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Relevant bibliographies by topics / Phylogenetic footprints

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Academic literature on the topic 'Phylogenetic footprints'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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Journal articles on the topic "Phylogenetic footprints"

1

Witt, Ulrich, and Georg Schwesinger. "Phylogenetic footprints in organizational behavior." Journal of Economic Behavior & Organization 90 (June 2013): S33—S44. http://dx.doi.org/10.1016/j.jebo.2012.12.011.

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Matthews, Philippa C., Alasdair J. Leslie, Aris Katzourakis, Hayley Crawford, Rebecca Payne, Andrew Prendergast, Karen Power, et al. "HLA Footprints on Human Immunodeficiency Virus Type 1 Are Associated with Interclade Polymorphisms and Intraclade Phylogenetic Clustering." Journal of Virology 83, no. 9 (February 25, 2009): 4605–15. http://dx.doi.org/10.1128/jvi.02017-08.

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ABSTRACT The selection of escape mutations has a major impact on immune control of infections with viruses such as human immunodeficiency virus (HIV). Viral evasion of CD8+ T-cell responses leaves predictable combinations of escape mutations, termed HLA “footprints.” The most clearly defined footprints are those associated with HLA alleles that are linked with successful control of HIV, such as HLA-B*57. Here we investigated the extent to which HLA footprint sites in HIV type 1 (HIV-1) are associated with viral evolution among and within clades. First, we examined the extent to which amino acid differences between HIV-1 clades share identity with sites of HLA-mediated selection pressure and observed a strong association, in particular with respect to sites of HLA-B selection (P < 10−6). Similarly, the sites of amino acid variability within a clade were found to overlap with sites of HLA-selected mutation. Second, we studied the impact of HLA selection on interclade phylogeny. Removing the sites of amino acid variability did not significantly affect clade-specific clustering, reflecting the central role of founder effects in establishing distinct clades. However, HLA footprints may underpin founder strains, and we show that amino acid substitutions between clades alter phylogeny, underlining a potentially substantial role for HLA in driving ongoing viral evolution. Finally, we investigated the impact of HLA selection on within-clade phylogeny and demonstrate that even a single HLA allele footprint can result in significant phylogenetic clustering of sequences. In conclusion, these data highlight the fact that HLA can be a strong selection force for both intra- and interclade HIV evolution at a population level.

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Lautrédou, A. C., D. D. Hinsinger, C. Gallut, C. H. C. Cheng, M. Berkani, C. Ozouf-Costaz, C. Cruaud, G. Lecointre, and A. Dettai. "Phylogenetic footprints of an Antarctic radiation: The Trematominae (Notothenioidei, Teleostei)." Molecular Phylogenetics and Evolution 65, no. 1 (October 2012): 87–101. http://dx.doi.org/10.1016/j.ympev.2012.05.032.

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Schallau, Anna, Irina Kakhovskaya, Anne Tewes, Andreas Czihal, Jens Tiedemann, Michaela Mohr, Ivo Grosse, Renate Manteuffel, and Helmut Bäumlein. "Phylogenetic footprints in fern spore- and seed-specific gene promoters." Plant Journal 53, no. 3 (October 30, 2007): 414–24. http://dx.doi.org/10.1111/j.1365-313x.2007.03354.x.

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Leung, J. Y., F. E. McKenzie, A. M. Uglialoro, P. O. Flores-Villanueva, B. C. Sorkin, E. J. Yunis, D. L. Hartl, and A. E. Goldfeld. "Identification of phylogenetic footprints in primate tumor necrosis factor-alpha promoters." Proceedings of the National Academy of Sciences 97, no. 12 (June 6, 2000): 6614–18. http://dx.doi.org/10.1073/pnas.97.12.6614.

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Sevillya, Gur, and Sagi Snir. "Synteny footprints provide clearer phylogenetic signal than sequence data for prokaryotic classification." Molecular Phylogenetics and Evolution 136 (July 2019): 128–37. http://dx.doi.org/10.1016/j.ympev.2019.03.010.

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Prohaska, Sonja J., Claudia Fried, Christoph Flamm, Günter P. Wagner, and Peter F. Stadler. "Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications." Molecular Phylogenetics and Evolution 31, no. 2 (May 2004): 581–604. http://dx.doi.org/10.1016/j.ympev.2003.08.009.

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Shelton, David A., Lauren Stegman, Ross Hardison, Webb Miller, Jeffery H. Bock, Jerry L. Slightom, Morris Goodman, and Deborah L. Gumucio. "Phylogenetic Footprinting of Hypersensitive Site 3 of the β-Globin Locus Control Region." Blood 89, no. 9 (May 1, 1997): 3457–69. http://dx.doi.org/10.1182/blood.v89.9.3457.

