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  • 1
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    Repetitive DNA Sequences (2021)
    MDPI - Multidisciplinary Digital Publishing Institute
    Details
    Publication Date: 2024-04-05
    Description: Repetitive DNA is ubiquitous in eukaryotic genomes, and, in many species, comprises the bulk of the genome. Repeats include transposable elements that can self-mobilize and disperse around the genome, and tandemly-repeated satellite DNAs that increase in copy number due to replication slippage and unequal crossing over. Despite their abundance, repetitive DNA is often ignored in genomic studies due to technical challenges in their identification, assembly, and quantification. New technologies and methods are now providing the unprecedented power to analyze repetitive DNAs across diverse taxa. Repetitive DNA is of particular interest because it can represent distinct modes of genome evolution. Some repetitive DNA forms essential genome structures, such as telomeres and centromeres, which are required for proper chromosome maintenance and segregation, whereas others form piRNA clusters that regulate transposable elements; thus, these elements are expected to evolve under purifying selection. In contrast, other repeats evolve selfishly and produce genetic conflicts with their host species that drive adaptive evolution of host defense systems. However, the majority of repeats likely accumulate in eukaryotes in the absence of selection due to mechanisms of transposition and unequal crossing over. Even these neutral repeats may indirectly influence genome evolution as they reach high abundance. In this Special Issue, the contributing authors explore these questions from a range of perspectives.
    Keywords: QH426-470 ; QH301-705.5 ; Q1-390 ; transgene ; zebra finch ; transcription ; endogenous retrovirus ; transposable element ; centromere drive ; arthropods ; PSR (Paternal sex ratio) ; Alu ; gene evolution ; nuclear rDNA ; epigenetics ; heterochromatin ; alpha satellite ; Su(Hw) ; repeated elements ; karyotype ; piRNA cluster ; gene duplication ; super-Mendelian ; estrildidae ; genomic conflict ; GC-content ; segregation ; CENP-A ; drift ; germline ; hobo ; I element ; repetitive DNA ; transposons ; human satellites ; retrotransposons ; genome assembly ; LTR retrotransposons ; satellite DNA ; structural variation ; selection ; host genome ; Uraeginthus cyanocephalus ; LINE-1 ; B chromosomes ; ERV ; arms race ; sequence variation ; secondary structure ; HeT-A and TART telomeric retrotransposons ; database ; genetic conflict ; coevolution ; ncRNAs (non coding RNAs) ; repeat ; centromeric transcription ; nucleolus ; satellite ; insulator ; Rhino ; population genetics ; centromere ; genome annotation ; horizontal transfer ; rRNA ; genome elimination ; genome evolution ; evolution ; chromosome evolution ; genome size ; genome ; drosophila ; transposable elements ; selfish elements ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical)
    Language: English
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  • 2
    Electronic Resource
    Electronic Resource
    The structure of human mitochondrial DNA variation (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 543-555 
    Details
    ISSN: 1432-1432
    Keywords: Mitochondrial DNA ; Human evolution ; Population genetics ; Molecular anthropology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Restriction analysis of mitochondrial DNA (mtDNA) of 3065 humans from 62 geographic samples identified 149 haplotypes and 81 polymorphic sites. These data were used to test several aspects of the evolutionary past of the human species. A dendrogram depicting the genetic relatedness of all haplotypes shows that the native African populations have the greatest diversity and, consistent with evidence from a variety of sources, suggests an African origin for our species. The data also indicate that two individuals drawn, at random from the entire sample will differ at approximately 0.4% of their mtDNA nucleotide sites, which is somewhat higher than previous estimates. Human mtDNA also exhibits more interpopulation heterogeneity (GST=0.351±0.025) than does nuclear DNA (GST=0.12). Moreover, the virtual absence of intermediate levels of linkage disequilibrium between pairs of sites is consistent with the absence of genetic recombination and places constraints on the rate of mutation. Tests of the selective neutrality of mtDNA variation, including the Ewens-Watterson and Tajima tests, indicate a departure in the direction consistent with purifying selection, but this departure is more likely due to the rapid growth of the human population and the geographic heterogeneity of the variation. The lack of a good fit to neutrality poses problems for the estimation of times of coalescence from human mtDNA data.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02102807
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  • 3
    Electronic Resource
    Electronic Resource
    Comparisons of the Nucleotide Substitution Process Among Repetitive Segments of the α- and β-Spectrin Genes (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. 492 -500 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Spectrin — Substitution pattern — Substitution rate — Elliptocytosis — Spherocytosis — Maximum likelihood — Gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The actin–cross-linking protein spectrin is a prominent component of the membrane cytoskeleton. Spectrin is a tetramer of two antiparallel αβ-dimers which share a unique and ancient gene structure. The α-spectrin and β-spectrin genes are composed primarily of tandemly repeated 106-amino-acid segments, each of which forms a triple α-helical coiled coil. Both the genes and the repeats themselves are homologous. The two genes are thought to be the result of a gene duplication event, and each gene is the product of duplications of the 106-amino-acid repeats. In this work we compare the process of molecular evolution across the repeated segments of the α- and β-spectrin genes. We find that the α-spectrin segments have, for the most part, evolved in a homogeneous fashion, while considerable heterogeneity is found among β-spectrin segments. Several segments with unique known functions are found to have evolved differently than the others. On the basis of heterogeneity of the evolutionary process, we suggest that at least one repeat has a unique function that has yet to be documented. We also present new statistical methods for comparing the evolutionary process between different regions of DNA sequences.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006173
