, but this requires accurate sequence assembly of the X and Y (or Z and W) chromosomes, which may be difficult if they are recently diverged. Results Here we produce a haplotype-resolved genome assembly of zig-zag eel (Mastacembelus armatus), an aquaculture fish, at the chromosomal scale. The diploid assembly is nearly gap-free, and in most chromosomes, we resolve the centromeric and subtelomeric heterochromatic sequences. In particular, the Y chromosome, including its highly repetitive short arm, has zero gaps. Using resequencing data, we identify a ~7 Mb fully sex-linked region (SLR), spanning the sex chromosome centromere and almost entirely embedded in the pericentromeric heterochromatin. The SLRs on the X and Y chromosomes are almost identical in sequence and gene content, but both are repetitive and heterochromatic, consistent with zero or low recombination. We further identify an HMG-domain containing gene HMGN6 in the SLR as a candidate sex-determining gene that is expressed at the onset of testis development. Conclusions Our study supports the idea that preexisting regions of low recombination, such as pericentromeric regions, can give rise to SLR in the absence of structural variations between the proto-sex chromosomes.

scholarly journals A Gradual Process of Recombination Restriction in the Evolutionary History of the Sex Chromosomes in Dioecious Plants

PLoS Biology ◽  
2004 ◽  
Vol 3 (1) ◽  
pp. e4 ◽  
Author(s):  
Michael Nicolas ◽  
Gabriel Marais ◽  
Vladka Hykelova ◽  
Bohuslav Janousek ◽  
Valérie Laporte ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Evolutionary History ◽  
Dioecious Plants ◽  
Gradual Process ◽  
History Of

Education as Arikara Spiritual Renewal and Cultural Evolution

2014 ◽  
Vol 54 (3) ◽  
pp. 303-322 ◽  
Author(s):  
KuuNUx TeeRIt Kroupa
Keyword(s):  
Deep Understanding ◽  
Cultural Development ◽  
Human Beings ◽  
Old People ◽  
New Beginning ◽  
The People ◽  
History Of ◽  
The Creation ◽  
First Time ◽  
The Universe

In May 2009, the Arikara returned to the land of their ancestors along the Missouri River in South Dakota. For the first time in more than a half century, a Medicine Lodge was built for ceremony. The lodge has returned from its dormant state to regain its permanent place in Arikara culture. This event will be remembered as a significant moment in the history of the Arikara because it symbolizes a new beginning and hope for the people. Following this historic event, Arikara spiritual leader Jasper Young Bear offered to share his experience and deep insight into Arikara thought: You have to know that the universe is the Creator's dream, the Creator's mind, everything from the stars all the way to the deepest part of the ocean, to the most microscopic particle of the creation, to the creation itself, on a macro level, on a micro level. You have to understand all of those aspects to understand what the lodge represents. The lodge is a fractal, a symbolic representation of the universe itself. How do we as human beings try to make sense of that? That understanding, of how the power in the universe flows, was gifted to us through millennia of prayer and cultural development… It is important for us to internalize our stories, internalize the star knowledge, internalize those things and make that your way, make that your belief, because we're going to play it out inside the lodge. It only lives by us guys interacting with it and praying with it and bringing it to life… We're going to play out the wise sayings of the old people… So you see that it's an Arikara worldview. A learning process of how the universe functions is what you're actually experiencing [inside the Medicine Lodge]. What the old people were describing was the functioning of how we believed the universe behaves. And we had a deep, deep understanding of what that meant and how it was for us. So that's what you're actually seeing in the Medicine Lodge.

Notes on Professor Karlgren's System for Dating Chinese Bronzes

1936 ◽  
Vol 68 (03) ◽  
pp. 463-473
Author(s):  
Herrlee Glessner Creel
Keyword(s):  
Chinese Culture ◽  
Deep Understanding ◽  
Central Place ◽  
Chinese History ◽  
History Of ◽  
Oracle Bones

The pre-Confucian period has come, during the last decade, to occupy a central place in the attention of students of the history of Chinese culture. Research on the oracle bones, scientific excavations at Anyang and elsewhere, and other investigations and discoveries have not served merely to throw light on the civilization of late Shang and early Chou times. They have also shown us that those periods saw the laying of the foundations of the whole structure of Chinese culture, as it has persisted even to our own day, so that to understand them is no mere concern of antiquarians, but a vital necessity for any deep understanding of the currents of Chinese history.

scholarly journals Formal Functions of Metric Dissonance in Rock Music

2014 ◽  
Vol 20 (2) ◽  
Author(s):  
Nicole Biamonte
Keyword(s):  
Cross Section ◽  
Rock Music ◽  
Phrase Structure ◽  
Comparative Analyses ◽  
Metric Dissonance ◽  
Corpus Studies ◽  
History Of

This article explores the interactions of metric dissonance with phrase structure and form in rock music, offers categorization schemes for common formal functions of metric dissonance, and presents several corpus studies of metric dissonance in the works of single artists and bands as well as in a cross-section of rock songs. These data allow for comparative analyses of the metric profile of a given artist or band, suggest genre correlations with particular metric patterns, and demonstrate a trend of increasing metric dissonance throughout the history of rock.

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