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Morphological Characters from the Genome: SINE Insertion Polymorphism and Phylogenies
Published on Jan 1, 2006
· DOI :10.1007/7050_018
Agnès Dettaï3
Estimated H-index: 3
Jean-Nicolas Volff37
Estimated H-index: 37
(University of Würzburg)
For the last fifteen years, researchers have been using SINE (short interspersed elements; non-autonomous retroposons) insertion polymorphism as characters for phylogeny. Although the collection of these characters is much less straightforward and much more work intensive than for classical sequence data, they are subject to very little homoplasy, and therefore allow more reliable determination of the phylogeny of species. As reversions are very rare, and the ancestral state (absence of the insertion) is known, these characters are orientated a priori. They are also good markers for population genetics. Because of their almost complete lack of homoplasy, character conflict in these characters is a better indicator of incomplete lineage sorting and hybridization than other types of data, even for ancient divergences. Only a few examples of convergencies and reversions have been identified, and after looking through hundreds of characters; moreover, most instances of homoplasy are identifiable as such, so SINE insertion polymorphism can still be regarded as very high quality characters. Constant progress has been made through the years for the isolation of new SINEs as well as for the isolation of new insertion loci, both by bioinformatic methods and by benchwork. Numerous dedicated computer programs are available, and the newly sequenced complete genomes allow their full scale utilization. SINE insertion polymorphism data has proved its interest on complex phylogenetic problems where morphological and sequence data were not resolutive. The improvements in its portability encourage an enlargement of its application to new taxa, where it will provide novel and high quality phylogenetic information.
  • References (161)
  • Cited By (4)
Published on Jan 1, 2001in Nature 41.58
Eric S. Lander240
Estimated H-index: 240
Lauren Linton7
Estimated H-index: 7
Bruce Birren50
Estimated H-index: 50
1,571 Citations
Published on Dec 15, 1999
David B. Goldstein1
Estimated H-index: 1
Christian Schlötterer39
Estimated H-index: 39
1: Hancock: Microsatellites and other simple sequences 2: Kashi and Soller: Functional roles of microsatellites and minisatellites 3: Armour et al: Microsatellites and mutation processes in tandemly repetitive DNA 4: Eisen: Mechanistic basis for microsatellite instability 5: Estoup and Cornuet: Microsatellite evolution: inferences from population data 6: Amos: A comparative approach to the study of microsatellite evolution 7: Rubinsztein: Trinucleotide expansion mutations cause diseases which do...
827 Citations
Published on Jun 1, 1998in Journal of Mammalian Evolution 2.75
W. Patrick Luckett4
Estimated H-index: 4
Nancy Hong3
Estimated H-index: 3
A character analysis of selected conservative morphological traits from extant and fossil artiodactyls and cetaceans was combined with a similar analysis of conservative nucleotide positions from the complete mitochondrial cytochrome b sequences of available extant artiodactyls, cetaceans, sirenians, perissodactyls, and other mammals. This combined analysis focuses on the evidence that supports conflicting hypotheses of artiodactyl monophyly, including the affinities of hippopotamids and the mon...
55 Citations Source Cite
Published on Sep 10, 1998
Christopher J. Humphries4
Estimated H-index: 4
Ian J. Kitching33
Estimated H-index: 33
Peter L. Forey4
Estimated H-index: 4
Preface Ch. 1 - Introduction to cladistic concepts Ch. 2 - Characters and character coding Ch. 3 - Cladogram construction, character polarity, and rooting Ch. 4 - Optimization and the effects of missing values Ch. 5 - Measures of character fit and character weighting Ch. 6 - Support and confidence statistics for cladograms and groups Ch. 7 - Consensus trees Ch. 8 - Simultaneous and partitioned analysis Ch. 9 - Three-item statements analysis References Glossary Appendix: Computer programs
353 Citations
Published on Aug 1, 1999in Plant Molecular Biology 3.54
T. Schmidt55
Estimated H-index: 55
(University of Kiel)
Retroelements and remnants thereof constitute a large fraction of the repetitive DNA of plant genomes. They include LTR (long terminal repeat) retrotransposons such as Ty1-copia and Ty3-gypsy retrotransposons, which are widespread in plant genomes and show structural similarity to retroviruses. Recently, non-LTR retrotransposons, lacking the long terminal repeats and subdivided into LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements), have been discovered a...
71 Citations Source Cite
Published on Jun 1, 2000in Journal of Molecular Evolution 1.96
Jerzy K. Kulski30
Estimated H-index: 30
(University of Western Australia),
Silvana Gaudieri33
Estimated H-index: 33
(University of Western Australia),
Roger L. Dawkins38
Estimated H-index: 38
(University of Western Australia)
The class I region of the major histocompatibility complex contains two subgenomic blocks (250–350 kb each), known as the alpha and beta blocks. These blocks contain members of multicopy gene families including HLA class I, HERV-16 (previously called P5 sequences), and PERB11 (MIC). We have previously shown that each block consists of imperfect duplicated segments (duplicons) containing linked members of different gene families, retroelements and transposons that have coevolved as part of two se...
