PMC:55343 / 15484-16990
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/55343","sourcedb":"PMC","sourceid":"55343","source_url":"http://www.ncbi.nlm.nih.gov/pmc/55343","text":"Materials and Methods\n\nLineages\nWe have manually sequenced 33 complete mtDNA genomes from available samples previously assigned to major haplogroups. To include lacking haplogroups we added 9 published sequences to the analyses (Table 1).\n\nComplete mtDNA sequences\nComplete mtDNA were amplified in 32 overlapping fragments with primers and PCR conditions described in Table 2. The same primers were utilized to directly sequence both strands of the fragments using the Promega fmol® DNA Cycle Sequencing System and the Usb Thermo Sequenase Radiolabelled Terminator Cycle Sequencing Kits.\nTable 2 Oligonucleotide pairs used in the amplification and sequencing\n\nStatistic analyses\nSequences were aligned manually. Phylogenetic relationships were estimated using median-joining networks [32] as implemented in Network 2.0d and refined by hand. The same topology was obtained using the neighbor-joining method [33]. A chimpanzee sequence (GenBank accession n° D38113) was added to root the networks. Statistical significance of the branches were accomplished by bootstrap resampling with 1000 replications (PHYLIP Package 3.5c, ). Minimum estimates of coalescence ages, and 95% confidence intervals, were based on mean divergence among lineages for the coding region and a constant evolutionary rate of 1.7 × 10-8 per site per year that has been inferred for this region on the basis of 53 complete mtDNA sequences [7].\n\nAccesion numbers\nSequences are available in GenBank (accession nos. AF381981-AF382013) ","divisions":[{"label":"Title","span":{"begin":0,"end":21}},{"label":"Section","span":{"begin":23,"end":238}},{"label":"Title","span":{"begin":23,"end":31}},{"label":"Section","span":{"begin":240,"end":662}},{"label":"Title","span":{"begin":240,"end":264}},{"label":"Table caption","span":{"begin":588,"end":661}},{"label":"Section","span":{"begin":661,"end":1417}},{"label":"Title","span":{"begin":661,"end":679}},{"label":"Section","span":{"begin":1419,"end":1505}},{"label":"Title","span":{"begin":1419,"end":1435}}],"tracks":[{"project":"2_test","denotations":[{"id":"11553319-10331250-10000869","span":{"begin":786,"end":788},"obj":"10331250"},{"id":"11553319-3447015-10000870","span":{"begin":909,"end":911},"obj":"3447015"},{"id":"11553319-11130070-10000871","span":{"begin":1414,"end":1415},"obj":"11130070"}],"attributes":[{"subj":"11553319-10331250-10000869","pred":"source","obj":"2_test"},{"subj":"11553319-3447015-10000870","pred":"source","obj":"2_test"},{"subj":"11553319-11130070-10000871","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ec93ce","default":true}]}]}}