Phylogeny and the Tree of Life

Phylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life

Figure 26.1 What is this organism?
A: Legless Lizard: Pygopus lepidopodus

Overview: Investigating the Tree of Life
Phylogeny is the evolutionary history of a species or group of related species. The discipline of systematics classifies organisms and determines their evolutionary relationships. Systematists use fossil, molecular, and genetic data to infer evolutionary relationships.

Figure 26.2 An unexpected family tree

Concept 26.1: Phylogenies show evolutionary relationships
Taxonomy is the ordered division and naming of organisms.

Binomial Nomenclature
In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances. Two key features of his system remain useful today: two-part names for species and hierarchical classification.

The two-part scientific name of a species is called a binomial.
The first part of the name is the genus. The second part, called the specific epithet, is unique for each species within the genus. The first letter of the genus is capitalized, and the entire species name is italicized. Both parts together name the species (not the specific epithet alone).

Hierarchical Classification
Linnaeus introduced a system for grouping species in increasingly broad categories. The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species. A taxonomic unit at any level of hierarchy is called a taxon.

Figure 26.3 Hierarchical classification
Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Figure 26.3 Hierarchical classification Phylum: Chordata Kingdom: Animalia Bacteria Domain: Eukarya Archaea

Class: Mammalia Phylum: Chordata Kingdom: Animalia Bacteria
Fig. 26-3a Class: Mammalia Phylum: Chordata Figure 26.3 Hierarchical classification Kingdom: Animalia Bacteria Domain: Eukarya Archaea

Species: Panthera pardus Genus: Panthera Family: Felidae
Fig. 26-3b Species: Panthera pardus Genus: Panthera Figure 26.3 Hierarchical classification Family: Felidae Order: Carnivora

Linking Classification and Phylogeny
Systematists depict evolutionary relationships in branching phylogenetic trees.

Canis lupus Order Family Genus Species Felidae Panthera Pantherapardus
Fig. 26-4 Order Family Genus Species Felidae Panthera Pantherapardus Taxidea Taxidea taxus Carnivora Mustelidae Lutra lutra Lutra Figure 26.4 The connection between classification and phylogeny Canis latrans Canidae Canis Canis lupus

Linnaean classification and phylogeny can differ from each other.
Systematists have proposed the PhyloCode, which recognizes only groups that include a common ancestor and all its descendents.

A phylogenetic tree represents a hypothesis about evolutionary relationships.
Each branch point represents the divergence of two species. Sister taxa are groups that share an immediate common ancestor.

A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree.
A polytomy is a branch from which more than two groups emerge.

Branch point (node) Taxon A Taxon B Sister taxa Taxon C ANCESTRAL
Figure 26.5 How to read a phylogenetic tree Branch point (node) Taxon A Taxon B Sister taxa Taxon C ANCESTRAL LINEAGE Taxon D Taxon E Figure 26.5 How to read a phylogenetic tree Taxon F Common ancestor of taxa A–F Polytomy

What We Can and Cannot Learn from Phylogenetic Trees
Phylogenetic trees do show patterns of descent Phylogenetic trees do not indicate when species evolved or how much genetic change occurred in a lineage. It shouldn’t be assumed that a taxon evolved from the taxon next to it.

Applying Phylogenies Phylogeny provides important information about similar characteristics in closely related species. A phylogeny was used to identify the species of whale from which “whale meat” originated.

Fig. 26-6 RESULTS Minke (Antarctica) Minke (Australia) Unknown #1a, 2, 3, 4, 5, 6, 7, 8 Minke (North Atlantic) Unknown #9 Humpback (North Atlantic) Humpback (North Pacific) Unknown #1b Gray Blue (North Atlantic) Figure 26.6 What is the species identity of food being sold as whale meat? Blue (North Pacific) Unknown #10, 11, 12 Unknown #13 Fin (Mediterranean) Fin (Iceland)

