Phylogenetic Trees. Bret Larget. Departments of Botany and of Statistics University of Wisconsin Madison. September 8, 2009

Transcription

1 Phylogenetic Trees ret Larget epartments of otany and of Statistics University of Wisconsin Madison September 8, 2009 Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

2 rief History arwin Phylogenetics and arwin In 1837, shortly after his famous five-year voyage as naturalist on the eagle, arwin sketched a tree diagram in one of his notebooks. This simple sketch is remarkably similar to modern diagrams of phylogenies. In addition, the sole figure in The Origin of Species (1859) is a phylogeny. Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

3 arwin s Trees rief History arwin Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

4 rief History arly History arly History Shortly after the 1859 publication of The Origin of Species, many biologists came to accept the truth of a universal Tree of Life. rnst Haeckel and many others created highly stylized trees that were based on expert opinion. century passed before development of formal scientific methods for estimating phylogenies began. Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

5 Haeckel s Trees rief History arly History Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

6 rief History What is the Origin of Whales? Modern Phylogenetics dolphin TGTGTTTTT giant sperm whale TGTGTTTTTTT bowhead whale TGTGTTTTTT right whale TGTGGTTTTTT minke whale TGTGTTTTT fin whale TGTGTTTGT blue whale TGTGTTTT humpback whale TGTGTTTTT... hippopotamus TGTGTTTTTTTT camel TGTGTTTTTTT pig TGTGTTTTTT cow TGTTTGGTTTTTGT sheep TGTTGTTTTGT goat TGTGGTTTTTGT Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

7 rief History n stimated Whale Phylogeny Modern Phylogenetics Scienceirect - ull Size Image 09/04/ :10 M LOS urlversion=0&_userid=443835&md5=df655f7ee732c807488f9262b841bcfc Page 1 of 2 Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

8 rief History Uses of Phylogenies Why is Phylogenetics Important? It is an exaggeration to say phylogenetics are everywhere, but phylogenetic trees are used in many areas of biology beyond the obvious area of systematics. Other areas include forensics and developmental biology. rom a statistical point of view, the evolutionary history of organisms means that species should not be treated as independent samples. ven if evolutionary relationships are not of primary interest, a good statistical analysis might need to account for the phylogeny to explain some part of the dependence among observations from different species. Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

9 rief History Uses of Phylogenies Why is Phylogenetics Important? It is an exaggeration to say phylogenetics are everywhere, but phylogenetic trees are used in many areas of biology beyond the obvious area of systematics. Other areas include forensics and developmental biology. rom a statistical point of view, the evolutionary history of organisms means that species should not be treated as independent samples. ven if evolutionary relationships are not of primary interest, a good statistical analysis might need to account for the phylogeny to explain some part of the dependence among observations from different species. Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

10 rief History Uses of Phylogenies Why is Phylogenetics Important? It is an exaggeration to say phylogenetics are everywhere, but phylogenetic trees are used in many areas of biology beyond the obvious area of systematics. Other areas include forensics and developmental biology. rom a statistical point of view, the evolutionary history of organisms means that species should not be treated as independent samples. ven if evolutionary relationships are not of primary interest, a good statistical analysis might need to account for the phylogeny to explain some part of the dependence among observations from different species. Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

11 rief History Uses of Phylogenies Why is Phylogenetics Important? It is an exaggeration to say phylogenetics are everywhere, but phylogenetic trees are used in many areas of biology beyond the obvious area of systematics. Other areas include forensics and developmental biology. rom a statistical point of view, the evolutionary history of organisms means that species should not be treated as independent samples. ven if evolutionary relationships are not of primary interest, a good statistical analysis might need to account for the phylogeny to explain some part of the dependence among observations from different species. Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

12 rief History orensic Phylogenetic Tree Uses of Phylogenies Reviews 30 HIV orensics igure 2 R RV 10% US3 31 SMHS8 P896 SMHS7 NVVG SMHS2 S YU2 NVUSR2 NY5G S14 US2 JH32 NVV WU160 JRS M1 H HX2 S128 L50 L49 SMHS1 L1 SMHS20 85WIPR54 MNG US4 89SP061 US1 S2 NVV PHI HN WR M200 G M925 M18 TH MN 3 RL42 PHI L47 L46 OYI M36 L45 L igure 2. Neighbor-joining phylogram representing the reconstruction of the phylogenetic relationships between the env (2-V5) sequences obtained from the index case (31-44), the alleged recipient (22-29), three local controls (L45 and L48; L46 and L47; and L49 and L50) and 48 sequences chosen from Genank. Ten iterations of random sequence addition were used. Scale bar represents 10% genetic distance. ootstrap values are shown at nodes with greater than 70% support. Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

13 Trees ctivity 1: xample Tree Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

14 Trees ctivity 2: ompare Trees Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

15 Trees ctivity 3: Unrooted Tree Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13

16 Trees ctivity 4: Labeled Histories Genetics/otany 629 (all 2009) Phylogenetic Trees September 8, / 13