ArticleGenome research2005
Orthologous repeats and mammalian phylogenetic inference.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Evolutionary conservation of an ancient retroviralJournal of virology · 2023Article
- Genomic Signature in Evolutionary Biology: A Review.Biology · 2023Review
- Cross-species transmission of an ancient endogenous retrovirus and convergent co-option of its envelope gene in two mammalian orders.PLoS genetics · 2022Article
- Article
- Cross-Species Transmission and Differential Fate of an Endogenous Retrovirus in Three Mammal Lineages.PLoS pathogens · 2015Article
- Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics.Molecular biology and evolution · 2012Article
- MicroRNAome of porcine pre- and postnatal development.PloS one · 2010Article
- 2x genomes--depth does matter.Genome biology · 2010Article
- Historical constraints on vertebrate genome evolution.Genome biology and evolution · 2009Article
- Confirming the phylogeny of mammals by use of large comparative sequence data sets.Molecular biology and evolution · 2008Article
- Dog as an outgroup to human and mouse.PLoS computational biology · 2007Article
- Using genomic data to unravel the root of the placental mammal phylogeny.Genome research · 2007Article
- Microinversions in mammalian evolution.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Retroposed elements as archives for the evolutionary history of placental mammals.PLoS biology · 2006Article
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Authors and funding
4 authors.
Funding
Abstract
Determining phylogenetic relationships between species is a difficult problem, and many phylogenetic relationships remain unresolved, even among eutherian mammals. Repetitive elements provide excellent markers for phylogenetic analysis, because their mode of evolution is predominantly homoplasy-free and unidirectional. Historically, phylogenetic studies using repetitive elements have relied on biological methods such as PCR analysis, and computational inference is limited to a few isolated repeats. Here, we present a novel computational method for inferring phylogenetic relationships from partial sequence data using orthologous repeats. We apply our method to reconstructing the phylogeny of 28 mammals, using more than 1000 orthologous repeats obtained from sequence data available from the NISC Comparative Sequencing Program. The resulting phylogeny has robust bootstrap numbers, and broadly matches results from previous studies which were obtained using entirely different data and methods. In addition, we shed light on some of the debatable aspects of the phylogeny. With rapid expansion of available partial sequence data, computational analysis of repetitive elements holds great promise for the future of phylogenetic inference.
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