RESULTS Minke (Antarctica) Minke (Australia) Unknown #1a,
Fig. 26-6a RESULTS Minke (Antarctica) Minke (Australia) Unknown #1a, 2, 3, 4, 5, 6, 7, 8 Minke (North Atlantic) Figure 26.6 What is the species identity of food being sold as whale meat? Unknown #9

Humpback (North Atlantic) Humpback (North Pacific) Unknown #1b Gray
Fig. 26-6b Humpback (North Atlantic) Humpback (North Pacific) Unknown #1b Gray Figure 26.6 What is the species identity of food being sold as whale meat? Blue (North Atlantic) Blue (North Pacific)

Unknown #10, 11, 12 Unknown #13 Fin (Mediterranean) Fin (Iceland)
Fig. 26-6c Unknown #10, 11, 12 Unknown #13 Fin (Mediterranean) Fin (Iceland) Figure 26.6 What is the species identity of food being sold as whale meat?

Phylogenies of anthrax bacteria helped researchers identify the source of a particular strain of anthrax.

Fig. 26-UN1 A B D B D C C C B D A A (a) (b) (c)

Concept 26.2: Phylogenies are inferred from morphological and molecular data.
To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms.

Morphological and Molecular Homologies
Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences.

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.

Fig. 26-7 Figure 26.7 Convergent evolution of analogous burrowing characteristics

Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages.

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.

Evaluating Molecular Homologies
Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms.

Deletion Insertion 1 2 3 4 Fig. 26-8
Figure 26.8 Aligning segments of DNA 4

Fig. 26-8a 1 Deletion 2 Figure 26.8 Aligning segments of DNA Insertion

Fig. 26-8b 3 4 Figure 26.8 Aligning segments of DNA

It is also important to distinguish homology from analogy in molecular similarities.
Mathematical tools help to identify molecular homoplasies, or coincidences. Molecular systematics use DNA and other molecular data to determine evolutionary relationships.

Figure 26.9 A molecular homoplasy

Concept 26.3: Shared characters are used to construct phylogenetic trees.
Once homologous characters have been identified, they can be used to infer a phylogeny.

Cladistics Cladistics groups organisms by common descent. A clade is a group of species that includes an ancestral species and all its descendants. Clades can be nested in larger clades, but not all groupings of organisms qualify as clades.

A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants.

(a) Monophyletic group (clade) (b) Paraphyletic group
Fig A A A B Group I B B C C C D D D E E Group II E Group III F F F G G G Figure Monophyletic, paraphyletic, and polyphyletic groups (a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group

(a) Monophyletic group (clade)
Fig a A B Group I C D E F Figure 26.10a Monophyletic, paraphyletic, and polyphyletic groups G (a) Monophyletic group (clade)

A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants.

(b) Paraphyletic group
Fig b A B C D Group II E F Figure 26.10b Monophyletic, paraphyletic, and polyphyletic groups G (b) Paraphyletic group

A polyphyletic grouping consists of various species that lack a common ancestor.

(c) Polyphyletic group
Fig c A B C D Group III E F Figure 26.10c Monophyletic, paraphyletic, and polyphyletic groups G (c) Polyphyletic group

Shared Ancestral and Shared Derived Characters
In comparison with its ancestor, an organism has both shared and different characteristics.

A shared ancestral character is a character that originated in an ancestor of the taxon.
A shared derived character is an evolutionary novelty unique to a particular clade. A character can be both ancestral and derived, depending on the context.

Inferring Phylogenies Using Derived Characters
When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared.

Figure 26.11 Constructing a phylogenetic tree
TAXA Lancelet (outgroup) (outgroup) Lancelet Salamander Lamprey Leopard Lamprey Tuna Turtle Vertebral column (backbone) Tuna 1 1 1 1 1 Vertebral column Hinged jaws 1 1 1 1 Salamander Hinged jaws CHARACTERS Four walking legs 1 1 1 Turtle Four walking legs Amniotic (shelled) egg 1 1 Figure Constructing a phylogenetic tree Amniotic egg Leopard Hair 1 Hair (a) Character table (b) Phylogenetic tree

