Chapter 26
Phylogeny and the Tree of Life
Investigating the Tree of Life (Page 1)
Phylogenies show evolutionary relationships
Northern pygmy owl is more closely related to dinosaurs than to crocodiles
Phylogenies are inferred from morphological and molecular data
Shared characters are used to construct phylogenetic trees
Molecular clocks help track evolutionary time
Our understanding of the tree of life continues to change based on new data
Early feathered dinosaur fossils (Page 2)
Fossil specimens of oviraptorosaur Similicaudipteryx and proto-feather preserved in amber provide evidence of feather structures
Internal organs, such as the heart, rarely fossilize
Fossilized dinosaur eggs and nests support the prediction of brooding in dinosaurs
Molecular characteristics are used to determine evolutionary relationships
DNA or protein sequence information from extinct organisms is a challenge to obtain
Connective tissue protein (collagen) from fossilized soft tissue supports the bird-dinosaur grouping
Phylogenies show evolutionary relationships (Page 2)
Organisms share characteristics due to common ancestry
Phylogenies are hypotheses of the evolutionary history between different organisms
Phylogenies can be used to make predictions and test hypotheses
Practical applications of evolutionary history can be derived from phylogenies
Page 3: Organisms and Classification
Organisms are named and classified in the scientific discipline of taxonomy.
Linnaean classification is a common method used to classify organisms.
Taxonomy involves placing species in groups within more inclusive groups.
Diagrams representing evolutionary history can be used to interpret and understand taxonomy.
Common names for organisms can be misleading and cause confusion.
Biologists use Latin scientific names to avoid ambiguity in communication.
The scientific name consists of two parts: the genus and the specific epithet.
The first letter of the genus is capitalized and the entire binomial is italicized.
Linnaeus assigned over 10,000 binomials, many of which are still used today.
The hierarchical classification system groups species into increasingly inclusive categories called taxa.
Taxa include species, genus, family, order, class, phylum, kingdom, and domain.
Related genera are placed in the same family, and related families are placed in the same order.
Classifying species helps structure our understanding of the world.
Taxonomists use specific characters to define higher levels of classification.
Higher levels of classification, such as genera and families, are not italicized but capitalized.
Page 588: The Evolutionary History of Biological Diversity
Biological classification is like a postal address that identifies an organism's place in the hierarchy.
Classification involves placing organisms in kingdoms, phyla, classes, orders, families, genera, and species.
Taxonomists have determined that pines and firs are different enough to be placed in separate genera but similar enough to be grouped into the same family, Pinaceae.
Higher levels of classification are defined by specific characters chosen by taxonomists.
The evolutionary history of biological diversity is represented by the classification system.
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Larger categories in classification may not be comparable between lineages
An order of snails does not have the same diversity as an order of mammals
Some systematists propose classification based on evolutionary relationships
Names are only assigned to groups that include a common ancestor and all of its descendants
Difficulties in aligning Linnaean classification with phylogeny
Classification does not necessarily reflect evolutionary history
Birds evolved from reptiles, so Aves would be considered a subgroup of Reptilia
Linking Classification and Phylogeny
Phylogenetic tree represents the evolutionary history of a group of organisms
Branching pattern in the tree often matches how taxonomists have classified groups
Misclassification may occur when a species has lost a key feature shared by its close relatives
DNA or other evidence may lead to reclassification to reflect evolutionary history
Visualizing Phylogenetic Relationships
Phylogenetic tree represents a hypothesis about evolutionary relationships
Branch points represent common ancestors of lineages
Tree topology is the pattern of branching
Sister taxa are groups of organisms that share a common ancestor not shared by any other group
Branches of a tree can be rotated without changing the relationships shown in the tree
Basal taxon is a lineage that diverges early in the history of the group
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Phylogenetic tree visually represents the relationship between groups of organisms
Branch points represent common ancestors
Horizontal branches represent evolutionary lineages
Length of the branch is arbitrary unless specified
Frogs are most closely related to lizards and chimps
