UNIT III A. Descent with Modification(Ch9) B. Phylogeny (Ch2) C. Evolution of Populations (Ch2) D. Origin of Species or Speciation (Ch22)
Classification in broad term simply means putting things in classes or groups. Humans seem unable to resist the urge to classify. It's one of the most basic activities of any science, because it's easier to think about a few groups of things than about lots of separate things. Taxonomy means giving names to things. It tends to go hand in hand with classification, but need not. You can arrange things without naming them, or name them without arranging them, but the most helpful schemes name things in a way the reflects their classification. Phylogeny is the evolutionary tree of life, the hierarchical structure by which every life-form is related to every other life-form. Systematics is the study of making these trees
Phylogenetics We had this species naming scheme as developed by who? Later we realized that this way of classifying (sorting) organisms and naming them often reflected their true evolutionary relationships (or phylogenies). Our goal today is to make our classification system and our naming system (taxonomic system) reflect the organisms' evolutionary history. Bad practice to have a bunch of organisms in a Family, one of which does not have shared ancestry with the others.
Problems cropped up when we were naming or classifying due to phenetics
Figure 2.2 Sorting homologous and analogous traits No limbs Eastern glass lizard Monitor lizard Iguanas ANCESTRAL LIZARD (with limbs) No limbs Snakes Geckos
Figure 2.7
We make this mistake all the time..
Why does simple phenetics based on morphology cause confusion? Look same due to similar Synapsids way of life! Monotremes Marsupials Dolphins 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 Primates Rodents Dinosaurs Birds Ichthyosaurs Lizards.5 m.5 m
Synapsids Monotremes Marsupials Common dolphin Dolphins 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 Primates Rodents Dinosaurs Birds Ichthyosaurs Lizards Ichthyosaur.5 m.5 m Convergent characteristics
Analogous characters=look same but really are not the same from an evolutionary standpoint=show homoplasy Are gliding flaps between front and back limbs. analogous traits? or homologous traits? How about thorns and small leaves? Homologous characters= really shared =shared due to shared ancestry
Campbell.. Adaptation can obscure homologies. Convergence can create misleading analogies.
To get away from this problem of overall similarity (phenetics-which can be misleading) Hennig said.. Groups (clades) should share only very specific morphological traits that are evolutionarily new or novel also called derived traits or synapomorphies These are shared characteristics that no one else has.
Figure 2.5 Branch point: where lineages diverge Taxon A 2 3 4 Taxon B Taxon C Taxon D Sister taxa ANCESTRAL LINEAGE 5 Taxon E Taxon F This branch point represents the common ancestor of taxa A G. Taxon G This branch point forms a polytomy: an unresolved pattern of divergence. Basal taxon
All groups should be monophyletic (includes an ancestor with all descendent species) A clade is Cladistics! Ucmp berkeley
Which boxes (which groups) show clades or monophyletic groups?
Which boxes (which groups) show clades or monophyletic groups?
Figure 2. Which boxes (which groups) show clades or monophyletic groups? (a) Monophyletic group (clade) A (b) Paraphyletic group A (c) Polyphyletic group A B Group I B C C B C Group III D D D E F 2 E F Group II 2 E F G G G
Do the clip test what are monophyletic groups here?
Making a phylogenetic tree based on morphological characters CHARACTERS Vertebral column (backbone) Hinged jaws Four walking legs Amnion Hair Lancelet (outgroup) (a) Character table Lamprey TAXA Bass Frog Turtle Leopard Vertebral column You are given derived Lancelet (outgroup) characters or Lamprey synapomorphies in a table! Hinged jaws Bass Frog Use an outgroup to figure Four walking legs Turtle out what your starting Amnion Leopard point -what your Hair ancestral state is. (b) Phylogenetic tree Figure 2. Focus on order of branching.
