Indel-Based Evolutionary Distance and MouseâHuman Divergence Export

@article{citeulike:1652922, abstract = {10.1101/gr.2450504 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\^{a}€“human divergence exceeds rat\^{a}€“mouse divergence by a factor of 4, so that mouse\^{a}€“human evolutionary distance in terms of selectively neutral indels is 0.056. Because in mammals, indels are \^{a}ˆ¼14 times less frequent than nucleotide substitutions, mouse\^{a}€“human evolutionary distance in terms of selectively neutral substitutions is \^{a}ˆ¼0.8.}, author = {Ogurtsov, Aleksey Y. and Sunyaev, Shamil and Kondrashov, Alexey S.}, citeulike-article-id = {1652922}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.2450504}, citeulike-linkout-1 = {http://genome.cshlp.org/content/14/8/1610.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/14/8/1610.full.pdf}, citeulike-linkout-3 = {http://www.genome.org/cgi/content/abstract/14/8/1610}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/15289479}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=15289479}, day = {1}, doi = {10.1101/gr.2450504}, journal = {Genome Research}, keywords = {intron, length}, month = {August}, number = {8}, pages = {1610--1616}, posted-at = {2009-11-04 10:27:29}, priority = {2}, title = {Indel-Based Evolutionary Distance and Mouse\^{a}€“Human Divergence}, url = {http://dx.doi.org/10.1101/gr.2450504}, volume = {14}, year = {2004} }

TY - JOUR ID - citeulike:1652922 L3 - citeulike-article-id:1652922 N2 - 10.1101/gr.2450504 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 ∼14 times less frequent than nucleotide substitutions, mouse–human evolutionary distance in terms of selectively neutral substitutions is ∼0.8. IS - 8 JF - Genome Research EP - 1616 TI - Indel-Based Evolutionary Distance and Mouse–Human Divergence VL - 14 SP - 1610 KW - intron KW - length AU - Ogurtsov, Aleksey AU - Sunyaev, Shamil AU - Kondrashov, Alexey PY - 2004/08/01/ UR - http://dx.doi.org/10.1101/gr.2450504 ER -