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Green","year":"2010","journal-title":"Science"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1016\/j.ajhg.2011.09.005","article-title":"Denisova admixture and the first modern human dispersals into southeast Asia and oceania.","volume":"89","author":"D Reich","year":"2011","journal-title":"Am J Hum Genet"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/S0092-8674(00)80310-4","article-title":"Neandertal DNA sequences and the origin of modern humans.","volume":"90","author":"M Krings","year":"1997","journal-title":"Cell"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1016\/j.cell.2008.06.021","article-title":"A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing.","volume":"134","author":"RE Green","year":"2008","journal-title":"Cell"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1086\/302219","article-title":"When less is more: gene loss 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Nachman","year":"2000","journal-title":"Genetics"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1098\/rstb.1995.0078","article-title":"A composite estimate of primate phylogeny.","volume":"348","author":"A Purvis","year":"1995","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/nature05634","article-title":"The delayed rise of present-day mammals.","volume":"446","author":"OR Bininda-Emonds","year":"2007","journal-title":"Nature"},{"key":"ref82","first-page":"555","article-title":"PAML: a program package for phylogenetic analysis by maximum likelihood.","volume":"13","author":"Z Yang","year":"1997","journal-title":"Comput Appl Biosci"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: Phylogenetic Analysis by Maximum Likelihood.","volume":"24","author":"Z Yang","year":"2007","journal-title":"Mol Biol 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Nielsen","year":"1998","journal-title":"Genetics"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/genetics\/155.1.431","article-title":"Codon-substitution models for heterogeneous selection pressure at amino acid sites.","volume":"155","author":"Z Yang","year":"2000","journal-title":"Genetics"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1093\/oxfordjournals.molbev.a004148","article-title":"Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages.","volume":"19","author":"Z Yang","year":"2002","journal-title":"Mol Biol Evol"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1093\/molbev\/msi097","article-title":"Bayes empirical bayes inference of amino acid sites under positive selection.","volume":"22","author":"Z Yang","year":"2005","journal-title":"Mol Biol 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