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?

Overview: Investigating the Tree of Life
Legless lizards have evolved independently in several different groups © 2011 Pearson Education, Inc.

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 © 2011 Pearson Education, Inc.

Figure 26.2 Figure 26.2 An unexpected family tree.

Concept 26.1: Phylogenies show evolutionary relationships
Taxonomy is the ordered division and naming of organisms © 2011 Pearson Education, Inc.

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 © 2011 Pearson Education, Inc.

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) © 2011 Pearson Education, Inc.

Damn King Philip Can Order Freaking Good Salmon Species:
Figure 26.3 Damn King Philip Can Order Freaking Good Salmon Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Figure 26.3 Linnaean classification. Phylum: Chordata Kingdom: Animalia Domain: Bacteria Domain: Archaea Domain: Eukarya

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 Taxonomy is concerned with taxa. Nomenclature is concerned with names. © 2011 Pearson Education, Inc.

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

Linking Classification and Phylogeny
Systematists depict evolutionary relationships in branching phylogenetic trees © 2011 Pearson Education, Inc.

Order Family Genus Species Panthera pardus (leopard) Felidae Panthera
Figure 26.4 Order Family Genus Species Panthera pardus (leopard) Felidae Panthera Taxidea taxus (American badger) Taxidea Carnivora Mustelidae Lutra lutra (European otter) Lutra Figure 26.4 The connection between classification and phylogeny. Canis latrans (coyote) Canidae Canis Canis lupus (gray wolf)

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 descendants (Its current version is specifically designed to regulate the naming of clades) © 2011 Pearson Education, Inc.

Each branch point represents the divergence of two species
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 © 2011 Pearson Education, Inc.

- Snake and lizard are sister taxa
The branches leading to them meet at node 1 (red arrow) to form clade a Bird and crocodile are sister taxa (members of clade b, who share node 2,as their common ancestor) According to this cladogram, a bird or crocodile are equally closely related to a lizard (or a snake), because they are related by way of the common ancestor at node 3. - Clade a and clade b are sister taxa

A polytomy is a branch from which more than two groups emerge
A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree A basal taxon diverges early in the history of a group and originates near the common ancestor of the group A polytomy is a branch from which more than two groups emerge © 2011 Pearson Education, Inc.

where lineages diverge Taxon A
Figure 26.5 Branch point: where lineages diverge Taxon A Taxon B Sister taxa Taxon C Taxon D Taxon E ANCESTRAL LINEAGE Taxon F Figure 26.5 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.

What We Can and Cannot Learn from Phylogenetic Trees
Phylogenetic trees show patterns of descent, not phenotypic similarity Phylogenetic trees do not indicate when species evolved or how much change occurred in a lineage It should not be assumed that a taxon evolved from the taxon next to it © 2011 Pearson Education, Inc.

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 © 2011 Pearson Education, Inc.

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

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 © 2011 Pearson Education, Inc.

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 © 2011 Pearson Education, Inc.

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 © 2011 Pearson Education, Inc.

Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages © 2011 Pearson Education, Inc.

Figure 26.7 Figure 26.7 Convergent evolution of analogous burrowing characteristics.

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 © 2011 Pearson Education, Inc.

Evaluating Molecular Homologies
Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms © 2011 Pearson Education, Inc.

Figure 1 1 2 Figure 26.8 Aligning segments of DNA.

1 1 2 Deletion 2 1 2 Insertion Figure 26.8-2
Figure 26.8 Aligning segments of DNA.

1 1 2 Deletion 2 1 2 Insertion 3 1 2 Figure 26.8-3
Figure 26.8 Aligning segments of DNA. 2

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

It is also important to distinguish homology from analogy in molecular similarities
Mathematical tools help to identify molecular homoplasies, or coincidences Molecular systematics uses DNA and other molecular data to determine evolutionary relationships © 2011 Pearson Education, Inc.

Figure 26.9 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 © 2011 Pearson Education, Inc.

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 © 2011 Pearson Education, Inc.

A taxon is equivalent to a clade ONLY if it is
monophyletic

A polyphyletic (Many tribes) grouping consists of various species with different ancestors
© 2011 Pearson Education, Inc.

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

Shared Ancestral and Shared Derived Characters
In comparison with its ancestor, an organism has both shared and different characteristics © 2011 Pearson Education, Inc.

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 © 2011 Pearson Education, Inc.

Inferring Phylogenies Using Derived Characters
When inferring evolutionary relationships, it is useful to know in which clade a shared derived character “first” appeared © 2011 Pearson Education, Inc.

