CHAPTER 20 PHYLOGENY Looks like a snake. How can it be a lizard?

CHAPTER 20 PHYLOGENY Looks like a snake. How can it be a lizard?
Figure 20.1 Looks like a snake. How can it be a lizard? Figure 20.1 What kind of organism is this? CHAPTER 20 PHYLOGENY © 2016 Pearson Education, Inc.

Eastern Glass Lizard Lacks 3 traits found in all snakes
Highly mobile jaw Large number of vertebrae Short post-anal tail They also have eyelids and external ear openings © 2016 Pearson Education, Inc.

Most legless lizards burrow or live in grasslands
Snake-like body form evolved independently in more than one group of lizards Most legless lizards burrow or live in grasslands Pattern of evolution: convergent Mechanism: natural selection © 2016 Pearson Education, Inc.

Biologists reconstruct and interpret phylogenies using systematics
phylogeny - evolutionary history of a species or group of related species systematics - classifies organisms and determines their evolutionary relationships © 2016 Pearson Education, Inc. 4

Concept 20.1: Phylogenies show evolutionary relationships
Organisms share many characteristics because of common ancestry Taxonomy – system for classifying and naming of organisms Most taxonomies based on visible characteristics, ex similarities in morphology No specific intent to reflect evolutionary relationships between organisms 5

COMMON NAMES ARE CONFUSING AND VARY FROM PLACE TO PLACE
Peacock Mantis Shrimp Not a peacock Not a mantis Also…. Not a shrimp © 2016 Pearson Education, Inc.

Linnaean Taxonomic System
18th century, Carolus Linnaeus system of taxonomy based on visible similarities 2 key features: two-part names for species and hierarchical classification © 2016 Pearson Education, Inc. 7

Binomial nomenclature two-part scientific name of a species
1st part: genus (plural genera) 2nd part: specific epithet, unique for each species within genus Capitalize 1st letter of genus, italicized entire name Do not capitalize specific epithet, do italicize Both parts together name the species Scientific names are “latinized” Example: Homo sapiens – humans Quercus alba – white oak Drosophila melanogaster - fruitfly 8

Hierarchical Classification
Groups species in increasingly broad categories called taxon (pl. taxa) From most specific to most general: species, genus, family, order, class, phylum, kingdom, and domain 9

How many taxonomic units are shared by all three animals?

At what taxon do the ferrets and cats diverge?

To which animal is Mustela furo most closely related?

Linking Classification and Phylogeny
Systematists propose that classification be based entirely on evolutionary relationships Systematists depict evolutionary relationships in branching phylogenetic trees The trees may match the “nested” classification of taxonomists WHY do Linnaean classification and phylogeny often differ from each other? © 2016 Pearson Education, Inc. 13

Linking Classification and Phylogeny
WHAT DO YOU NEED TO BE ABLE TO DO? YOU must learn to represent and interpret evolutionary relationships in tree diagrams YOU must understand that organisms that are closer together on the tree are more closely related YOU must be able to interpret a variety of evidence used to inform and justify these representations INTERPRET TREES, MAKE TREES, AND PROVIDE EVIDENCE FOR CLAIMS ABOUT TREES © 2016 Pearson Education, Inc. 14

For general purposes, not much
What's the difference between a phylogeny, an evolutionary tree, a phylogenetic tree, and a cladogram? For general purposes, not much Many biologists, use these terms interchangeably — all of them essentially mean a tree structure that represents the evolutionary relationships within a group of organisms. For some biologist these terms are used in a more narrow purpose WHAT DO YOU NEED TO KNOW? © 2016 Pearson Education, Inc.

Possible evolutionary relationships within Order Carnivora
Figure 20.4 Order Family Genus Species Possible evolutionary relationships within Order Carnivora Does classification match phylogeny? Panthera Felidae Panthera pardus (leopard) Taxidea Carnivora Taxidea taxus (American badger) Mustelidae Lutra Lutra lutra (European otter) Figure 20.4 The connection between classification and phylogeny Canis latrans (coyote) Canidae Canis Canis lupus (gray wolf) © 2016 Pearson Education, Inc.

