{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,30]],"date-time":"2025-08-30T17:10:03Z","timestamp":1756573803833},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: We suggest the use of Poisson regression for time inference and hypothesis testing on a bifurcating Phylogenetic tree with known topology. This method is computationally simple and naturally accommodates variable substitution rates across different sites, without requiring the estimation of these rates. We identify the assumptions under which this is a maximum-likelihood inference approach and show that in some realistic situations\u2014in particular, when the probability of repeated mutation within each branch of the tree is small\u2014these assumptions hold with high probability.<\/jats:p><jats:p>Results: Our motivating domain is human mitochondrial DNA trees, and we illustrate our method on a problem of estimating the time to most recent common ancestor of all non-African mtDNA, using publicly available data. We test for molecular clock violations using multiple comparisons, and conclude that the global molecular clock hypothesis cannot be rejected based on these data.<\/jats:p><jats:p>Contact: \u00a0srosset@us.ibm.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl306","type":"journal-article","created":{"date-parts":[[2007,1,19]],"date-time":"2007-01-19T18:51:12Z","timestamp":1169232672000},"page":"e142-e147","source":"Crossref","is-referenced-by-count":12,"title":["Efficient inference on known phylogenetic trees using Poisson regression"],"prefix":"10.1093","volume":"23","author":[{"given":"Saharon","family":"Rosset","sequence":"first","affiliation":[{"name":"IBM T.J. Watson Research Center, Yorktown Heights \u00a0 NY 10598, USA"}]}],"member":"286","published-online":{"date-parts":[[2007,1,15]]},"reference":[{"key":"2023041107143665700_","volume-title":"Statistical Inference","author":"Casella","year":"2001","edition":"2 edn"},{"key":"2023041107143665700_","doi-asserted-by":"crossref","DOI":"10.1201\/9780429246593","volume-title":"An Introduction to the Bootstrap","author":"Efron","year":"1994"},{"key":"2023041107143665700_","volume-title":"Inferring Phylogenies","author":"Felsenstein","year":"2003"},{"key":"2023041107143665700_","first-page":"406","article-title":"Toward defining the course of evolution: minimum change for a specified tree topology","volume":"20","author":"Fitch","year":"1971","journal-title":"J. Mol. Evol."},{"key":"2023041107143665700_","first-page":"935","article-title":"Origin and evolution of native american mtdna variation: a reappraisal","volume":"59","author":"Forster","year":"1996","journal-title":"Am. J. Hum. 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