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 Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation

2012 ◽  
Vol 109 (4) ◽  
pp. 693-708 ◽  
Author(s):  
Jonathan Corbi ◽  
Julien Y. Dutheil ◽  
Catherine Damerval ◽  
Maud I. Tenaillon ◽  
Domenica Manicacci
Keyword(s):  
Evolutionary History ◽  
Accelerated Evolution ◽  
History Of

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

scholarly journals The early evolutionary history of neo-sex chromosomes in Neotropical grasshoppers, Boliviacris noroestensis (Orthoptera: Acrididae: Melanoplinae)

2014 ◽  
Vol 111 (3) ◽  
pp. 321-327 ◽  
Author(s):  
Elio R.D. CASTILLO ◽  
Alberto TAFFAREL ◽  
Dardo A. MARTI
Keyword(s):  
Sex Chromosomes ◽  
Evolutionary History ◽  
History Of

The conservation of number and location of 18S sites indicates the relative stability of rDNA in species of Pentatomomorpha (Heteroptera)

Genome ◽  
2013 ◽  
Vol 56 (7) ◽  
pp. 425-429 ◽  
Author(s):  
Vanessa Bellini Bardella ◽  
Thiago Fernandes ◽  
André Luís Laforga Vanzela
Keyword(s):  
Sex Chromosomes ◽  
18S Rdna ◽  
Fluorescent In Situ Hybridization ◽  
Evolutionary History ◽  
Conclusive Evidence ◽  
Fish Analysis ◽  
Comparative Cytogenetics ◽  
Rdna Sites ◽  
History Of

Fluorescent in situ hybridization (FISH) with rDNA probes has been used for comparative cytogenetics studies in different groups of organisms. Although heteropterans are a large suborder within Hemiptera, studies using rDNA are limited to the infraorder Cimicomorpha, in which rDNA sites are present in the autosomes or sex chromosomes. We isolated and sequenced a conserved 18S rDNA region of Antiteuchus tripterus (Pentatomidae) and used it as a probe against chromosomes of 25 species belonging to five different families of Pentatomomorpha. The clone pAt05, with a length of 736 bp, exhibited a conserved stretch of 590 bp. FISH analysis with the probe pAt05 always demonstrated hybridization signals in sub-terminal positions, except for Euschistus heros. Apparently, there is a tendency for 18S rDNA sites to locate in autosomes, except for Leptoglossus gonagra and Euryophthalmus rufipennis, which showed signals in the m- and sex chromosomes, respectively. Although FISH has produced evidence that rearrangements are involved in rDNA repositioning, whether in different autosomes or between sex and m-chromosomes, we have no conclusive evidence of what were the pathways of these rearrangements based on the evolutionary history of the species studied here. Nevertheless, the diversity in the number of species analyzed here showed a tendency of 18S rDNA to remain among the autosomes.

scholarly journals Characterization of the bovine pseudoautosomal boundary: Documenting the evolutionary history of mammalian sex chromosomes

2008 ◽  
Vol 18 (12) ◽  
pp. 1884-1895 ◽  
Author(s):  
A.-S. Van Laere ◽  
W. Coppieters ◽  
M. Georges
Keyword(s):  
Sex Chromosomes ◽  
Evolutionary History ◽  
History Of ◽  
Pseudoautosomal Boundary

scholarly journals Evolutionary History of Alpha Satellite DNA Repeats Dispersed within Human Genome Euchromatin

2020 ◽  
Vol 12 (11) ◽  
pp. 2125-2138
Author(s):  
Isidoro Feliciello ◽  
Željka Pezer ◽  
Dušan Kordiš ◽  
Branka Bruvo Mađarić ◽  
Đurđica Ugarković
Keyword(s):  
Satellite Dna ◽  
Evolutionary History ◽  
Genomic Sequence ◽  
Sequence Divergence ◽  
Dna Repeats ◽  
Alpha Satellite ◽  
Alpha Satellite Dna ◽  
Satellite Repeats ◽  
Number Variation ◽  
History Of

Abstract Major human alpha satellite DNA repeats are preferentially assembled within (peri)centromeric regions but are also dispersed within euchromatin in the form of clustered or short single repeat arrays. To study the evolutionary history of single euchromatic human alpha satellite repeats (ARs), we analyzed their orthologous loci across the primate genomes. The continuous insertion of euchromatic ARs throughout the evolutionary history of primates starting with the ancestors of Simiformes (45–60 Ma) and continuing up to the ancestors of Homo is revealed. Once inserted, the euchromatic ARs were stably transmitted to the descendant species, some exhibiting copy number variation, whereas their sequence divergence followed the species phylogeny. Many euchromatic ARs have sequence characteristics of (peri)centromeric alpha repeats suggesting heterochromatin as a source of dispersed euchromatic ARs. The majority of euchromatic ARs are inserted in the vicinity of other repetitive elements such as L1, Alu, and ERV or are embedded within them. Irrespective of the insertion context, each AR insertion seems to be unique and once inserted, ARs do not seem to be subsequently spread to new genomic locations. In spite of association with (retro)transposable elements, there is no indication that such elements play a role in ARs proliferation. The presence of short duplications at most of ARs insertion sites suggests site-directed recombination between homologous motifs in ARs and in the target genomic sequence, probably mediated by extrachromosomal circular DNA, as a mechanism of spreading within euchromatin.

