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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 Dettai20
Estimated H-index: 20
,
Jean-Nicolas Volff37
Estimated H-index: 37
(University of Würzburg)
Abstract
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.
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  • Citations (4)
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References161
Newest
Published on May 1, 2006in Molecular Biology and Evolution 10.22
Masato Nikaido27
Estimated H-index: 27
,
Healy Hamilton16
Estimated H-index: 16
+ 6 AuthorsNorihiro Okada54
Estimated H-index: 54
Baleen whales (suborder Mysticeti) comprise 11 extant species that are classified into four families. Although several phylogenetic hypotheses about these taxa have been proposed, their phylogenetic relationships remain confused. We addressed this problem using short interspersed repetitive element (SINE) insertion data, which now are regarded as almost ideal shared, derived characters at the molecular level. We reconstructed the phylogenetic relationships of baleen whales by characterizing 36 i...
63 Citations Source Cite
Published on Mar 14, 2006in PLOS Biology 9.16
Jan Ole Kriegs12
Estimated H-index: 12
(University of Münster),
Gennady Churakov18
Estimated H-index: 18
(University of Münster)
+ 3 AuthorsJürgen Schmitz31
Estimated H-index: 31
(University of Münster)
Reconstruction of the placental mammalian (eutherian) evolutionary tree has undergone diverse revisions, and numerous aspects remain hotly debated. Initial hierarchical divisions based on morphology contained many misgroupings due to features that evolved independently by similar selection processes. Molecular analyses corrected many of these misgroupings and the superordinal hierarchy of placental mammals was recently assembled into four clades. However, long or rapid evolutionary periods, as w...
216 Citations Source Cite
Published on Feb 1, 2006in Systematic Biology 8.52
Wayne P. Maddison45
Estimated H-index: 45
(University of British Columbia),
L. Lacey Knowles39
Estimated H-index: 39
(University of Michigan)
It is now well known that incomplete lineage sorting can cause serious difficulties for phylogenetic inference, but little attention has been paid to methods that attempt to overcome these difficulties by explicitly considering the processes that produce them. Here we explore approaches to phylogenetic inference designed to consider retention and sorting of ancestral polymorphism. We examine how the reconstructability of a species (or population) phylogeny is affected by (a) the number of loci u...
733 Citations Source Cite
Published on Jan 15, 2006in Bioinformatics 5.48
Aleksandr Morgulis6
Estimated H-index: 6
(National Institutes of Health),
E. Michael Gertz14
Estimated H-index: 14
(National Institutes of Health)
+ 1 AuthorsRicha Agarwala39
Estimated H-index: 39
(National Institutes of Health)
Motivation: Matches to repetitive sequences are usually undesirable in the output of DNA database searches. Repetitive sequences need not be matched to a query, if they can be masked in the database. RepeatMasker/Maskeraid (RM), currently the most widely used software for DNA sequence masking, is slow and requires a library of repetitive template sequences, such as a manually curated RepBase library, that may not exist for newly sequenced genomes. Results: We have developed a software tool calle...
117 Citations Source Cite
Published on Jan 1, 2006in Gene 2.50
Jianxin Wang18
Estimated H-index: 18
(Roswell Park Cancer Institute),
Lei Song3
Estimated H-index: 3
(Roswell Park Cancer Institute)
+ 5 AuthorsPing Liang32
Estimated H-index: 32
(Roswell Park Cancer Institute)
Alu elements are the most active and predominant type of short interspersed elements (SINEs) in the human genome. Recently inserted polymorphic (for presence/absence) Alu elements contribute to genome diversity among different human populations, and they are useful genetic markers for population genetic studies. The objective of this study is to identify polymorphic Alu insertions through an in silico comparative genomics approach and to analyze their distribution pattern throughout the human ge...
44 Citations Source Cite
Published on Dec 1, 2005in Gene 2.50
David A. Ray31
Estimated H-index: 31
(West Virginia University),
Dale J. Hedges32
Estimated H-index: 32
(Louisiana State University)
+ 6 AuthorsMark A. Batzer83
Estimated H-index: 83
(Louisiana State University)
Interspersed repeats are a major component of most eukaryotic genomes and have an impact on genome size and stability, but the repetitive element landscape of crocodilian genomes has not yet been fully investigated. In this report, we provide the first detailed characterization of an interspersed repeat element in any crocodilian genome. Chompy is a putative miniature inverted-repeat transposable element (MITE) family initially recovered from the genome of Alligator mississippiensis (American al...