Sister taxa are groups that share a common ancestor not shared by any other group
Trees can be drawn vertically or diagonally without changing the relationships
Rotating branches around a branch point does not change the relationships conveyed by the tree
Page 6: CONCEPT CHECK 26.1
Humans share certain visual skills with beavers
Humans and beavers share levels of classification in Figure 26.4
Both have a long body, large front paws, small eyes, and a pad of thickened skin that protects the nose
Porcupines and naked mole-rats are sister taxa
New evidence suggests they share a more recent common ancestor
Redraw the tree in Figure 26.5 to include porcupines
CONCEPT 26.2: Phylogenies are inferred from morphological and molecular data
Phylogenies are inferred from morphological and molecular data
Systematists gather information about morphology, genes, and biochemistry
Features that result from common ancestry reflect evolutionary relationships
Morphological and Molecular Homologies
Phenotypic and genetic similarities due to shared ancestry are called homologies
Similarity in bone structure in mammals is an example of a morphological homology
Genes or DNA sequences are homologous if they are descended from a common ancestor
Distinguishing between homology and analogy
Complexity of characters being compared can help distinguish between homology and analogy
More similar elements in complex structures indicate a common ancestor
Similar morphologies or DNA sequences suggest closer relatedness
Evaluating Molecular Homologies
Comparing DNA molecules poses technical challenges
Sequencing and aligning comparable sequences from different species
Distantly related species have different bases at many sites and may have different lengths
Sorting Homology from Analogy
Convergent evolution can lead to similarity between organisms due to similar environmental pressures
Insertions and deletions accumulate over time, leading to differences in nucleic acid sequences
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Researchers have developed computer programs to align DNA sequences of different lengths
These programs help address problems caused by deletions or insertions in DNA sequences
Molecular comparisons reveal base substitutions and other differences in comparable genes of different species
These differences indicate divergence since their common ancestor
Similar gene sequences indicate close relation, despite morphological differences
Sequencing of over 110 billion bases of DNA has fueled the study of phylogeny
New data has supported hypotheses and clarified relationships
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Cladistics is a widely used method for inferring phylogeny from homologous characters
It uses shared ancestry as the primary criterion for classification
Clades are groups that include an ancestral species and all of its descendants
Taxa are equivalent to clades only if they are monophyletic
Monophyletic groups consist of an ancestral species and all of its descendants
Paraphyletic groups consist of an ancestral species and some, but not all, of its descendants
Polyphyletic groups include distantly related species but not their most recent common ancestor
Biologists avoid defining polyphyletic groups and reclassify members if necessary
Page 9: Inferring Phylogenies Using Derived Characters
Shared derived characters are unique to particular clades.
Derived characters are evolutionary novelties unique to a clade.
Ancestral characters can also be considered shared derived characters at deeper branch points.
By comparing members of the ingroup with each other and with the outgroup, we can determine which characters were derived at different branch points of vertebrate evolution.
A backbone can qualify as a shared derived character at a deeper branch point that distinguishes all vertebrates from other animals.
Hinged jaws are absent in the outgroup and lampreys, but present in all other members of the ingroup, indicating that hinged jaws arose in a lineage leading to all members of the ingroup except lampreys.
Lampreys are the sister taxon to the other vertebrates in the ingroup.
Maximum Parsimony and Maximum Likelihood
As the database of DNA sequences grows, building the most accurate phylogenetic tree becomes more difficult.
There are a vast number of possible ways to arrange species into a tree, making it impossible to find the most accurate tree in large data sets.
Systematists can narrow down the possibilities by applying the principles of maximum parsimony and maximum likelihood.
Figure 26.12: Constructing a phylogenetic tree
The derived characters used in this example include the amnion, hinged jaws, vertebral column, four walking legs, and hair.
The presence or absence of these characters is indicated in the character table.
Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny.
In the phylogenetic tree, the most inclusive clade for which a hinged jaw is a shared ancestral character is circled.
