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Phylogenetics We had this naming scheme as developed by who? when? Later we realized that this way of classifying (naming) organisms often reflected their.

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Presentation on theme: "Phylogenetics We had this naming scheme as developed by who? when? Later we realized that this way of classifying (naming) organisms often reflected their."— Presentation transcript:

1 Phylogenetics We had this naming scheme as developed by who? when? Later we realized that this way of classifying (naming) organisms often reflected their true evolutionary relationships..or phylogenies Our goal today is to make a classification system that reflects the organisms' evolutionary history. Problems cropped up due to phenetics…

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3 Figure 20.7

4 Synapsids This node represents the common ancestor of dolphins and ichthyosaurs. It is unlikely that it had a streamlined body, long jaws filled with sharp teeth, or fins and flippers because few of its descendants did Dolphins and ichthyosaurs evolved their similar features independently Monotremes Marsupials Dolphins Primates Rodents Dinosaurs Birds Lizards Ichthyosaurs 0.5 m Why does simple phenetics based on morphology cause confusion?

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6 Figure 20.2 ANCESTRAL LIZARD (with limbs) Eastern glass lizard Monitor lizard Snakes Geckos No limbs Iguanas No limbs Sorting homologous and analogous traits

7 Synapsids This node represents the common ancestor of dolphins and ichthyosaurs. It is unlikely that it had a streamlined body, long jaws filled with sharp teeth, or fins and flippers because few of its descendants did Dolphins and ichthyosaurs evolved their similar features independently Monotremes Marsupials Dolphins Primates Rodents Dinosaurs Birds Lizards Ichthyosaurs Common dolphin Ichthyosaur 0.5 m Convergent characteristics

8 Are gliding flaps between front and back limbs …. analogous traits? or homologous traits? Homologous characters=“really shared”=shared due to shared ancestry Analogous characters=look same but really are not the same from an evolutionary standpoint=show homoplasy

9 Campbell.. Adaptation can obscure homologies. Convergence can create misleading analogies.

10 To get away from this problem Hennig said we should only gather groups together that share “special traits” that are evolutionarily new or novel derived traits or characters All groups should be monophyletic (includes an ancestor with all descendent species) A clade is… Cladistics! Ucmp berkeley

11 Which boxes (which groups) show clades or monophyletic groups?

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13 Figure 20.10 B C A D E F G Group I (a) Monophyletic group (clade) 11 B C A D E F G Group II (b) Paraphyletic group (c) Polyphyletic group B C A D E F G Group III 22 Which boxes (which groups) show clades or monophyletic groups?

14 Do the clip test…what are monophyletic groups here?

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18 MM=1460 MN=2550 NN=990 We can calculate the allele frequencies as: Frequency of M =.547=p Frequency of N =.453=q We can now calculate our expected genotype frequencies. How many would we expect to have if “nothing is going on” MM = p 2 = (.547) 2 =.299, or 1496 individuals in the sample MN = 2pq = 2 x (.547 x 0.453 =.496, or 2478 individuals NN = q 2 = (.453) 2 =.205, or 1026 individuals

19 Figure 20.11 Leopard Turtle Frog Bass Lamprey Lancelet (outgroup) Hair Amnion Four walking legs Hinged jaws Vertebral column Leopard Turtle Frog BassLamprey Lancelet (outgroup) Hair Amnion Four walking legs Hinged jaws Vertebral column (backbone) CHARACTERS TAXA (b) Phylogenetic tree (a) Character table 01 0 1 0 1 0 1 0 10 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 Making a phylogenetic tree…

20 Figure 20.11 Leopard Turtle Frog Bass Lamprey Lancelet (outgroup) Hair Amnion Four walking legs Hinged jaws Vertebral column Leopard Turtle Frog BassLamprey Lancelet (outgroup) Hair Amnion Four walking legs Hinged jaws Vertebral column (backbone) CHARACTERS TAXA (b) Phylogenetic tree (a) Character table 01 0 1 0 1 0 1 0 10 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 Making a phylogenetic tree… “principle of parsimony” assume the fewest number of evolutionary changes or events- simplest explanation given data

