ArticleGenome research2009
Mosaic retroposon insertion patterns in placental mammals.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
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- SINE-Based Phylogenomics Reveal Extensive Introgression and Incomplete Lineage Sorting inGenes · 2022Article
- Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation.Genome biology and evolution · 2020Article
- Retrotransposons spread potential cis-regulatory elements during mammary gland evolution.Nucleic acids research · 2019Article
- Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation.Mobile DNA · 2019Article
- The Volcano Rabbit in the Phylogenetic Network of Lagomorphs.Genome biology and evolution · 2019Article
- Global Rate Variation in Bony Vertebrates.Genome biology and evolution · 2018Article
- Lineage-independent retrotransposition of UTP14 associated with male fertility has occurred multiple times throughout mammalian evolution.Royal Society open science · 2017Article
- Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes.Genome biology and evolution · 2017Article
- Speciation network in Laurasiatheria: retrophylogenomic signals.Genome research · 2017Article
- Resolving the relationships of Paleocene placental mammals.Biological reviews of the Cambridge Philosophical Society · 2017Article
- Mammal madness: is the mammal tree of life not yet resolved?Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Review
- Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans.Molecular biology and evolution · 2016Article
- Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data.PLoS computational biology · 2016Article
- The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference.Genome biology and evolution · 2016Article
- Article
- Determining the Position of Storks on the Phylogenetic Tree of Waterbirds by Retroposon Insertion Analysis.Genome biology and evolution · 2015Article
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6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One and a half centuries after Charles Darwin and Alfred Russel Wallace outlined our current understanding of evolution, a new scientific era is dawning that enables direct observations of genetic variation. However, pure sequence-based molecular attempts to resolve the basal origin of placental mammals have so far resulted only in apparently conflicting hypotheses. By contrast, in the mammalian genomes where they were highly active, the insertion of retroelements and their comparative insertion patterns constitute a neutral, virtually homoplasy-free archive of evolutionary histories. The "presence" of a retroelement at an orthologous genomic position in two species indicates their common ancestry in contrast to its "absence" in more distant species. To resolve the placental origin controversy we extracted approximately 2 million potentially phylogenetically informative, retroposon-containing loci from representatives of the major placental mammalian lineages and found highly significant evidence challenging all current single hypotheses of their basal origin. The Exafroplacentalia hypothesis (Afrotheria as the sister group to all remaining placentals) is significantly supported by five retroposon insertions, the Epitheria hypothesis (Xenarthra as the sister group to all remaining placentals) by nine insertion patterns, and the Atlantogenata hypothesis (a monophyletic clade comprising Xenarthra and Afrotheria as the sister group to Boreotheria comprising all remaining placentals) by eight insertion patterns. These findings provide significant support for a "soft" polytomy of the major mammalian clades. Ancestral successive hybridization events and/or incomplete lineage sorting associated with short speciation intervals are viable explanations for the mosaic retroposon insertion patterns of recent placental mammals and for the futile search for a clear root dichotomy.
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