PHYLOGENETIC TREE - A HYPOTHESIS ABOUT EVOLUTIONARY RELATIONSHIPS
branch points represent the divergence of two taxa from a common ancestor; a dichotomy – division into 2 parts Sister taxa - groups that share an immediate common ancestor © 2016 Pearson Education, Inc. 17

Rooted tree has a branch to represent the most recent common ancestor of all taxa in the tree
Basal taxon diverges early in the history of a group and originates near the common ancestor of the group Polytomy - branch from which more than two groups emerge; evolutionary relationship currently unclear © 2016 Pearson Education, Inc. 18

where lineages diverge Taxon A
Figure 20.5 Branch point: where lineages diverge Taxon A Taxon B Sister taxa Taxon C Taxon D MOST RECENT COMMON ANCESTOR OF TAXON A-G A “rooted” tree Taxon E Taxon F Figure 20.5 How to read a phylogenetic tree Basal taxon Taxon G This branch point represents the common ancestor of taxa A–G. This branch point forms a polytomy: an unresolved pattern of divergence. © 2016 Pearson Education, Inc.

READ FROM BASE TO TIPS REGARDLESS OF HOW TREES IS ORIENTED
READ FROM BASE TO TIPS REGARDLESS OF HOW TREES IS ORIENTED. DO NOT READ ACROSS THE TIPS! © 2016 Pearson Education, Inc.

TREE BRANCES CAN ROTATE AROUND A BRANCH POINT WITHOUT CHANGING THEIR EVOLUTIONARY RELATIONSHIPS.
© 2016 Pearson Education, Inc.

Figure 20.UN01 WHICH OF THE TREES DEPICTS AN EVOLUTIONARY HISTORY DIFFERENT FROM THE OTHER TWO? EXPLAIN. A B D B D C C C B D A A Figure 20.UN01 Concept check 20.1, p. 399 (a) (b) (c) © 2016 Pearson Education, Inc.

HOW DOES THE TREE REPRESENT TIME
HOW DOES THE TREE REPRESENT TIME? HOW DOES THE TREE REPRESENT EXTANT SPECIES? © 2016 Pearson Education, Inc.

What We Can and Cannot Learn from Phylogenetic Trees
show patterns of descent, not phenotypic similarity – they may not resemble each other Lineages evolve at different rates Lineages faced different environmental conditions © 2016 Pearson Education, Inc. 24

do not generally indicate when a species evolved or how much change occurred in a lineage Show only most recent common ancestor IT IS possible to provide information about the dates of splits; ex. Length of line proportional to time Assume you are only seeing pattern of descent unless you are given specific information © 2016 Pearson Education, Inc. 25

Figure 20.4 Order Family Genus Species Panthera Felidae Panthera pardus (leopard) Taxidea Carnivora Taxidea taxus (American badger) Mustelidae Lutra Lutra lutra (European otter) Wolves and coyotes share a common ancestor – one did not evolve from the other Figure 20.4 The connection between classification and phylogeny Canis latrans (coyote) Canidae Canis Canis lupus (gray wolf) © 2016 Pearson Education, Inc.

Applying Phylogenies Phylogeny provides important information about similar characteristics in closely related species Phylogenetic trees based on DNA sequences can be used to infer species identities For example: A phylogeny was used to identify the species of whale from which “whale meat” originated © 2016 Pearson Education, Inc. 28

Results Minke (Southern Hemisphere) mtDNA Unknown mtDNA #1a,
Figure 20.6 Results Minke (Southern Hemisphere) mtDNA Unknown mtDNA #1a, 2, 3, 4, 5, 6, 7, 8 Minke (North Atlantic) mtDNA Unknown mtDNA #9 Humpback mtDNA Unknown mtDNA #1b Figure 20.6 Inquiry: What is the species identity of food being sold as whale meat? Blue mtDNA Unknown mtDNA #10, 11, 12, 13 Fin mtDNA © 2016 Pearson Education, Inc.

Concept 20.2: Phylogenies are inferred from morphological and molecular data
The similarities used to infer phylogenies must result from shared ancestry © 2016 Pearson Education, Inc. 30

Morphological and Molecular Homologies
Phenotypic and genetic similarities due to shared ancestry are called homologies Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences © 2016 Pearson Education, Inc. 31

Sorting Homology from Analogy
When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy Homology is similarity due to shared ancestry Analogy is similarity due to convergent evolution © 2016 Pearson Education, Inc. 32

Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages © 2016 Pearson Education, Inc. 33

Australian marsupial mole
Figure 20.7 Australian marsupial mole Figure 20.7 Convergent evolution in burrowers North American eutherian mole © 2016 Pearson Education, Inc.

