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Lec6-Phylogeny2007 - YPCO92 120888 Sfl2457T YP91001 238664...

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ECH3937 20431 ECH3937 20167 ECH3937 14722 ECH3937 17419 ECH3937 18541 ECH3937 17896 ECH3937 17863 PlTTO1 141022 SCRI1043 50855 SCRI1043 53164 SCRI1043 54408 SCRI1043 57558 ECH3937 17662 ECH3937 17665 ECH3937 17668 ECH3937 17672 ECH3937 17674 SCRI1043 58972 SCRI1043 59598 SCRI1043 59602 SCRI1043 59605 SCRI1043 59608 ECH3937 16585 SCRI1043 48415 ECH3937 18892 SCRI1043 48511 ECH3937 18585 SCRI1043 58061 ECH3937 18765 SCRI1043 52036 ECH3937 15168 SCRI1043 58277 SenLT2 95332 MG1655 4744 EcoRIM 131994 EDL933 26073 Sfl301 88087 Sfl2457T 72554 YPCO92 120790 YPCO92 120791 ECH3937 16436 ECH3937 17090 ECH3937 17537 SCRI1043 50312 YP91001 236316 YPCO92 119344 YPKIM 32701 ECH3937 16979 SCRI1043 51018 ECH3937 14618 SCRI1043 54897 ECH3937 19858 ECH3937 19855 ECH3937 19852 ECH3937 19851 SCRI1043 51623 ECH3937 19306 ECH3937 19050 SCRI1043 54545 SCRI1043 54551 ECH3937 17097 SCRI1043 47533 ECH3937 20252 ECH3937 15600 ECH3937 15603 ECH3937 16115 SCRI1043 47561 YP91001 243830 YPCO92 129020 YPKIM 33881 ECH3937 15513 SCRI1043 53830 YP91001 241164 YPCO92 117982 YPKIM 32953 ECH3937 19309 ECH3937 14726 EcoRIM 134012 EDL933 28099 MG1655 10087 CFT073 79997 Sfl301 89357 Sfl2457T 74510 SenCT18 112185 SenLT2 100002 SenTy2 84856 ECH3937 14843 SCRI1043 57364 YP91001 238556 YPCO92 120760 YPKIM 31500 ECH3937 14536 SCRI1043 52281 ECH3937 19790 SCRI1043 47806 SCRI1043 47811 SenLT2 99999 SenCT18 112182 SenTy2 84855 ECH3937 19718 SCRI1043 56439 ECH3937 18754 SCRI1043 52063 ECH3937 46680 SCRI1043 48500 ECH3937 14824 SCRI1043 57403 ECH3937 18502 SCRI1043 57501 ECH3937 18511 SCRI1043 57474 EcoRIM 132579 EDL933 26681 MG1655 6288 Sfl301 88220 Sfl2457T 73134 PlTTO1 141025 YP91001 238664 YPCO92 120888 YPKIM 31533 MG1655 6290 CFT073 78420 EcoRIM 132580 EDL933 26682 Sfl301 88221 Sfl2457T 73135 SenCT18 109228 SenLT2 96205 SenTy2 82672 SenLT2 103914 EcoRIM 135436 EDL933 29529 MG1655 14282 CFT073 81646 Sfl301 90598 Sfl2457T 76001 SenCT18 107948 SenLT2 95413 SenTy2 83275 SenCT18 112064 SenLT2 99818 SenCT18 113896 SenLT2 101078 SenTy2 85671 YP91001 238660 YPCO92 120881 YPKIM 31532 SCRI1043 53573 ECH3937 16380 Phylogeny
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Vocabulary of Phylogenetic Trees Graph of edges and nodes that illustrates the evolutionary relationships among “Operational Taxonomic Units or OTUs” Topology refers to the branching pattern http://www.ncbi.nlm.nih.gov/About/primer/phylo.html
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Rooting and Scaling – Same tree, different look? http://www.ncbi.nlm.nih.gov/About/primer/phylo.html
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Three different rooted trees consistent with a four taxon unrooted tree What is the total number of possible rooted trees consistent with this unrooted tree? http://www.ncbi.nlm.nih.gov/About/primer/phylo.html
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How many possible trees for n taxa? Number of Rooted Trees = (2 n -3)! (2 n -2 ) ( n -2)! Number of Unrooted Trees = (2 n -5)! (2 n -3 ) ( n -3)!
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Phylogeny and Genomics A species tree provides a framework for analyzing presence and absence of genes in genomes (or traits in organisms) The species tree may be unknown A genome is a (comprehensive) source of DNA and (predicted) protein sequences to use for phylogenetic reconstruction Different regions of the genome may support different trees Trees are useful for examining evolutionary history of gene families Knowledge of the species tree affects interpretation of gene family trees.
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Erwinia carotovora Knowing the relationship between strains and species provides a framework for interpretation Pantoea stewartii Salmonella enterica Yersinia pestis
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Erwinia carotovora A reasonable guess based on the character “host type” Pantoea stewartii Salmonella enterica Yersinia pestis But is this a good choice if the goal is to reconstruct the “species tree”?
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