25 Citations Source Cite
Published on Jan 1, 1992in Human Biology 0.60
Nicole T. Perna39
Estimated H-index: 39
Mark A. Batzer82
Estimated H-index: 82
+ 1 AuthorsMark Stoneking80
Estimated H-index: 80
A PCR-based method was used to screen 462 individuals from Japan, Papua New Guinea, Indonesia, and Australia for an Alu family insertion polymorphism. The frequency of this Alu insertion shows significant heterogeneity among island subgroups of the Indonesian sample and between the Japanese-Indonesian populations and the Australian-New Guinean populations. The simple, rapid PCR-based screening technique and the significant frequency differences among populations demonstrate that Alu insertion po...
94 Citations
Published on Dec 1, 1999in Genetica 1.37
Astrid M. Roy3
Estimated H-index: 3
(Tulane University),
Marion L. Carroll8
Estimated H-index: 8
(Louisiana State University)
+ 4 AuthorsPrescott L. Deininger48
Estimated H-index: 48
(Tulane University)
Alu elements undergo amplification through retroposition and integration into new locations throughout primate genomes. Over 500,000 Alu elements reside in the human genome, making the identification of newly inserted Alu repeats the genomic equivalent of finding needles in the haystack. Here, we present two complementary methods for rapid detection of newly integrated Alu elements. In the first approach we employ computational biology to mine the human genomic DNA sequence databases in order to...
87 Citations Source Cite
Published on Jan 1, 2005in Methods in Enzymology 1.98
James A. Cotton33
Estimated H-index: 33
Abstract Paralogy (common ancestry through gene duplication rather than speciation) is widely recognized as an important problem for molecular systematists. This chapter introduces the concepts of paralogy and orthology and explains why paralogy can complicate both systematic work and other studies of molecular evolution. The definition of paralogy is explicitly phylogenetic, and phylogenetic methods are crucial in elucidating the pattern of paralogy. In particular, knowledge of the species phyl...
11 Citations Source Cite
Published on Jan 1, 1980
Daniel L. Hartl89
Estimated H-index: 89
Andrew G. Clark96
Estimated H-index: 96
Genetic and Phenotypic Variation Organisation of Genetic Variation Random Genetic Drift Mutation and the Neutral Theory Darwinian Selection Inbreeding, Population Subdivision, and Migration Molecular Population Genetics Evolutionary Quantitative Genetics Population Genomics Human Population Genetics
4,191 Citations
Cited By4
Published on Jan 1, 2006
D.-H. Lankenau1
Estimated H-index: 1
(Ladenburg Thalmann)
Replicative double-strand break (DSB) repair has been predominantly studied in single-celled organisms such as bacteria and fungi who lack the germline of metazoans. In contrast, most studies concerning DNA repair in mammals focused on somatic cells while only few authors engaged in embryonic stem cells. Drosophila represents a field of in vivo biochemistry systems linking DNA repair research with the power of classical genetics and modern developmental, molecular and cellular biology. In additi...
9 Citations Source Cite
Published on Sep 3, 2015in Molecular Biology and Evolution 10.22
Liliya Doronina4
Estimated H-index: 4
(University of Münster),
Gennady Churakov18
Estimated H-index: 18
(University of Münster)
+ 4 AuthorsJürgen Schmitz28
Estimated H-index: 28
(University of Münster)
Freed from the competition of large raptors, Paleocene carnivores could expand their newly acquired habitats in search of prey. Such changing conditions might have led to their successful distribution and rapid radiation. Today, molecular evolutionary biologists are faced, however, with the consequences of such accelerated adaptive radiations, because they led to sequential speciation more rapidly than phylogenetic markers could be fixed. The repercussions being that current genealogies based on...
14 Citations Source Cite
Published on Oct 1, 2011in Molecular Genetics and Genomics 2.73
Giampaolo Zampicinini2
Estimated H-index: 2
(University of Turin),
Piero Cervella10
Estimated H-index: 10
(University of Turin)
+ 1 AuthorsGabriella Sella20
Estimated H-index: 20
(University of Turin)
The dipteran Chironomus riparius is found across the entire Palearctic region; its larvae are among the most abundant macroinvertebrates inhabiting inland waterbodies. Chironomid larvae have been extensively used in ecotoxicological and cytogenetic research, but relatively little is known on the population structure of this species. Transposable elements (TEs) are DNA sequences that are capable of autonomous replication; the number and genomic location of TE insertions varies across individuals;...
3 Citations Source Cite
Published on Jan 1, 2011
Dirk-Henner Lankenau2
Estimated H-index: 2
(Ladenburg Thalmann)
All modern organisms depend on genomes that encode a diversity of RNA molecules functioning in a plethora of physiological, regulatory, and fundamental functions. Processes like gene transcription into mRNA, ribozyme catalyzed translation in the heart of ribosomes, RNA interference (RNAi), reverse transcription and defense of transposons, retroelements, homing mobility of introns, and many other characteristics of life represent the smoking gun of primordial RNA based, complementary base pairing...
2 Citations Source Cite
View next paperIncomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data.