Bat and bird wings are homologous as forelimbs, but analogous as functional wings
Analogous structures or molecular sequences that evolved independently are also called homoplasies Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity The more complex two similar structures are, the more likely it is that they are homologous © 2016 Pearson Education, Inc. 35

Evaluating Molecular Homologies
Molecular homologies based on degree of similarity in nucleotide sequence between taxa Computer programs analyze similarities and differences between comparable DNA segments from different organisms The program will align similar sequences Closely related species will have few difference in their nucleotide sequence © 2016 Pearson Education, Inc. 36

There are 4 nucleotide bases in DNA: Adenine, Thymine, Cytosine, Guanine

Species 1 and 2 began with identical sequences
Figure 20.8-s1 1 C A T G Species 1 and 2 began with identical sequences 2 C A T G Sequence of nucleotide bases in a short segment of DNA Figure 20.8-s1 Aligning segments of DNA (step 1) © 2016 Pearson Education, Inc.

STRANDS BEGIN TO ACCUMULATE DIFFERENCES DUE TO MUTATIONS
Figure 20.8-s2 1 C A T G 2 C A T G Deletion 1 C A T G 2 C A T G G T A Insertion STRANDS BEGIN TO ACCUMULATE DIFFERENCES DUE TO MUTATIONS Mutations are changes in base sequence of DNA Mistakes are made when DNA is replicated Environmental factors such as radiation can cause mutations Figure 20.8-s2 Aligning segments of DNA (step 2) © 2016 Pearson Education, Inc.

ORANGE HIGHLIGHTS REGIONS WHICH NO LONGER ALIGN
Figure 20.8-s3 1 C A T G 2 C A T G Deletion 1 C A T G 2 C A T G G T A Insertion 1 C A T G Figure 20.8-s3 Aligning segments of DNA (step 3) 2 C A T G ORANGE HIGHLIGHTS REGIONS WHICH NO LONGER ALIGN © 2016 Pearson Education, Inc.

Computer realigns the bases – 11 of original 12 bases have not changed
Figure 20.8-s4 1 C A T G 2 C A T G Deletion 1 C A T G 2 C A T G G T A Insertion 1 C A T G Figure 20.8-s4 Aligning segments of DNA (step 4) 2 C A T G Computer realigns the bases – 11 of original 12 bases have not changed 1 C A T G 2 C A T G © 2016 Pearson Education, Inc.

2 organisms not closely related
Figure 20.9 A molecular homoplasy 2 organisms not closely related Coincidentally have 23% of bases in common So how do we know its analogy not homology Statistics! A C G G A T A G T C C A C T A G G C A C T A T C A C C G A C A G G T C T T T G A C T A G Figure 20.9 A molecular homoplasy © 2016 Pearson Education, Inc.

Concept 20.3: Shared characters are used to construct phylogenetic trees
You have identified homologous features The ones that reflect evolutionary history You are ready to infer phylogeny from data Morphology(could come from fossils), DNA, biochemistry, behavior, ecology, biogeography, and more! You need a method to classify the organisms by common descent CLADISTICS – systematists place species into groupings called clades (Greek for branch) © 2016 Pearson Education, Inc. 44

Cladistics clade - a group of species that includes ancestor and all its descendants Clades can be nested within larger clades Not all groupings are clades Figure 20.4 the taxon Carnivora is the largest clade Felidae, Mustelidae, and Canidae are nested within the larger clade Carnivora 45

CLADES ARE monophyletic “single tribe”
Include only ancestor species & all its descendants © 2016 Pearson Education, Inc.

CLADES ARE NOT paraphyletic “beside the tribe”
Includes ancestral species but only some of the descendants © 2016 Pearson Education, Inc.

CLADES ARE NOT polyphyletic “many tribes”
Includes distantly related species but not the most recent common ancestor © 2016 Pearson Education, Inc.

Figure 20.10 (a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group A A A B Group I B B Group III C C C D D D E E Group II E Figure Monophyletic, paraphyletic, and polyphyletic groups F F F G G G Paraphyletic includes most recent common ancestor – Polyphyletic does not © 2016 Pearson Education, Inc.

Clade - monophyletic Clade - monophyletic NOT polyphyletic Clade
NOT paraphyletic Clade © 2016 Pearson Education, Inc.

Do not look alike but in same clade
Figure 20.11 Paraphyletic group Common ancestor of even-toed ungulates Other even-toed ungulates Hippopotamuses Do not look alike but in same clade Cetaceans Look alike but NOT in same clade Seals Figure Paraphyletic vs. polyphyletic groups Bears Other carnivores Polyphyletic group © 2016 Pearson Education, Inc.