Amniotic (shelled) egg 1 1
Fig a TAXA (outgroup) Lancelet Salamander Lamprey Leopard Tuna Turtle Vertebral column (backbone) 1 1 1 1 1 Hinged jaws 1 1 1 1 CHARACTERS Four walking legs 1 1 1 Figure Constructing a phylogenetic tree Amniotic (shelled) egg 1 1 Hair 1 (a) Character table

Vertebral column Hinged jaws Four walking legs Amniotic egg Lancelet
Fig b Lancelet (outgroup) Lamprey Tuna Vertebral column Salamander Hinged jaws Figure Constructing a phylogenetic tree Turtle Four walking legs Amniotic egg Leopard Hair (b) Phylogenetic tree

An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied. Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics.

Homologies shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor.

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.

Figure 26.12 Branch lengths can indicate relative amounts of genetic change
Drosophila Lancelet Zebrafish Frog Chicken Human Figure Branch lengths can indicate relative amounts of genetic change Mouse

In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record.

Figure 26.13 Branch lengths can indicate time
Drosophila Lancelet Zebrafish Frog Chicken Human Figure Branch lengths can indicate time Mouse PALEOZOIC MESOZOIC CENOZOIC 542 251 65.5 Present Millions of years ago

Maximum Parsimony and Maximum Likelihood
Systematists can never be sure of finding the best tree in a large data set. They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood.

Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely. The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events.

Figure 26.14 Trees with different likelihoods
Human Mushroom Tulip Human 30% 40% Mushroom 40% Tulip Figure Trees with different likelihoods (a) Percentage differences between sequences 15% 5% 5% Figure Trees with different likelihoods 15% 15% 10% 20% 25% Tree 1: More likely Tree 2: Less likely (b) Comparison of possible trees

Human Mushroom Tulip Human 30% 40% Mushroom 40% Tulip Figure Trees with different likelihoods (a) Percentage differences between sequences

15% 5% 5% 15% 15% 10% 20% 25% Figure Trees with different likelihoods Tree 1: More likely Tree 2: Less likely (b) Comparison of possible trees

Computer programs are used to search for trees that are parsimonious and likely.

Three phylogenetic hypotheses: I I III
Figure Applying parsimony to a problem in molecular systematics Species I Species II Species III Three phylogenetic hypotheses: Figure Applying parsimony to a problem in molecular systematics I I III II III II III II I

Figure 26.15 Applying parsimony to a problem in molecular systematics
Site 1 2 3 4 1/C Species I C T A T I I III 1/C Species II C T T C II III II 1/C Species III A G A C III II I 1/C 1/C Ancestral sequence A G T T Figure Applying parsimony to a problem in molecular systematics

Site 1 2 3 4 1/C Species I C T A T I I III 1/C Species II C T T C II III II 1/C Species III A G A C III II I 1/C 1/C Ancestral sequence A G T T 3/A 2/T 3/A I I III 2/T 3/A 4/C II III II 4/C 4/C 2/T III II I 3/A 4/C 2/T 4/C 2/T 3/A Figure Applying parsimony to a problem in molecular systematics

Site 1 2 3 4 1/C Species I C T A T I I III 1/C Species II C T T C II III II 1/C Species III A G A C III II I 1/C 1/C Ancestral sequence A G T T 3/A 2/T 3/A I I III 2/T 3/A 4/C II III II 4/C 4/C 2/T III II I 3/A 4/C 2/T 4/C 2/T 3/A Figure Applying parsimony to a problem in molecular systematics I I III II III II III II I 6 events 7 events 7 events

Phylogenetic Trees as Hypotheses
The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil. Phylogenetic bracketing allows us to predict features of an ancestor from features of its descendents.