21 Making a tree using cladistic analysis Pull out derived characters or synapomorphies in a table! Then use an outgroup to figure out what your starting point-what your ancestral state is. Use principle of parsimony-assumes the fewest number of evolutionary changes or events-simplest explanation given data

22 Different tree!

23 ://www.nsf.gov/news/news_images.jsp?cntn_id=115520&org=NSF

24 Figure 27-4 The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group. Artiodactyls Whale Camel Peccary Pig HippoDeer Cow Gain of pulley- shaped astragalus Astragalus (ankle bone) If whales are related to hippos, then two changes occurred in the astragalus. Artiodactyls Camel Peccary Pig Hippo Whale Deer Cow Gain of pulley- shaped astragalus Data on the presence and absence of SINE genes support the close relationship between whales and hippos. Loss of pulley- shaped astragalus 0 = gene absent 1 = gene present ? = still undetermined Whales and hippos share four unique SINE genes (4, 5, 6, and 7) Most parsimonious- but wrong! Less parsimonious but right! Natural selection can obscure homologies..!

25 Figure 27-4 The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group. Artiodactyls Whale Camel Peccary Pig HippoDeer Cow Gain of pulley- shaped astragalus Astragalus (ankle bone) If whales are related to hippos, then two changes occurred in the astragalus. Artiodactyls Camel Peccary Pig Hippo Whale Deer Cow Gain of pulley- shaped astragalus Data on the presence and absence of SINE genes support the close relationship between whales and hippos. Loss of pulley- shaped astragalus 0 = gene absent 1 = gene present ? = still undetermined Whales and hippos share four unique SINE genes (4, 5, 6, and 7) Most parsimonious- but wrong! Less parsimonious but right! Natural selection can obscure homologies..!

26 Figure 27-4 The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group. Artiodactyls Whale Camel Peccary Pig HippoDeer Cow Gain of pulley- shaped astragalus Astragalus (ankle bone) If whales are related to hippos, then two changes occurred in the astragalus. Artiodactyls Camel Peccary Pig Hippo Whale Deer Cow Gain of pulley- shaped astragalus Data on the presence and absence of SINE genes support the close relationship between whales and hippos. Loss of pulley- shaped astragalus 0 = gene absent 1 = gene present ? = still undetermined Whales and hippos share four unique SINE genes (4, 5, 6, and 7) Most parsimonious- but wrong! Less parsimonious but right! Natural selection can obscure homologies..!

27 Figure 27-4 The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group. Artiodactyls Whale Camel Peccary Pig HippoDeer Cow Gain of pulley- shaped astragalus Astragalus (ankle bone) If whales are related to hippos, then two changes occurred in the astragalus. Artiodactyls Camel Peccary Pig Hippo Whale Deer Cow Gain of pulley- shaped astragalus Data on the presence and absence of SINE genes support the close relationship between whales and hippos. Loss of pulley- shaped astragalus 0 = gene absent 1 = gene present ? = still undetermined Whales and hippos share four unique SINE genes (4, 5, 6, and 7) Most parsimonious- but wrong! Less parsimonious but right! Natural selection can obscure homologies..! Leopard Turtle Frog Bass Lamprey Lancelet (outgroup) Hair Amnion Four walking legs Hinged jaws Vertebral column Leopard Turtle Frog BassLamprey Lancelet (outgroup) Hair Amnion Four walking legs Hinged jaws Vertebral column (backbone) CHARACTERS TAXA (b) Phylogenetic tree (a) Character table 01 0 1 0 1 0 1 0 10 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1

28 Molecular data was used to inform the situation and led us to the likely correct tree!

29 What can you not assume given a tree that looks like this?? Will those close to each other always look phenotypically or morphologically similar? Why or Why not? Figure 20.15 Ornithischian dinosaurs Birds Crocodilians Lizards and snakes Saurischian dinosaurs Common ancestor of crocodilians, dinosaurs, and birds