Figure 2. Making a phylogenetic tree CHARACTERS Vertebral column (backbone) Hinged jaws Four walking legs Amnion Lancelet (outgroup) Lamprey Bass TAXA Frog Turtle Leopard Vertebral column Hinged jaws Four walking legs Lancelet (outgroup) Lamprey Bass Frog Turtle Hair Amnion Hair Leopard (a) Character table (b) Phylogenetic tree
Figure 2. Making a phylogenetic tree CHARACTERS Vertebral column (backbone) Hinged jaws Four walking legs Amnion Lancelet (outgroup) Lamprey Bass TAXA Frog Turtle Leopard Vertebral column Hinged jaws Four walking legs Lancelet (outgroup) Lamprey Bass Frog Turtle Hair Amnion Hair Leopard (a) Character table (b) Phylogenetic tree
principle of parsimony assume the fewest number of evolutionary changes or eventssimplest explanation given data Figure 2. Making a phylogenetic tree Now rotate your nodes.. CHARACTERS Vertebral column (backbone) Hinged jaws Four walking legs Amnion Lancelet (outgroup) Lamprey Bass TAXA Frog Turtle Leopard Vertebral column Hinged jaws Four walking legs Lancelet (outgroup) Lamprey Bass Frog Turtle Hair Amnion Hair Leopard (a) Character table (b) Phylogenetic tree
Different tree style! Mostly we don t use these anymore why???
://www.nsf.gov/news/news_images.jsp?cntn_id=552&org=nsf
Figure 27-4 The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group. Artiodactyls Whale Camel Peccary Pig Hippo Deer Cow Gain of pulleyshaped astragalus Astragalus (ankle bone) If whales are related to hippos, then two changes occurred in the astragalus. Artiodactyls Most parsimonious But wrong! Camel Peccary Pig Hippo Whale Deer Cow Gain of pulleyshaped astragalus Loss of pulleyshaped astragalus Natural selection can obscure homologies..! Less parsimonious but right! Data on the presence and absence of SINE genes support the close relationship between whales and hippos. = gene present = gene absent? = still undetermined Whales and hippos share four unique SINE genes (4, 5, 6, and 7)
Figure 27-4 The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group. Artiodactyls Whale Camel Peccary Pig Hippo Deer Cow Gain of pulleyshaped 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 Loss of pulleyshaped astragalus Most parsimoniousbut wrong! Natural selection can obscure homologies..! Less parsimonious but right! Gain of pulleyshaped astragalus Data on the presence and absence of SINE genes support the close relationship between whales and hippos. = gene present = gene absent? = still undetermined Whales and hippos share four unique SINE genes (4, 5, 6, and 7)
Figure 27-4 The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group. Artiodactyls Whale Camel Peccary Pig Hippo Deer Cow Gain of pulleyshaped 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 Loss of pulleyshaped astragalus Most parsimoniousbut wrong! Natural selection can obscure homologies..! Less parsimonious but right! Gain of pulleyshaped astragalus Data on the presence and absence of SINE genes support the close relationship between whales and hippos. = gene present = gene absent? = still undetermined Whales and hippos share four unique SINE genes (4, 5, 6, and 7)
Molecular data was used to inform the situation and led us to the likely correct tree!
Figure 27-4 The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group. Artiodactyls Characters can be morphological or molecular data! CHARACTERS Vertebral column (backbone) Whale Camel Peccary Pig Hippo Deer Cow Gain of pulleyshaped astragalus Astragalus (ankle bone) If whales are related to hippos, then two changes occurred in the astragalus. Artiodactyls Hinged jaws Four walking legs Camel Peccary Pig Hippo Whale Deer Cow Amnion Hair Lancelet (outgroup) (a) Character table Lamprey Bass TAXA Frog Turtle Leopard Vertebral column Gain of pulleyshaped astragalus Hinged jaws Four walking legs Loss of pulleyshaped astragalus Amnion (b) Phylogenetic tree Lancelet (outgroup) Most parsimoniousbut Lamprey wrong! Bass Natural selection Frog can obscure homologies..! Turtle Leopard Less parsimonious but right! Data on the presence and absence of SINE genes support the close relationship between whales and hippos. Hair = gene present = gene absent? = still undetermined Whales and hippos share four unique SINE genes (4, 5, 6, and 7)
Things to remember
Will those close to each other on a tree always look phenotypically or morphologically similar? Why or Why not? Figure 2.5 Lizards and snakes Crocodilians Common ancestor of crocodilians, dinosaurs, and birds Ornithischian dinosaurs Saurischian dinosaurs Birds
It is not the case that the Long Branch shows No Change! Figure 2.5 Lizards and snakes Crocodilians Common ancestor of crocodilians, dinosaurs, and birds Ornithischian dinosaurs Saurischian dinosaurs Birds
Figure 2.4 Meaning is only conveyed in branching order. Rotate at nodes. Order Carnivora Family Genus Felidae Mustelidae Canidae Panthera Taxidea Lutra Canis 2 Species Panthera pardus (leopard) Taxidea taxus (American badger) Lutra lutra (European otter) Canis latrans (coyote) Canis lupus (gray wolf)
There are also different kinds of trees! Previous trees were cladograms show order of divergence. Presence or absence of traits.