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  • 4
    Electronic Resource
    Electronic Resource
    Natural selection on protein-coding genes in the human genome (2005)
    [s.l.] : Nature Publishing Group
    Nature 437 (2005), S. 1153-1157 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Comparisons of DNA polymorphism within species to divergence between species enables the discovery of molecular adaptation in evolutionarily constrained genes as well as the differentiation of weak from strong purifying selection. The extent to which weak negative and positive darwinian ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature04240
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  • 5
    Electronic Resource
    Electronic Resource
    Evolutionary changes in cis and trans gene regulation (2004)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 430 (2004), S. 85-88 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Differences in gene expression are central to evolution. Such differences can arise from cis-regulatory changes that affect transcription initiation, transcription rate and/or transcript stability in an allele-specific manner, or from trans-regulatory changes that modify the activity or ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature02698
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  • 6
    Electronic Resource
    Electronic Resource
    Population genetics Malaria variorum (2002)
    [s.l.] : Nature Publishing Group
    Nature 418 (2002), S. 283-285 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Understanding genetic variation in the malarial parasite, Plasmodium falciparum, is of major importance to public health, especially as we contemplate widespread programmes of vaccination. If a vaccine controls only part of the P. falciparum population, then it might alter the genetic composition ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/418283a
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  • 7
    Electronic Resource
    Electronic Resource
    Evolutionary biology Protamine wars (2000)
    [s.l.] : Macmillan Magazines Ltd.
    Nature 403 (2000), S. 261-263 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Proteins that evolve with unusual speed pique our interest because the mere rapidity of their change may be a clue to their function and adaptive significance. Proteins involved in sexual reproduction are particularly exciting because of their potential function in determining the success of ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/35002236
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  • 8
    Electronic Resource
    Electronic Resource
    Genetic recombination Intron size and natural selection (1999)
    [s.l.] : Macmillan Magazines Ltd.
    Nature 401 (1999), S. 344-344 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Intron sizes vary widely among different genes and among homologous genes of different species. The distribution of intron sizes may be maintained in a steady state, reflecting the processes of insertion and deletion of gene sequences, or it may be that the distribution is constrained by ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/43827
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  • 9
    Electronic Resource
    Electronic Resource
    Population Genetic Aspects of Gametophytic Self incompatibility (1996)
    Oxford, UK : Blackwell Publishing Ltd
    Plant species biology 11 (1996), S. 0 
    Details
    ISSN: 1442-1984
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract In gametophytic self-incompatibility, the S-locus encodes an S-protein whose expression results in successful pollination only when the pollen allele differs from both maternal alleles. Analysis of nucleotide and amino acid sequences of a number of S-alleles has revealed extraordinary allelic sequence divergence and an excess of interspecific shared polymorphism. Population genetic theory and analysis of the distribution of the number of shared polymorphic sites verifies that the sequence diversity is consistent with the alleles being extraordinarily old. Theory also predicts that S-alleles will exhibit less population structuring in a subdivided population than will a neutral locus, and data are being collected to test this. Self-incompatibility must involve two features - a pollen component that specifies the identity of the pollen and a pistil component that recognizes and elicits a response to self-pollen. The S-locus clearly determines the pistil component, but lack of expression of S in pollen leaves open the possibility that there may be another pollen factor. Experiments with transgenic plants have demonstrated that the S-protein expression in the pistil is necessary and sufficient to determine the pistil phenotype. However, several lines of evidence suggest that the degree of elimination of self-pollen in plants with gametophytic self-incompatibility depends on additional genetic factors besides the S-locus. Modifiers may affect self-incompatibility by affecting either the pollen component, the pistil component or both. Population genetic models that test the consequences of modification of these two components are reviewed and extended. Conditions for invasion of reduced degree of self-incompatibility depend in part on the level of inbreeding depression.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1442-1984.1996.tb00104.x
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  • 10
    Electronic Resource
    Electronic Resource
    Conjuring SNPs to detect associations (2007)
    [s.l.] : Nature Publishing Group
    Nature genetics 39 (2007), S. 815-816 
    Details
    ISSN: 1546-1718
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Genetic mapping has always relied on statistical inference, but this enterprise has never been so utterly dependent on rigorous analytical methods as it is with genome-wide association studies (GWASs). For each of the nearly 500,000 SNPs in the human genome scored by widely used genotyping ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/ng0707-815
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