12 Citations Source Cite
Published on Dec 1, 2005in Molecular Phylogenetics and Evolution 4.41
Jinchuan Xing40
Estimated H-index: 40
(Louisiana State University),
Hui Wang11
Estimated H-index: 11
(Louisiana State University)
+ 7 AuthorsMark A. Batzer83
Estimated H-index: 83
(Louisiana State University)
SINEs (Short INterspersed Elements) are a class of non-autonomous mobile elements that are <500 bp in length and have no open reading frames. Individual SINE elements are essentially homoplasy free with known ancestral states, making them useful genetic systems for phylogenetic studies. Alu elements are the most successful SINE in primate genomes and have been utilized for resolving primate phylogenetic relationships and human population genetics. However, no Alu based phylogenetic analysis has ...
94 Citations Source Cite
Published on Sep 1, 2005in American Journal of Physical Anthropology 2.90
L.H. Mateus Pereira1
Estimated H-index: 1
(Florida International University),
A. Socorro1
Estimated H-index: 1
(Florida International University)
+ 6 AuthorsRene J. Herrera38
Estimated H-index: 38
(Florida International University)
This study attempts to ascertain genetic affinities between Native American and East Asian pop- ulations by analyzing four polymorphic Alu insertions (PAIs) and three L1 polymorphic loci. These two genetic systems demonstrated strong congruence when levels of diversity and genetic distances were considered. Overall, genetic relatedness within Native American groups does not correlate with geographical and linguistic structure, although strong grouping for Native Americans with East Asians was de...
19 Citations Source Cite
Published on Sep 1, 2005in Molecular Biology and Evolution 10.22
Hidenori Nishihara11
Estimated H-index: 11
(Tokyo Institute of Technology),
Yoko Satta40
Estimated H-index: 40
+ 3 AuthorsNorihiro Okada54
Estimated H-index: 54
(Tokyo Institute of Technology)
Recent comprehensive studies of DNA sequences support the monophyly of Afrotheria, comprising elephants, sirenians (dugongs and manatees), hyraxes, tenrecs, golden moles, aardvarks, and elephant shrews, as well as that ofPaenungulata, comprising elephants, sirenians, and hyraxes. However, phylogenetic relationships among paenungulates, as well as among nonpaenungulates, have remained ambiguous. Here we applied an extensive retroposon analysis to these problems to support the monophyly of aardvar...
71 Citations Source Cite
Published on Aug 18, 2005in Genome Research 10.10
Louie N. van de Lagemaat14
Estimated H-index: 14
(University of Edinburgh),
Liane Gagnier15
Estimated H-index: 15
+ 1 AuthorsDixie L. Mager52
Estimated H-index: 52
Insertion of transposable elements is a major cause of genomic expansion in eukaryotes. Less is understood, however, about mechanisms underlying contraction of genomes. In this study, we show that retroelements can, in rare cases, be precisely deleted from primate genomes, most likely via recombination between 10- to 20-bp target site duplications (TSDs) flanking the retroelement. The deleted loci are indistinguishable from pre-integration sites, effectively reversing the insertion. Through huma...
102 Citations Source Cite
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Published on Sep 3, 2015in Molecular Biology and Evolution 10.22
Liliya Doronina5
Estimated H-index: 5
(University of Münster),
Gennady Churakov18
Estimated H-index: 18
(University of Münster)
+ 4 AuthorsJürgen Schmitz31
Estimated H-index: 31
(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...
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Published on Oct 1, 2011in Molecular Genetics and Genomics 2.73
Giampaolo Zampicinini3
Estimated H-index: 3
(University of Turin),
Piero Cervella12
Estimated H-index: 12
(University of Turin)
+ 1 AuthorsGabriella Sella22
Estimated H-index: 22
(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;...
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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...
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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...
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