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Abstract Hypersensitive site 3 (HS3) of the β-like globin locus control region has been implicated as an important regulator of the β-like globin genes, but the trans factors that bind HS3 have only been partially characterized. Using a five-species alignment (human, galago, rabbit, goat, and mouse) that represents 370 million years of evolution, we have identified 24 phylogenetic footprints in the HS3 core and surrounding regions. Probes corresponding to the human sequence at each footprint have been used in binding studies to identify the nuclear factors that bind within and near these conserved sequence elements. Among the high-affinity interactions observed were several binding sites for proteins with repressor activity, including YY1, CCAAT displacement protein, and G1/G2 complexes (uncharacterized putative repressors) and several binding sites for the stage selector protein. To complement this analysis, orthologous galago sequences were also used to derive probes and the pattern of proteins binding to human and galago probes was compared. Binding interactions differing between these two species could be responsible for the different expression patterns shown by the two γ genes (galago γ is embryonic; human γ is fetal). Alternatively, binding interactions that are conserved in the two species may be important in the regulation of common expression patterns (eg, repression of γ in adult life).

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Kim, Jung-whan, Karen I. Zeller, Yunyue Wang, Anil G. Jegga, Bruce J. Aronow, Kathryn A. O'Donnell, and Chi V. Dang. "Evaluation of Myc E-Box Phylogenetic Footprints in Glycolytic Genes by Chromatin Immunoprecipitation Assays." Molecular and Cellular Biology 24, no. 13 (July 1, 2004): 5923–36. http://dx.doi.org/10.1128/mcb.24.13.5923-5936.2004.

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ABSTRACT Prediction of gene regulatory sequences using phylogenetic footprinting has advanced considerably but lacks experimental validation. Here, we report whether transcription factor binding sites predicted by dot plotting or web-based Trafac analysis could be validated by chromatin immunoprecipitation assays. MYC overexpression enhances glycolysis without hypoxia and hence may contribute to altered tumor metabolism. Because the full spectrum of glycolytic genes directly regulated by Myc is not known, we chose Myc as a model transcription factor to determine whether it binds target glycolytic genes that have conserved canonical Myc binding sites or E boxes (5′-CACGTG-3′). Conserved canonical E boxes in ENO1, HK2, and LDHA occur in 31- to 111-bp islands with high interspecies sequence identity (>65%). Trafac analysis revealed another region in ENO1 that corresponds to a murine region with a noncanonical E box. Myc bound all these conserved regions well in the human P493-6 B lymphocytes. We also determined whether Myc could bind nonconserved canonical E boxes found in the remaining human glycolytic genes. Myc bound PFKM, but it did not significantly bind GPI, PGK1, and PKM2. Binding to BPGM, PGAM2, and PKLR was not detected. Both GAPD and TPI1 do not have conserved E boxes but are induced and bound by Myc through regions with noncanonical E boxes. Our results indicate that Myc binds well to conserved canonical E boxes, but not nonconserved E boxes. However, the binding of Myc to unpredicted genomic regions with noncanonical E boxes reveals a limitation of phylogenetic footprinting. In aggregate, these observations indicate that Myc is an important regulator of glycolytic genes, suggesting that MYC plays a key role in a switch to glycolytic metabolism during cell proliferation or tumorigenesis.

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Oleksyk, Taras K., Michael W. Smith, and Stephen J. O'Brien. "Genome-wide scans for footprints of natural selection." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1537 (January 12, 2010): 185–205. http://dx.doi.org/10.1098/rstb.2009.0219.

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Detecting recent selected ‘genomic footprints’ applies directly to the discovery of disease genes and in the imputation of the formative events that molded modern population genetic structure. The imprints of historic selection/adaptation episodes left in human and animal genomes allow one to interpret modern and ancestral gene origins and modifications. Current approaches to reveal selected regions applied in genome-wide selection scans (GWSSs) fall into eight principal categories: (I) phylogenetic footprinting, (II) detecting increased rates of functional mutations, (III) evaluating divergence versus polymorphism, (IV) detecting extended segments of linkage disequilibrium, (V) evaluating local reduction in genetic variation, (VI) detecting changes in the shape of the frequency distribution (spectrum) of genetic variation, (VII) assessing differentiating between populations ( F ST ), and (VIII) detecting excess or decrease in admixture contribution from one population. Here, we review and compare these approaches using available human genome-wide datasets to provide independent verification (or not) of regions found by different methods and using different populations. The lessons learned from GWSSs will be applied to identify genome signatures of historic selective pressures on genes and gene regions in other species with emerging genome sequences. This would offer considerable potential for genome annotation in functional, developmental and evolutionary contexts.

