ArticleGenome research2004
Indel-based evolutionary distance and mouse-human divergence.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Detecting Interspecific Positive Selection Using Convolutional Neural Networks.Molecular biology and evolution · 2025Article
- Single-character insertion-deletion model preserves long indels in ancestral sequence reconstruction.BMC bioinformatics · 2024Article
- Conserved regions in long non-coding RNAs contain abundant translation and protein-RNA interaction signatures.NAR genomics and bioinformatics · 2019Article
- Minimum InDel pattern analysis of the Zika virus.BMC genomics · 2018Article
- Split-inducing indels in phylogenomic analysis.Algorithms for molecular biology : AMB · 2018Article
- EvalMSA: A Program to Evaluate Multiple Sequence Alignments and Detect Outliers.Evolutionary bioinformatics online · 2016Article
- Complete Plastid Genome Sequencing of Four Tilia Species (Malvaceae): A Comparative Analysis and Phylogenetic Implications.PloS one · 2015Article
- Next-generation sequencing of colorectal cancers in chinese: identification of a recurrent frame-shift and gain-of-function Indel mutation in the TFDP1 gene.Omics : a journal of integrative biology · 2014Article
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- The vast, conserved mammalian lincRNome.PLoS computational biology · 2013Article
- Armless mitochondrial tRNAs in Enoplea (Nematoda).RNA biology · 2012Article
- A model of genetic search for beneficial mutations: estimating the constructive capacities of mutagenesis.Journal of molecular evolution · 2011Article
- Triplet repeat length bias and variation in the human transcriptome.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- INDELible: a flexible simulator of biological sequence evolution.Molecular biology and evolution · 2009Article
- Fast statistical alignment.PLoS computational biology · 2009Article
- Problems and solutions for estimating indel rates and length distributions.Molecular biology and evolution · 2009Article
- Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance.BMC evolutionary biology · 2009Article
- Somatic microindels in human cancer: the insertions are highly error-prone and derive from nearby but not adjacent sense and antisense templates.Human molecular genetics · 2008Article
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3 authors.
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Abstract
We propose a method for estimating the evolutionary distance between DNA sequences in terms of insertions and deletions (indels), defined as the per site number of indels accumulated in the course of divergence of the two sequences. We derive a maximal likelihood estimate of this distance from differences between lengths of orthologous introns or other segments of sequences delimited by conservative markers. When indels accumulate, lengths of orthologous introns diverge only slightly slower than linearly, because long indels occur with substantial frequencies. Thus, saturation is not a major obstacle for estimating indel-based evolutionary distance. For introns of medium lengths, our method recovers the known evolutionary distance between rat and mouse, 0.014 indels per site, with good precision. We estimate that mouse-human divergence exceeds rat-mouse divergence by a factor of 4, so that mouse-human evolutionary distance in terms of selectively neutral indels is 0.056. Because in mammals, indels are approximately 14 times less frequent than nucleotide substitutions, mouse-human evolutionary distance in terms of selectively neutral substitutions is approximately 0.8.
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