Why does this tree look different than the previous trees? It is looking at the number of changes in homologous genes. Branch lengths are proportional to genetic change. Figure 2.2 Drosophila Lancelet Zebrafish Frog Chicken Human Mouse
Branch lengths are proportional to change so different branch lengths indicate that the gene has evolved at different rates in different lineages-you can calculate that rate by anchoring to fossil record. Which lineages below show more rapid evolution? Figure 2.2.2 5 differences 2 differences 6.5 differences Drosophila Lancelet Zebrafish Frog Chicken Human Mouse
Figure 2.3 We can often anchor nodes at specific dates based on the fossil record! Drosophila Lancelet Zebrafish Frog Chicken Human 542 PALEOZOIC MESOZOIC 25 Millions of years ago CENOZOIC 65.5 Present Mouse
Then we can divide length measured in previous tree by time.. (2 differences/54my) to calculate an actual rate of change. Then we can graph. Drosophila Lancelet Zebrafish Frog Chicken Human 542 PALEOZOIC MESOZOIC 25 Millions of years ago CENOZOIC 65.5 Present Mouse
Molecular Clock! Here number of accumulated mutations in 7 proteins in mammals (who are green dots?) Number of mutations 9 6 3 3 6 9 Divergence time (millions of years) 2
Molecular Clock! Here number of accumulated mutations in 7 proteins in mammals (Who are green dots? Is the mutation rate for this group lower or higher than the norm for mammals?) Number of mutations 9 6 3 3 6 9 Divergence time (millions of years) 2
Do all parts of the genome evolve at a consistent rate? No! Strong selection pressure can slow or speed up change. If you want to look at very deep divisions in Eukaryotes would you use a slow or fast evolving part of the genome?
DNA that codes for ribosomal RNA (rrna) evolves so we use to look at ancient/recent divergences. (s 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. Why?
How do we use phylogenetic trees? How do trees help us make predictions about behavior of extinct dinos? If crocodiles brood eggs and birds do too then dinos? Lizards and snakes Crocodilians Common ancestor of crocodilians, dinosaurs, and birds Ornithischian dinosaurs Saurischian dinosaurs Birds
How do trees help us make predictions about the emergence and spread of infectious pathogens? Do you remember the Antibiotic Resistance video?
SARS virus 22 and 23 But where did this mystery virus come from? Airborne germ caused 774 deaths and more than 8 cases of illness. Scientists immediately suspected that it had jumped to humans from some other organism. In May of 23, 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 25, 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. http://evolution.berkeley.edu/evolibrary/news/6_batsars
HIV is in Humans SIV is in Monkeys There are several kinds of HIV ( and 2) and each of those has several strains What can we learn from this phylogenetic tree? https://www.pbs.org/wgbh/ pages/frontline/aids/virus/ tree.html
Figure 2.9 How do they use molecular clocks to establish origination dates of HIV virus? Imagine a freezer filled with samples Index of base changes between HIV gene sequences.5..5 9 HIV Adjusted best-fit line (accounts for uncertain dates of HIV sequences Range 92 94 96 Year 98 2