Lizards and snakes Crocodilians Ornithischian dinosaurs Common
Figure A phylogenetic tree of birds and their close relatives Lizards and snakes Crocodilians Ornithischian dinosaurs Common ancestor of crocodilians, dinosaurs, and birds Saurischian dinosaurs lFigure A phylogenetic tree of birds and their close relatives Birds

Animation: The Geologic Record
This has been applied to infer features of dinosaurs from their descendents: birds and crocodiles. Animation: The Geologic Record

(a) Fossil remains of Oviraptor and eggs
Front limb Hind limb Figure Fossils support a phylogenetic prediction: Dinosaurs built nests and brooded their eggs Eggs (a) Fossil remains of Oviraptor and eggs Figure Fossils support a phylogenetic prediction: Dinosaurs built nests and brooded their eggs (b) Artist’s reconstruction of the dinosaur’s posture

(a) Fossil remains of Oviraptor and eggs
Figure Fossils support a phylogenetic prediction: Dinosaurs built nests and brooded their eggs Front limb Hind limb Figure Fossils support a phylogenetic prediction: Dinosaurs built nests and brooded their eggs Eggs (a) Fossil remains of Oviraptor and eggs

(b) Artist’s reconstruction of the dinosaur’s posture
Figure Fossils support a phylogenetic prediction: Dinosaurs built nests and brooded their eggs Figure Fossils support a phylogenetic prediction: Dinosaurs built nests and brooded their eggs (b) Artist’s reconstruction of the dinosaur’s posture

Concept 26.4: An organism’s evolutionary history is documented in its genome.
Comparing nucleic acids or other molecules to infer relatedness is a valuable tool for tracing organisms’ evolutionary history. DNA that codes for rRNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago. mtDNA evolves rapidly and can be used to explore recent evolutionary events .

Gene Duplications and Gene Families
Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes. Like homologous genes, duplicated genes can be traced to a common ancestor.

Orthologous genes are found in a single copy in the genome and are homologous between species.
They can diverge only after speciation occurs.

Paralogous genes result from gene duplication, so are found in more than one copy in the genome.
They can diverge within the clade that carries them and often evolve new functions.

Figure 26.18 How two types of homologous genes originate
Ancestral gene Ancestral species Figure How two types of homologous genes originate Speciation with divergence of gene Orthologous genes Species A Species B (a) Orthologous genes Species A Figure How two types of homologous genes originate Gene duplication and divergence Paralogous genes Species A after many generations (b) Paralogous genes

Speciation with divergence of gene
Fig a Ancestral gene Ancestral species Speciation with divergence of gene Figure How two types of homologous genes originate Orthologous genes Species A Species B (a) Orthologous genes

Gene duplication and divergence
Fig b Species A Gene duplication and divergence Figure How two types of homologous genes originate Paralogous genes Species A after many generations (b) Paralogous genes

Genome Evolution Orthologous genes are widespread and extend across many widely varied species. Gene number and the complexity of an organism are not strongly linked. Genes in complex organisms appear to be very versatile and each gene can perform many functions.

Concept 26.5: Molecular clocks help track evolutionary time.
To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time.

Molecular Clocks A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change. In orthologous genes, nucleotide substitutions are proportional to the time since they last shared a common ancestor. In paralogous genes, nucleotide substitutions are proportional to the time since the genes became duplicated.

Molecular clocks are calibrated against branches whose dates are known from the fossil record.

Divergence time (millions of years)
Figure A molecular clock for mammals 90 60 Number of mutations 30 Figure A molecular clock for mammals 30 60 90 120 Divergence time (millions of years)

Neutral Theory Neutral theory states that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection. It states that the rate of molecular change in these genes and proteins should be regular like a clock.

Difficulties with Molecular Clocks
The molecular clock does not run as smoothly as neutral theory predicts. Irregularities result from natural selection in which some DNA changes are favored over others. Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty. The use of multiple genes may improve estimates.

Applying a Molecular Clock: The Origin of HIV
Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates. Comparison of HIV samples throughout the epidemic shows that the virus evolved in a very clocklike way. Application of a molecular clock to one strain of HIV suggests that that strain spread to humans during the 1930s.