30 What can you not assume given a tree that looks like this?? Will those close to each other always look phenotypically similar? Figure 20.15 Ornithischian dinosaurs Birds Crocodilians Lizards and snakes Saurischian dinosaurs Common ancestor of crocodilians, dinosaurs, and birds

31 Only conveys branching pattern, branching order. Rotate at nodes. Figure 20.4 Panthera pardus (leopard) Species Order FamilyGenus Taxidea taxus (American badger) Canis latrans (coyote) Lutra lutra (European otter) Canis lupus (gray wolf) Panthera Taxidea Canis Lutra Felidae Mustelidae Carnivora Canidae 12

32 Figure 20.12 Mouse Human Chicken Frog Zebrafish Lancelet Drosophila Why does this tree look different than the previous trees? IS looking at RATE of change of homologous genes. Branch lengths are proportional to genetic change. Since all are around today…what does the fact that there are different branch lengths mean??

33 Figure 20.12 Mouse Human Chicken Frog Zebrafish Lancelet Drosophila 15 units long 12 units 1.2 units 6.5 units

34 Figure 20.13 Mouse Human Chicken Frog Zebrafish Lancelet Drosophila Millions of years ago 65.5 Present542 PALEOZOIC 251 MESOZOIC CENOZOIC We can anchor those nodes at specific dates based on the fossil record!

35 Figure 20.13 Mouse Human Chicken Frog Zebrafish Lancelet Drosophila Millions of years ago 65.5 Present542 PALEOZOIC 251 MESOZOIC CENOZOIC Then we can divide length measured in previous tree by time.. (12 units/540my)

36 Figure 20.18 Divergence time (millions of years) Number of mutations 1209060300 90 60 30 0 Number of accumulated mutations in 7 proteins in mammals

37 When is a molecular clock not consistent! Selection pressure on certain proteins might mess things up…why? DNA that codes for ribosomal RNA (rRNA) evolves slowly so use to look at divergence that might have taken place 100s of millions of years ago.. DNA in mitochondria (mtDNA) evolves rapidly and can be used to explore rapid evolutionary events like differences within a species- You would end up with a really BAD tree if you tried to use mtDNA to look at deep divisions within mammals for example.

38 Beyond fossil record we often get into trouble.. Can get around by using many different regions and if all give same tree then probably correct.

39 Figure 20.15 Ornithischian dinosaurs Birds Crocodilians Lizards and snakes Saurischian dinosaurs Common ancestor of crocodilians, dinosaurs, and birds How do we use phylogenetic trees? Your text… How do they make predictions about behavior of extinct dinos

40 http://evolution.berkeley.edu/evolibrary/news/060101_batsars Airborne germ caused 774 deaths and more than 8000 cases of illness. Scientists immediately suspected that it had jumped to humans from some other organism. In May of 2003, attention focused in on cat-like mammals called civets. Infected civets were discovered at a live animal market in southern China (where they are occasionally eaten). However, since further searches failed to turn up more tainted civets, scientists concluded that they were not the original source of SARS and continued their quest. Then in the fall of 2005, two teams of researchers independently discovered large reservoirs of a SARS-like virus in Chinese horseshoe bats. Based on this evidence, biologists have come up with a plausible path of transmission: infected bats and uninfected civets came into contact at a market, the virus was transmitted to civets and then multiplied and evolved in civets (or other animals) in the public market, until eventually the virus hopped to humans. SARS virus 2002 and 2003 But where did this mystery virus come from?

41 Figure 20.19 Year Index of base changes between HIV gene sequences 194019201960 1900 0 0.15 0.10 0.05 19802000 HIV Range Adjusted best-fit line (accounts for uncertain dates of HIV sequences How do they use molecular clocks to establish origination dates of HIV virus?

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