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Principle of maximum parsimony
Organisms resemble each other due to common ancestry
Lineages may evolve at different rates or face different environmental conditions
Morphology and molecular data in phylogenetic trees
Most parsimonious tree requires fewest evolutionary events
Maximum likelihood approach identifies most likely tree based on DNA data
Different types of phylogenetic trees
Cladograms depict branch order, no additional information from branch lengths
Phylograms depict evolutionary change or times of events
Interpreting phylogenetic trees
Trees are hypotheses about relationships between organisms
Ancestor's characteristics can be inferred from fossil record or phylogenetic bracketing
Phylogenetic trees show patterns of descent, not phenotypic similarity
Phylogenetic trees as testable predictions
Allow scientists to make predictions about biology of clade members
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Applying parsimony to a molecular systematics problem
Identify most parsimonious hypothesis with fewest evolutionary events
Steps in identifying the most parsimonious tree
Draw possible phylogenies for the species
Tabulate molecular data for the species
Compare base changes at each site in the DNA sequence
Count total base-change events for each tree
Identifying the most parsimonious tree
Total base-change events to find the tree with the fewest events
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Figure 26.14: Interpreting cladograms and phylograms
Cladograms and phylograms depict evolutionary relationships
Cladograms:
Branching order is important
Branch length and order of terminal taxa are irrelevant
Phylograms:
Branch length is proportional to the degree of genetic divergence between species
Branch lengths can be calibrated to time with nodes mapped to dates based on fossil evidence
Phylograms with branch lengths proportional to genetic change are used for scientific and forensic purposes
Squirrel-Monkey-Baboon-Gorilla-Orangutan-Chimpanzee-Human phylogenies
Constructing phylogenies using the sequence of DNA or protein sequences
Branch lengths indicate the degree of genetic divergence between pairs of taxa
Comparison of branch points with a timeline to determine when chimpanzees and humans shared a common ancestor
DNA barcoding for species identification
Dr. Paul Hebert proposed using the sequence of a mitochondrial gene as a universal "DNA barcode" for species identification
The cytochrome oxidase I (CO1) gene has shown promise as a DNA barcode for identifying species in many eukaryotic groups
Absolute branch length depends on the gene/protein sequences being compared and how the comparisons are calculated
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Figure 26.15: Research Method Using a Molecular Marker for Universal Species Identification
Identification of species can be difficult, especially when there is insufficient phenotypic diversity or morphology varies depending on conditions or life stage
Cytochrome oxidase (CO1) is used as a molecular marker for species identification
PCR is used to amplify a portion of the CO1 gene, which is then sequenced and compared to other CO1 sequences to determine species identity
The CO1 DNA barcode has been successful for species-level identification in animals
Large databases of reference barcode sequences combined with morphological analyses can be used to identify unknown species quickly and accurately
The CO1 DNA barcode approach provides a cheap, easy, and unbiased method for identifying species
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Molecular systematics can reveal evolutionary relationships that cannot be determined by nonmolecular methods
Comparisons of nucleic acids or other molecules can be used to deduce relatedness
Gene duplication plays an important role in evolution
Increases the number of genes in the genome, providing more opportunities for further evolutionary changes
Molecular techniques allow us to trace the phylogenies of gene duplications and their influence on genome evolution
Must account for repeated duplications that have resulted in gene families
Different genes can evolve at different rates
Molecular trees can represent short or long periods of time, depending on the genes used
Orthologous genes result from speciation events and occur between genes found in different species
Paralogous genes result from gene duplication and occur within a species
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Orthologous genes can only diverge after speciation has taken place
Paralogous genes can diverge within a species because they are present in more than one copy in the genome
Molecular clocks help track evolutionary time
Based on the observation that some genes and other regions of genomes appear to evolve at constant rates
The number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the species branched from their common ancestor
The number of substitutions in paralogous genes is proportional to the time since the ancestral gene was duplicated
The molecular clock of a gene can be calibrated by graphing the number of genetic differences against the dates of evolutionary branch points known from the fossil record
Humans have fewer genes than yeast, but many human genes are more versatile and can encode multiple proteins that perform different tasks in various body tissues
Page 16: Molecular Clocks and Evolutionary Relationships
Molecular clocks can be used to estimate evolutionary relationships and divergence times.
Molecular clocks are calibrated using data on the rates at which genes have evolved in different taxa.
Some portions of the genome evolve in irregular bursts that are not clocklike.
Using many genes instead of just one or a few can help average out fluctuations in evolutionary rate.
Molecular clocks can aid in understanding evolutionary relationships if used with care.
Researchers constructed molecular clocks of vertebrate evolution using sequence data for 658 nuclear genes.
Despite the broad period of time covered (nearly 600 million years), their estimates of divergence times agreed closely with fossil-based estimates.
Differences in clock speed are caused by the importance of a gene.
Genes that are essential for survival change slowly, while genes that are less critical change more quickly.
Applying a Molecular Clock: The Origin of HIV
Researchers have used a molecular clock to date the origin of HIV infection in humans.
HIV, the virus that causes AIDS, is descended from viruses that infect chimpanzees and other primates.
HIV has spread to humans more than once, resulting in multiple origins of the virus.