scholarly journals Complex evolutionary history of the Y chromosome in flies of the Drosophila obscura species group

2019 ◽  
Author(s):  
Ryan Bracewell ◽  
Doris Bachtrog
Keyword(s):  
X Chromosome ◽  
Sex Chromosomes ◽  
Evolutionary History ◽  
Sex Chromosome ◽  
Species Group ◽  
Genomic Environment ◽  
History Of ◽  
Chromosome Formation ◽  
Dramatic Variation ◽  
Complex Evolutionary History

The Drosophila obscura species group shows dramatic variation in karyotype, including transitions among sex chromosomes. Members of the affinis and pseudoobscura subgroups contain a neo-X chromosome (a fusion of the X with an autosome), and it was shown that ancestral Y genes of Drosophila have become autosomal in species that contain the neo-X. Detailed analysis in species of the pseudoobscura subgroup revealed a translocation of ancestral Y genes to the small dot chromosome of that group. Here, we show that the Y-dot translocation is restricted to the pseudoobscura subgroup, and translocation of Y genes in the affinis subgroup followed a different route. We find that most ancestral Y genes moved independently to autosomal or X-linked locations in different taxa of the affinis subgroup, and we propose a dynamic model of sex chromosome formation and turnover in the obscura species group. Our results show that Y genes can find unique paths to escape an unfavorable genomic environment.

scholarly journals Inversions shape the divergence of Drosophila pseudoobscura and D. persimilis on multiple timescales

2019 ◽  
Author(s):  
Katharine L Korunes ◽  
Carlos A Machado ◽  
Mohamed AF Noor
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Whole Genome Sequence ◽  
Drosophila Pseudoobscura ◽  
Ancestral Polymorphism ◽  
Chromosomal Inversions ◽  
History Of ◽  
Ancient Gene

AbstractBy shaping meiotic recombination, chromosomal inversions can influence genetic exchange between hybridizing species. Despite the recognized importance of inversions in evolutionary processes such as divergence and speciation, teasing apart the effects of inversions over time remains challenging. For example, are their effects on sequence divergence primarily generated through creating blocks of linkage-disequilibrium pre-speciation or through preventing gene flux after speciation? We provide a comprehensive look into the influence of chromosomal inversions on gene flow throughout the evolutionary history of a classic system: Drosophila pseudoobscura and D. persimilis. We use extensive whole-genome sequence data to report patterns of introgression and divergence with respect to chromosomal arrangements. Overall, we find evidence that inversions have contributed to divergence patterns between Drosophila pseudoobscura and D. persimilis over three distinct timescales: 1) pre-speciation segregation of ancestral polymorphism, 2) post-speciation ancient gene flow, and 3) recent gene flow. We discuss these results in terms of our understanding of evolution in this classic system and provide cautions for interpreting divergence measures in similar datasets in other systems.

Evolution of duplicated growth hormone genes in autotetraploid salmonid fishes

Genome ◽  
2004 ◽  
Vol 47 (4) ◽  
pp. 714-723 ◽  
Author(s):  
S J McKay ◽  
J Trautner ◽  
M J Smith ◽  
B F Koop ◽  
R H Devlin
Keyword(s):  
Growth Hormone ◽  
Evolutionary History ◽  
Sequence Divergence ◽  
Genome Doubling ◽  
Disomic Inheritance ◽  
A Genome ◽  
Gh Gene ◽  
Average Sequence Divergence ◽  
History Of ◽  
Homeologous Chromosomes

A defining character of the piscine family Salmonidae is autotetraploidy resulting from a genome-doubling event some 25–100 million years ago. Initially, duplicated genes may have undergone concerted evolution and tetrasomic inheritance. Homeologous chromosomes eventually diverged and the resulting reduction in recombination and gene conversion between paralogous genes allowed the re-establishment of disomic inheritance. Among extant salmonine fishes (e.g. salmon, trout, char) the growth hormone (GH) gene is generally represented by two functional paralogs, GH1 and GH2. Sequence analyses of salmonid GH genes from species of subfamilies Coregoninae (whitefish, ciscos) and Salmoninae were used to examine the evolutionary history of the duplicated GH genes. Two divergent GH gene paralogs were also identified in Coregoninae, but they were not assignable to the GH1 and GH2 categories. The average sequence divergence between the coregonine GH genes was more than twofold lower than the corresponding divergence between the salmonine GH1 and GH2. Phylogenetic analysis of the coregonine GH paralogs did not resolve their relationship to the salmonine paralogs. These findings suggest that disomic inheritance of two GH genes was established by different mechanisms in these two subfamilies.Key words: salmon, phylogeny, growth hormone, disomy, tetraploidy.

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.

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