Shared Ancestral and Shared Derived Characters
shared ancestral character - character originated in an ancestor of the taxon All mammals have backbones but so do all vertebrates What character could distinguish mammals from all other vertebrates? shared derived character - evolutionary novelty unique to a particular clade Hair is one character that would distinguish mammals from all other vertebrates © 2016 Pearson Education, Inc. 52

Shared Ancestral and Shared Derived Characters
A character can be both ancestral and derived, depending on the context ??????? Having a backbone can be a derived characteristic if you are trying to distinguish all vertebrates from other animals vertebrates invertebrates backbone Multicellular, heterotrophs Animal ancestor © 2016 Pearson Education, Inc. 53

Derived Characters can be used to INFER Phylogeny
Shared derived characters are unique to a clade i.e. hair is unique to the mammal clade Determine when the shared derived character first appeared in a clade Use this information to infer phylogeny © 2016 Pearson Education, Inc. 54

EXAMPLE INFER PHYLOGENY OF 5 VERTEBRATES Leopard (mammal)
Turtle (reptile) Frog (amphibian) Bass (bony fish with jaws) Lamprey (jawless fish, cartilaginous skeleton) © 2016 Pearson Education, Inc. 55

EXAMPLE Choose an outgroup Why do you need an outgroup?
A species closely related to those we are studying but diverged before the lineage that includes the species we are studying (ingroup) Why do you need an outgroup? To help determine which characters are ancestral and which are derived; characters shared by both outgroup and ingroup predate the divergence of both groups from a common ancestor © 2016 Pearson Education, Inc. 56

For example, the lancelet is a good choice: member of the chordate phylum but an invertebrate

EXAMPLE Choose derived characters that will help distinguish between the organisms you are studying It is helpful to place this in a character table Shared by all but outgroup © 2016 Pearson Education, Inc. 58

Lancelet (outgroup) Lamprey Bass Vertebral column Frog Hinged jaws
Figure Lancelet (outgroup) Lamprey Bass Vertebral column Frog Hinged jaws Figure Using derived characters to infer phylogeny (part 2: phylogenetic tree) Turtle Four limbs Amnion Leopard Hair (b) Phylogenetic tree © 2016 Pearson Education, Inc.

EXAMPLE Choose derived characters that will help distinguish between the organisms you are studying It is helpful to place this in a character table Lamprey do not have jaws but all other members do © 2016 Pearson Education, Inc. 60

EXAMPLE Choose derived characters that will help distinguish between the organisms you are studying It is helpful to place this in a character table Bass do not have 4 limbs © 2016 Pearson Education, Inc. 62

Keep in mind that the finished phylogenetic tree is a HYPOTHESIS
If you chose a different set of characters the phylogenetic tree could be different. Well that sounds kind of random! The tree is a hypothesis – an explanation on trial! © 2016 Pearson Education, Inc. 64

How do you know which tree is right?
That would be the tree that best illustrates ALL AVAILABLE EVIDENCE What would make the tree more valid? Evidence from multiple sources lead to the same conclusion. The more evidence the better our model will be. AND THAT, FOLKS, IS WHY WE CALL IT SCIENCE! © 2016 Pearson Education, Inc. 65

Phylogenetic Trees with Proportional Branch Lengths
In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence in that lineage Our previous trees gave relative time (order of events) not absolute time (association of event with a point in time) © 2016 Pearson Education, Inc. 66

Figure 20.13 Drosophila’s longer branch means more changes in DNA sequence have accumulated since divergence from the common ancestor than in the other groups. Drosophila Lancelet Zebrafish Frog Chicken Figure Branch lengths can represent genetic change. Human Mouse The gene that is being studied has evolved at different rates in different groups. © 2016 Pearson Education, Inc.

Zebrafish – longest line – length of line indicates degree of change
Figure 20.13 Among vertebrates, which lineage show the most rapid evolution of the gene? Zebrafish – longest line – length of line indicates degree of change Drosophila Lancelet Zebrafish Frog Chicken Figure Branch lengths can represent genetic change. Human Mouse © 2016 Pearson Education, Inc.

Figure 20.14 Drosophila Lancelet Zebrafish Frog This tree based on same molecular evidence as previous tree. BUT fossil evidence used to determine time of branch points Chicken Figure Branch lengths can indicate time. Human Mouse 500 400 300 200 100 Present Millions of years ago © 2016 Pearson Education, Inc.