Figure 26.11 TAXA (outgroup) Lancelet Lamprey Leopard Bass Frog Turtle Vertebral column (backbone) 1 1 1 1 1 Hinged jaws 1 1 1 1 Four walking legs CHARACTERS 1 1 1 Amnion 1 1 Figure Constructing a phylogenetic tree. Hair 1 (a) Character table

Figure 26.11 TAXA Lancelet (outgroup) (outgroup) Lancelet Lamprey Lamprey Leopard Bass Frog Turtle Vertebral column (backbone) 1 1 1 1 1 Bass Vertebral column Hinged jaws 1 1 1 1 Frog Hinged jaws Four walking legs CHARACTERS 1 1 1 Turtle Four walking legs Amnion 1 1 Figure Constructing a phylogenetic tree. Amnion Hair 1 Leopard Hair (a) Character table (b) Phylogenetic tree

The outgroup is a group that has diverged before the ingroup
An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied The outgroup is a group that has diverged before the ingroup Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics © 2011 Pearson Education, Inc.

C D A B C D Root A B A B C D is Outgroup C D A B Root

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 Lancelet Drosophila Zebrafish Frog Chicken Human Mouse © 2011 Pearson Education, Inc.

Phylogenetic Trees with Proportional Branch Lengths
In other trees, branch length can represent chronological time (sequence of events), and branching points can be determined from the fossil record Mouse Human Chicken Frog Zebrafish Lancelet Drosophila Present CENOZOIC MESOZOIC PALEOZOIC Millions of years ago 542 251 65.5 © 2011 Pearson Education, Inc.

So length of the branched can be proportional to “time” or
“number of changes” (ex, genetic changes)

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 © 2011 Pearson Education, Inc.

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 © 2011 Pearson Education, Inc.

Maximum parsimony: In general usage, parsimony means to be economical or thrifty. It is generally thought that a simpler, more parsimonious chain of events is more likely to occur than a more complicated, less parsimonious chain of events.

(a) Percentage differences between sequences
Figure 26.14 Human Mushroom Tulip Human 30% 40% Mushroom 40% Tulip (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

Number of possible trees for different number of species:
Computer programs are used to search for trees that are parsimonious and likely Number of possible trees for different number of species: # of Species # of possible trees 4 1x3= 3 5 1x3x5= 15 6 1x3x5x7= 105 7 1x3x5x7x9= 945 8 1x3x5x7x9x11= 10,395 9 1x3x5x7x9x11x13= 135,135 10 1x3x5x7x9x11x13x15= 2,025,027 © 2011 Pearson Education, Inc.

1 3 4 RESULTS    1/C 3/A 2/T 4/C 6 events 7 events 2 Species 
Ancestral sequence 1 3 4 Site C A T G Species  Species  Species  Three phylogenetic hypotheses: 1 3 TECHNIQUE    Figure Research Method: Applying parsimony to a problem in molecular systematics

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 descendants For example, phylogenetic bracketing allows us to infer characteristics of dinosaurs © 2011 Pearson Education, Inc.

Lizards and snakes Crocodilians Ornithischian dinosaurs Common
Figure 26.16 Lizards and snakes Crocodilians Ornithischian dinosaurs Common ancestor of crocodilians, dinosaurs, and birds Saurischian dinosaurs Figure A phylogenetic tree of birds and their close relatives. Birds

The fossil record supports nest building and brooding in dinosaurs
Birds and crocodiles share several features: four-chambered hearts, song, nest building, and 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 © 2011 Pearson Education, Inc.

(b) Artist’s reconstruction of the dinosaur’s
Figure 26.17 Front limb Hind limb Figure Fossil support for 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 based on the fossil findings

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 approach 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 © 2011 Pearson Education, Inc.

Gene Duplications and Gene Families
Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes Repeated gene duplications result in gene families Like homologous genes, duplicated genes can be traced to a common ancestor © 2011 Pearson Education, Inc.

They can diverge only after speciation occurs
Orthologous genes are found in a single copy in the genome and are homologous between species They can diverge only after speciation occurs © 2011 Pearson Education, Inc.

Speciation with divergence of gene
Figure 26.18a Formation of orthologous genes: a product of speciation Ancestral gene Ancestral species Speciation with divergence of gene Figure Two types of homologous genes. Orthologous genes Species A Species B

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 © 2011 Pearson Education, Inc.