Figure 26.20 Dating the origin of HIV-1 M with a molecular clock
0.20 Figure Dating the origin of HIV-1 M with a molecular clock 0.15 Computer model of HIV Index of base changes between HIV sequences 0.10 Range Figure Dating the origin of HIV-1 M with a molecular clock 0.05 1900 1920 1940 1960 1980 2000 Year

Concept 26.6: New information continues to revise our understanding of the tree of life.
Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics.

From Two Kingdoms to Three Domains
Early taxonomists classified all species as either plants or animals. Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia. More recently, the three-domain system has been adopted: Bacteria, Archaea, and Eukarya. The three-domain system is supported by data from many sequenced genomes. Animation: Classification Schemes

Figure 26.21 The three domains of life
EUKARYA Land plants Dinoflagellates Green algae Forams Ciliates Diatoms Red algae Amoebas Cellular slime molds Euglena Trypanosomes Animals Leishmania Fungi Sulfolobus Green nonsulfur bacteria Thermophiles (Mitochondrion) Figure The three domains of life Spirochetes Halophiles Chlamydia COMMON ANCESTOR OF ALL LIFE Green sulfur bacteria BACTERIA Methanobacterium Cyanobacteria ARCHAEA (Plastids, including chloroplasts)

BACTERIA Green nonsulfur bacteria (Mitochondrion) Spirochetes
Figure The three domains of life Green nonsulfur bacteria (Mitochondrion) Spirochetes Chlamydia COMMON ANCESTOR OF ALL LIFE Green sulfur bacteria Figure The three domains of life BACTERIA Cyanobacteria (Plastids, including chloroplasts)

ARCHAEA Sulfolobus Thermophiles Halophiles Methanobacterium
Figure The three domains of life Sulfolobus Thermophiles Halophiles Figure The three domains of life Methanobacterium ARCHAEA

EUKARYA Dinoflagellates Land plants Forams Ciliates Red algae Amoebas
Fig c Figure The three domains of life EUKARYA Land plants Dinoflagellates Green algae Forams Ciliates Diatoms Red algae Amoebas Cellular slime molds Euglena Trypanosomes Animals Leishmania Figure The three domains of life Fungi

A Simple Tree of All Life
The tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria. The tree of life is based largely on rRNA genes, as these have evolved slowly.

There have been substantial interchanges of genes between organisms in different domains.
Horizontal gene transfer is the movement of genes from one genome to another. Horizontal gene transfer complicates efforts to build a tree of life.

Bacteria Eukarya Archaea 4 3 2 1 Billions of years ago
Figure The role of horizontal gene transfer in the history of life Bacteria Eukarya Archaea Figure The role of horizontal gene transfer in the history of life 4 3 2 1 Billions of years ago

Is the Tree of Life Really a Ring?
Some researchers suggest that eukaryotes arose as an endosymbiosis between a bacterium and archaean. If so, early evolutionary relationships might be better depicted by a ring of life instead of a tree of life.

Eukarya Bacteria Archaea Figure 26.23 A ring of life

Node Taxon A Taxon B Sister taxa Taxon C Taxon D Taxon E Most recent
Fig. 26-UN2 Graphics Node Taxon A Taxon B Sister taxa Taxon C Taxon D Taxon E Most recent common ancestor Polytomy Taxon F

Monophyletic group A A A B B B C C C D D D E E E F F F G G G
Fig. 26-UN3 Graphics Monophyletic group A A A B B B C C C D D D E E E F F F G G G Paraphyletic group Polyphyletic group

Fig. 26-UN4 Graphics Salamander Lizard Goat Human

Fig. 26-UN5 Graphics

Fig. 26-UN10a Graphics

Fig. 26-UN10b Graphics

You should now be able to:
Explain the justification for taxonomy based on a PhyloCode. Explain the importance of distinguishing between homology and analogy. Distinguish between the following terms: monophyletic, paraphyletic, and polyphyletic groups; shared ancestral and shared derived characters; orthologous and paralogous genes.

Define horizontal gene transfer and explain how it complicates phylogenetic trees.
Explain molecular clocks and discuss their limitations.

Phylogeny and the Tree of Life

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