Maximum Parsimony Systematists can never be sure of finding the best tree in a large data set If you are analyzing 50 species, there are 3X1076 ways to arrange the tree! They narrow possibilities by applying the principle of maximum parsimony (Occam’s razor) THE SIMPLEST EXPLANATION IS PROBABLY THE CORRECT EXPLANATION © 2016 Pearson Education, Inc. 71

Computer programs are used to search for trees that are parsimonious
Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely Computer programs are used to search for trees that are parsimonious © 2016 Pearson Education, Inc. 73

Three phylogenetic hypotheses:
Figure 20.15 Technique 1/C 1/C I I III II III II 1/C III II I Species I Species II Species III 1/C 1/C Three phylogenetic hypotheses: 3/A 2/T 3/A I I III I I III 2/T 3/A 4/C II III II II III II 4/C 4/C 2/T III II I III II I 3/A 4/C 2/T 4/C 2/T 3/A Site Figure Research method: applying parsimony to a problem in molecular systematics 1 2 3 4 Results Species I C T A T I I III Species II C T T C II III II Species III A G A C III II I Ancestral sequence A G T T 6 events 7 events 7 events © 2016 Pearson Education, Inc.

Technique Species I Species II Species III
Figure Technique Species I Species II Species III Three phylogenetic hypotheses: Figure Research method: applying parsimony to a problem in molecular systematics (part 1: hypotheses) I I III II III II III II I © 2016 Pearson Education, Inc.

Technique Site 1 2 3 4 Species I C T A T Species II C T T C
Figure Research method: applying parsimony to a problem in molecular systematics (part 2: table) Species III A G A C Ancestral sequence A G T T © 2016 Pearson Education, Inc.

Technique 1/C I I III 1/C II III II 1/C III II I 1/C 1/C 3/A 2/T 3/A I
Figure Technique 1/C I I III 1/C II III II 1/C III II I 1/C 1/C 3/A 2/T 3/A I I III 2/T 3/A 4/C II III II Figure Research method: applying parsimony to a problem in molecular systematics (part 3: comparison) 4/C 4/C 2/T III II I 3/A 4/C 2/T 4/C 2/T 3/A © 2016 Pearson Education, Inc.

FEWEST CHANGES Results I I III II III II III II I 6 events 7 events
Figure FEWEST CHANGES Results I I III II III II III II I Figure Research method: applying parsimony to a problem in molecular systematics (part 4: results) 6 events 7 events 7 events © 2016 Pearson Education, Inc.

Phylogenetic Trees as Hypotheses
The best hypothesized phylogenetic tree fits the most data: morphological, molecular, and fossil Phylogenetic hypotheses are modified when new evidence arises © 2016 Pearson Education, Inc. 80

Phylogenetic bracketing allows us to predict features of ancestors and their extinct descendants based on the features of closely related living descendants For example, phylogenetic bracketing allows us to infer characteristics of dinosaurs based on shared characters in modern birds and crocodiles © 2016 Pearson Education, Inc. 81

†Saurischian dinosaurs other than birds
Figure 20.16 Lizards and snakes Crocodilians †Ornithischian dinosaurs Common ancestor of crocodilians, dinosaurs, and birds †Saurischian dinosaurs other than birds Figure A phylogenetic tree of birds and their close relatives Birds © 2016 Pearson Education, Inc.

Birds and crocodiles share several features: four-chambered hearts, song, nest building, and egg brooding These characteristics likely evolved in a common ancestor and were shared by all of its descendants, including dinosaurs The fossil record supports nest building and brooding in dinosaurs © 2016 Pearson Education, Inc. 83

(a) Fossil remains of Oviraptor and eggs
Figure 20.18 Front limb Hind limb Eggs Figure Fossil support for a phylogenetic prediction: Dinosaurs built nests and brooded their eggs. (a) Fossil remains of Oviraptor and eggs (b) Artist’s reconstruction of the dinosaur’s posture based on the fossil findings © 2016 Pearson Education, Inc.

(a) Fossil remains of Oviraptor and eggs
Figure Front limb Hind limb Figure Fossil support for a phylogenetic prediction: Dinosaurs built nests and brooded their eggs. (part 1: fossil) Eggs (a) Fossil remains of Oviraptor and eggs © 2016 Pearson Education, Inc.

CHAPTER 20 PHYLOGENY Looks like a snake. How can it be a lizard?

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