Formation of paralogous genes: within a species
Figure 26.18b Formation of paralogous genes: within a species Ancestral gene Species C Gene duplication and divergence Figure Two types of homologous genes. Paralogous genes Species C after many generations

Speciation with divergence of gene
Figure 26.18 Formation of orthologous genes: a product of speciation Formation of paralogous genes: within a species Ancestral gene Ancestral gene Ancestral species Species C Speciation with divergence of gene Gene duplication and divergence Figure Two types of homologous genes. Orthologous genes Paralogous genes Species A Species B Species C after many generations

Genome Evolution Orthologous genes are widespread and extend across many widely varied species For example, humans and mice diverged about 65 million years ago, and 99% of our genes are orthologous © 2011 Pearson Education, Inc.

Gene number and the complexity of an organism are not strongly linked
For example, humans have only four times as many genes as yeast, a single-celled eukaryote Genes in complex organisms appear to be very versatile, and each gene can perform many functions © 2011 Pearson Education, Inc.

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 © 2011 Pearson Education, Inc.

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 © 2011 Pearson Education, Inc.

Individual genes vary in how clocklike they are
Molecular clocks are calibrated against branches whose dates are known from the fossil record Individual genes vary in how clocklike they are © 2011 Pearson Education, Inc.

Divergence time (millions of years)
Figure 26.19 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 is not influenced by natural selection It states that the rate of molecular change in these genes and proteins should be regular like a clock © 2011 Pearson Education, Inc.

Problems 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 © 2011 Pearson Education, Inc.

Applying a Molecular Clock: The Origin of HIV
Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates HIV spread to humans more than once Comparison of HIV samples 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 © 2011 Pearson Education, Inc.

Index of base changes between HIV gene sequences
Figure 26.20 0.20 0.15 HIV Index of base changes between HIV gene sequences 0.10 Range Adjusted best-fit line (accounts for uncertain dates of HIV sequences) 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 © 2011 Pearson Education, Inc.

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 © 2011 Pearson Education, Inc.

Eukarya Bacteria Archaea Figure 26.21
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)

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 © 2011 Pearson Education, Inc.

Horizontal gene transfer complicates efforts to build a tree of life
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 occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms Horizontal gene transfer complicates efforts to build a tree of life © 2011 Pearson Education, Inc.

Two major episodes of horizontal gene transfer
Gene transfer between mitochondria ancestor and ancestor of Eukaryotes Gene transfer between chloroplast ancestor and ancestor of green plants Bacteria Eukarya Figure The role of horizontal gene transfer in the history of life. Archaea 4 3 2 1 Billions of years ago

Is the Tree of Life Really a Ring?
Some researchers suggest that eukaryotes arose as a fusion 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 © 2011 Pearson Education, Inc.

Figure 26.23 Archaea Eukarya Figure A ring of life. Bacteria

A B D B D C C C B D A A (a) (b) (c) Figure 26.UN01
Figure 26.UN01 Concept Check 26.1, question 3 (a) (b) (c)

Branch point Taxon A Most recent common ancestor Taxon B Sister taxa
Figure 26.UN02 Branch point Taxon A Most recent common ancestor Taxon B Sister taxa Taxon C Taxon D Taxon E Figure 26.UN02 Summary figure, Concept 26.1 Polytomy Taxon F Taxon G Basal taxon

Monophyletic group Polyphyletic group A A A B B B C C C D D D E E E F
Figure 26.UN03 Monophyletic group Polyphyletic group A A A B B B C C C D D D E E E Figure 26.UN03 Summary figure, Concept 26.3 F F F G G G Paraphyletic group

Salamander Lizard Goat Human Figure 26.UN04
Figure 26.UN04 Test Your Understanding, question 5 Human

Figure 26.UN05 Figure 26.UN05 Test Your Understanding, question 9

Figure 26.UN06 Figure 26.UN06 Appendix A: answer to Figure 26.5 legend question

Figure 26.UN07 Figure 26.UN07 Appendix A: answer to Figure legend question

Figure 26.UN08 Figure 26.UN08 Appendix A: answer to Concept Check 26.1, question 4

Figure 26.UN11 Figure 26.UN11 Appendix A: answer to Test Your Understanding, question 9

Phylogeny and the Tree of Life

Similar presentations

Presentation on theme: "Phylogeny and the Tree of Life"— Presentation transcript:

Similar presentations

About project

Feedback

Log in

Auth with social network:

Phylogeny and the Tree of Life

Similar presentations

Presentation on theme: "Phylogeny and the Tree of Life"— Presentation transcript:

Similar presentations

About project

Feedback