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Dissertations / Theses on the topic "Phylogenetic footprints"

1

Dwivedi, Bhakti. "Impact of molecular evolutionary footprints on phylogenetic accuracy a simulation study /." Dayton, Ohio : University of Dayton, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=dayton1250807136.

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Fried, Claudia, Wim Hordijk, Sonja J. Prohaska, Claus R. Stadler, and Peter F. Stadler. "The Footprint Sorting Problem." 2004. https://ul.qucosa.de/id/qucosa%3A32629.

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Phylogenetic footprints are short pieces of noncoding DNA sequence in the vicinity of a gene that are conserved between evolutionary distant species. A seemingly simple problem is to sort footprints in their order along the genomes. It is complicated by the fact that not all footprints are collinear: they may cross each other. The problem thus becomes the identification of the crossing footprints, the sorting of the remaining collinear cliques, and finally the insertion of the noncollinear ones at “reasonable” positions. We show that solving the footprint sorting problem requires the solution of the “Minimum Weight Vertex Feedback Set Problem”, which is known to be NP-complete and APX-hard. Nevertheless good approximations can be obtained for data sets of interest. The remaining steps of the sorting process are straightforward: computation of the transitive closure of an acyclic graph, linear extension of the resulting partial order, and finally sorting w.r.t. the linear extension. Alternatively, the footprint sorting problem can be rephrased as a combinatorial optimization problem for which approximate solutions can be obtained by means of general purpose heuristics. Footprint sortings obtained with different methods can be compared using a version of multiple sequence alignment that allows the identification of unambiguously ordered sublists. As an application we show that the rat has a slighly increased insertion/deletion rate in comparison to the mouse genome.

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Fried, Claudia, Sonja J. Prohaska, and Peter F. Stadler. "Independent Hox‐cluster duplications in lampreys." 2003. https://ul.qucosa.de/id/qucosa%3A32632.

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The analysis of the publicly available Hox gene sequences from the sea lamprey Petromyzon marinus provides evidence that the Hox clusters in lampreys and other vertebrate species arose from independent duplications. In particular, our analysis supports the hypothesis that the last common ancestor of agnathans and gnathostomes had only a single Hox cluster which was subsequently duplicated independently in the two lineages.

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Prohaska, Sonja J., Claudia Fried, Christoph Flamm, Günther P. Wagner, and Peter F. Stadler. "Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications." 2004. https://ul.qucosa.de/id/qucosa%3A31997.

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Evolutionarily conserved non-coding genomic sequences represent a potentially rich source for the discovery of gene regulatory regions. Since these elements are subject to stabilizing selection they evolve much slower than adjacent non-functional DNA. These so-called phylogenetic footprints can be detected by comparison of the sequences surrounding orthologous genes in different species. In this paper we present a new method and an effcient software tool for the identifcation of corresponding footprints in long sequences from multiple species. This allows the evolutionary study of the origin and loss of phylogenetic footprints if suffcient number and appropriately placed species are included. We apply this method to the published sequences of HoxA clusters of shark, human, and the duplicated zebrafish and Takifugu clusters as well as the published HoxB cluster sequences. We find that there is a massive loss of sequence conservation in the intergenic region of the HoxA clusters, consistent with the finding in [Chiu et al., PNAS 99, 5492-5497 (2002)]. We further propose a simple model to estimate the loss of sequence conservation that can be attributed to gene loss and other structural reasons. We find that the loss of conservation after cluster duplication is more extensive than expected by this model. This suggests that binding site turnover and/or adaptive modification may also contribute to the loss of sequence conservation. We conclude that this method is suitable for the large scale study of the evolution of (putative) cis-regulatory elements.

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Prohaska, Sonja J., Claudia Fried, Chris T. Amemiya, Frank H. Ruddle, Günter P. Wagner, and Peter F. Stadler. "The Shark HoxN Cluster is Homologous to the Human HoxD Cluster." 2004. https://ul.qucosa.de/id/qucosa%3A31998.

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The statistical analysis of phylogenetic footprints in the two known horn shark Hox clusters and the four mammalian clusters shows that the shark HoxN cluster is HoxD-like. This finding implies that the most recent common ancestor of jawed vertebrates had at least four Hox clusters, including those which are orthologous to the four mammalian Hox clusters.

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