HIV's genetic material is made of RNA, and like other RNA viruses, it evolves quickly.
The most widespread strain in humans is HIV-1 M, which first spread to humans during the 1930s according to the molecular clock.
Potential Problems with Molecular Clocks
Molecular clocks do not always run smoothly and can have irregularities.
Many irregularities are likely the result of natural selection, with certain DNA changes favored over others.
Some genes experiencing selection can still serve as approximate markers of elapsed time.
Molecular clocks cannot be extended beyond the time span documented by the fossil record.
Fossil records are limited, and estimates of divergence times beyond the fossil record are highly uncertain.
Concept Check 26.5
A molecular clock is a tool used to estimate evolutionary relationships and divergence times. The assumption underlying the use of a molecular clock is that mutations are selectively neutral.
Numerous base changes can occur in an organism's DNA without affecting its fitness if the changes are selectively neutral.
If a molecular clock dates the divergence of two taxa at 80 million years ago, but new fossil evidence shows that the taxa diverged at least 120 million years ago, this could happen if the molecular clock is not accurately reflecting the true divergence time due to irregularities or fluctuations in evolutionary rate.
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Three-domain system: Bacteria, Archaea, and Eukarya
Bacteria: contains most prokaryotes, including bacteria related to chloroplasts and mitochondria
Archaea: diverse group of prokaryotic organisms
Eukarya: organisms with cells containing true nuclei, includes single-celled organisms, plants, fungi, and animals
HIV-1 M originated in the 1930s based on gene's rate of change
Phylogenetic tree represents the three domains and their lineages
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Polytomy: branch point where relationship among species is uncertain
Horizontal gene transfer: genes transferred between species, can occur between prokaryotes and eukaryotes
Much of the history of life is about single-celled organisms
Eukarya and Archaea are more closely related to each other than to bacteria
Horizontal gene transfer has played a key role in the history of life
Overall:
Three-domain system: Bacteria, Archaea, and Eukarya
HIV-1 M originated in the 1930s
Phylogenetic tree represents the three domains and their lineages
Polytomy: branch point where relationship among species is uncertain
Horizontal gene transfer: genes transferred between species, can occur between prokaryotes and eukaryotes
Much of the history of life is about single-celled organisms
Eukarya and Archaea are more closely related to each other than to bacteria
Horizontal gene transfer has played a key role in the history of life
Page 19: Scientific Skills Exercise
Using Protein Sequence Data to Test an Evolutionary Hypothesis
Carotenoids are colored molecules with diverse functions in organisms
Pea aphids have genes for carotenoid synthesis, unlike other animals
Evolutionary biologists hypothesize that aphids acquired these genes through horizontal gene transfer
Scientists obtained DNA sequences for carotenoid-biosynthesis genes from various species
Amino acid sequences were aligned and compared to test the hypothesis
Data from the Experiment
Amino acid sequences of carotenoid-biosynthesis genes from different organisms were compared
The sequences for the aphid, fungi, bacteria, and plant were aligned
The first 60 amino acids of one polypeptide were analyzed
Organism Alignment of Amino Acid Sequences
Acyrthosiphon (aphid): IKIIIIGSGV GGTAAAARLS KKGFQVEVYE KNSYNGGRCS IIR-HNGHRF DQGPSL--YL
Ustilago (fungus): KKVVIIGAGA GGTALAARLG RRGYSVTVLE KNSFGGGRCS LIH-HDGHRW DQGPSL--YL
Gibberella (fungus): KSVIVIGAGV GGVSTAARLA KAGFKVTILE KNDFTGGRCS LIH-NDGHRF DQGPSL--LL
Staphylococcus (bacterium): MKIAVIGAGV TGLAAAARIA SQGHEVTIFE KNNNVGGRMN QLK-KDGFTF DMGPTI--VM
Pantoea (bacterium): KRTFVIGAGF GGLALAIRLQ AAGIATTVLE QHDKPGGRAY VWQ-DQGFTF DAGPTV--IT
Arabidopsis (plant): WDAVVIGGGH NGLTAAAYLA RGGLSVAVLE RRHVIGGAAV TEEIVPGFKF SRCSYLQGLL
How the Experiment Was Done
DNA sequences for carotenoid-biosynthesis genes were obtained from different species
Amino acid sequences of the encoded polypeptides were aligned and compared
Computer analysis was used to translate the DNA sequences into amino acid sequences
Concept Check 26.6
The kingdom Monera is no longer considered a valid taxon because it was divided into two domains: Bacteria and Archaea
Phylogenies based on different genes can yield different branching patterns for the tree of life
The origin of eukaryotes is thought to have involved a fusion of organisms and extensive horizontal gene transfer
Page 20: Chapter Review
Phylograms depict evolutionary relationships with branch lengths
Branch lengths are proportional to time or amount of genetic change
Cladograms are phylogenetic trees where only the patterns of descent are meaningful
Linnaeus's binomial classification system gives organisms two-part names: a genus plus a specific epithet
Species are grouped in increasingly broad taxa in the Linnaean system
Related genera are placed in the same family
Families in orders
Orders in classes
Classes in phyla
Phyla in kingdoms
Kingdoms in domains
Systematists depict evolutionary relationships as branching phylogenetic trees
Many systematists propose that classification be based entirely on evolutionary relationships
The most parsimonious tree is the one that requires the fewest evolutionary changes
The most likely tree is the one based on the most likely pattern of changes
Well-supported phylogenetic hypotheses are consistent with a wide range of data
CONCEPT 26.1 Monophyletic group Polyphyletic group Phylogenies show evolutionary relationships (pp. 587-591)
Explain the logic of using shared derived characters to infer phylogeny
CONCEPT 26.4 Polytomy Basal taxon (pp. 599-600)
An organism's evolutionary history is documented in its genome
Orthologous genes are homologous genes found in different species as a result of speciation
Paralogous genes are homologous genes within a species that result from gene duplication
Humans and chimpanzees are sister species
CONCEPT 26.2 Phylogenies are inferred from morphological and molecular data (pp. 591-592)
When reconstructing phylogenies, it is better to compare orthologous genes
Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with very different structures and genetic sequences
CONCEPT 26.5 Molecular clocks help track evolutionary time (pp. 600-602)
To infer phylogeny, homology must be distinguished from analogy
Some regions of DNA change at a rate consistent enough to serve as a molecular clock
Computer programs are used to align comparable DNA sequences and to distinguish molecular homologies from coincidental matches between taxa that diverged long ago
CONCEPT 26.6 Our understanding of the tree of life continues to change based on new data (pp. 602-604)
A clade is a monophyletic grouping that includes an ancestral species and all of its descendants
The tree of life consists of three great domains: Bacteria, Archaea, and Eukarya
Page 21
Phylogenies based on rRNA genes suggest that eukaryotes are most closely related to archaea, while data from some other genes suggest a closer relationship to bacteria.
Genetic analyses indicate that extensive horizontal gene transfer has occurred throughout the evolutionary history of life.
Darwin suggested looking at a species' close relatives to learn what its ancestors may have been like.
Recent methods such as phylogenetic bracketing and the use of outgroups in cladistic analysis anticipate Darwin's suggestion.
The five-kingdom system was abandoned for a three-domain system due to advancements in genetic analysis and the discovery of new organisms.
Page 21-22
Draw a phylogenetic tree based on the first five characters in the table.
Place hatch marks on the tree to indicate the origin(s) of each of the six characters.
Assume that tuna and dolphins are sister species and redraw the phylogenetic tree accordingly.
How many evolutionary changes are required in each tree?
Page 22
In a comparison of birds and mammals, having four limbs is a shared ancestral character.
To apply parsimony to constructing a phylogenetic tree, choose the tree that represents the fewest evolutionary changes, in either DNA sequences or morphology.
In Figure 26.5, the taxon that descended from the same common ancestor as Muroidea is Rodentia.
Page 22-23
In a short essay, explain how genetic information along with an understanding of the process of descent with modification enables scientists to reconstruct phylogenies that extend hundreds of millions of years back in time.
Three living species X, Y, and Z share a common ancestor T, as do extinct species U and V.
A grouping that consists of species T, X, Y, and Z (but not U or V) makes up a monophyletic clade.
Based on the given tree, the statement that is not correct is that salamanders are as closely related to goats as to humans.
Page 23
Manatees are considered tetrapods even though they lack hind limbs.
Manatees likely share traits with leopards and other mammals.
Early members of the manatee lineage may have differed from today's manatees.
Page 23-24
The relative lengths of the squirrel monkey and gorilla branches in the phylogeny indicate that gorillas evolved before squirrel monkeys.
For additional practice questions, check out the Dynamic Study Modules in