Campbell Biology Chapter 26 Review: Phylogeny and the Tree of Life

26.1 Naming, ranking and reading trees

pp. 537–540

On the AP exam? Yes

Topic 7.9 tests reading trees: what a node means, which groups are sister taxa and what a tree can't tell you. Scientific names and the Linnaean ranks are background, so you won't have to list the ranks.

In the course: Topic 7.9 Phylogeny (notes, videos and more questions)

Key points

Everyday names cause mix-ups: one name can cover several species, and one species can have many local names. So biologists give each species a two-part Latin name, its genus followed by a second word that's unique within that genus, like Acer rubrum for red maple.
In print, the genus is capitalized, the second word is lowercase, and the whole name is in italics.
The Linnaean system nests groups inside bigger groups: species, genus, family, order, class, phylum, kingdom and domain. A named group at any of these levels is a taxon. Ranks are human decisions, so an order of insects isn't equal to an order of mammals in any measurable way.
A phylogenetic tree is a hypothesis about evolutionary history. The tips are taxa, and each branch point (node) stands for the last ancestor shared by everything beyond it.
Sister taxa share a common ancestor that no other group on the tree shares. A polytomy is a node with three or more branches, which means the order of those splits isn't known yet. A basal taxon is a lineage that splits off near the root.
To judge relatedness, trace back to where two lineages meet. You can spin branches around any node without changing the tree, so how close two tips sit on the page means nothing.
A tree shows who descends from whom, not who looks alike. Unless the branch lengths are labeled as time, it doesn't give ages, and a tip never evolved from the tip beside it: both came from an ancestor that's usually extinct.

Key terms (13)

phylogeny: The branching history of a set of related species: who split from whom, and in what order.
systematics: The field that classifies organisms and works out how they're related, using evidence from fossils, anatomy and DNA.
taxonomy: The part of biology that names organisms and sorts them into groups.
binomial: A species' two-part scientific name: the genus first, then a word that picks out one species within that genus.
genus: The rank just above species. Species in the same genus share the first word of their scientific names.
specific epithet: The second word of a scientific name. Only one species in a genus can use a given epithet.
taxon: Any named group of organisms at any level, from one species to a whole domain. The plural is taxa.
phylogenetic tree: A branching diagram showing a hypothesis about how a set of organisms are related through common ancestors.
node (branch point): A spot where a tree splits. It stands for the latest ancestor shared by all the lineages beyond it.
sister taxa: Two groups that are closer to each other than to anything else on a tree, because they share an ancestor no other group shares.
rooted tree: A tree with a node that stands for the common ancestor of every taxon on it, so you can tell earlier splits from later ones.
basal taxon: A lineage that branches off early, close to the root of the tree.
polytomy: A node with three or more branches coming out of it. It means scientists can't yet tell in what order those lineages split.

Check yourself: 26.1 Naming, ranking and reading trees

4 questions on 26.1 Naming, ranking and reading trees. Pick an answer to see if you got it, and why.

Question 1 of 4

A field guide lists the white oak as Quercus alba and the northern red oak as Quercus rubra. Based on the names alone, what can you conclude?

Question 2 of 4

In a phylogenetic tree of four living species, the lineage leading to species P splits off at the root. The rest of the tree splits into species Q and a branch that later divides into species R and species S. Which statement is supported by the tree?

Question 3 of 4

A student says that species J and K must be close relatives because their names are printed next to each other at the tips of a tree. Which response best corrects the student?

Question 4 of 4

A tree of five coral species shows a single node from which four of the species branch at once. What does this most likely mean?

0 of 4 answered

26.2 Homology, analogy and DNA evidence

pp. 540–542

On the AP exam? Yes

Topic 7.6 tests homologous structures and DNA or protein comparisons as evidence, and convergent evolution comes up in Topic 7.10. How sequences are aligned, and the word homoplasy, are background.

In the course: Topic 7.6 Evidence of Evolution, Topic 7.9 Phylogeny, Topic 7.10 Speciation (notes, videos and more questions)

Key points

Only similarities inherited from a common ancestor, called homologies, tell you about relationships. They can be in body structure, development, proteins or DNA.
Usually, the more alike two species are in structure and DNA, the more closely related they are. But body form and genes can change at different speeds. Related species can look very different after a fast burst of change, while their DNA stays similar.
Analogy is similarity that evolved separately in different lineages, usually because they faced similar challenges (convergent evolution). The camera-like eyes of octopuses and vertebrates are an example. Analogous traits can trick you into grouping unrelated species.
Clues that a similarity is homologous: a complex structure matches part for part, it develops the same way in the embryo, and fossils or DNA point to the same ancestry. The more detailed the match, the less likely it arose twice.
Before DNA sequences can be compared, they have to be lined up (aligned). Insertions and deletions shift bases out of register, so computer programs add gaps to bring matching stretches back together.
With only four bases, two unrelated sequences still match at roughly one site in four just by chance. Statistical tests help tell real but distant homology apart from these accidental matches.
Molecular systematics uses DNA and other molecules to work out relationships. Sequences supply thousands of characters, so they now drive most tree-building.

Key terms (9)

homology: A similarity between species that comes from a shared ancestor, whether in bones, development, proteins or DNA.
analogy: A similarity that evolved independently in separate lineages, not inherited from a shared ancestor. It says nothing about relatedness.
convergent evolution: When unrelated lineages evolve similar features because they face similar challenges, like streamlined bodies in sharks and dolphins.
homoplasy: Any shared feature that wasn't inherited from a common ancestor, such as an analogous structure or a chance DNA match.
morphological homology: A homology in body form, such as the same set of limb bones showing up in very different animals.
molecular homology: DNA or protein sequences in different species that resemble each other because they descend from one ancestral sequence.
sequence alignment: Lining up DNA or protein sequences from different species so that positions descended from the same ancestral site sit together.
insertion and deletion: Mutations that add or remove bases. They shift the rest of a sequence, which is why aligned sequences sometimes need gaps.
molecular systematics: Working out evolutionary relationships by comparing DNA, RNA or protein sequences.

Check yourself: 26.2 Homology, analogy and DNA evidence

4 questions on 26.2 Homology, analogy and DNA evidence. Pick an answer to see if you got it, and why.

Question 1 of 4

A student builds a tree of six animals using only one trait, a camera-like eye with a lens. The tree places an octopus right next to a hawk, apart from the other mollusks. What most likely went wrong?

Question 2 of 4

Scorpions and wasps both have venomous stingers. Which finding would best show that the stingers are analogous rather than homologous?

Question 3 of 4

Species M and N have hind legs built from 14 bones that match one for one and are joined in the same order. Species M and P are both bright yellow. Which similarity is stronger evidence of shared ancestry?

Question 4 of 4

Here are two species' versions of the same short DNA region. Species 1: TTAGCCGATCAGGTA Species 2: TTAGCGATCAGGTA Compared position by position from the left, they match at only 6 of the first 14 sites. What is the best interpretation?

0 of 4 answered

26.3 Building trees from shared derived traits

pp. 542–548

On the AP exam? Yes

Topic 7.9 tests building a cladogram from shared derived characters, using an outgroup and choosing the tree that needs the fewest changes. The terms monophyletic, paraphyletic and polyphyletic, and maximum likelihood, are background.

In the course: Topic 7.9 Phylogeny (notes, videos and more questions)

Key points

Cladistics groups organisms by common ancestry. A clade (or monophyletic group) is an ancestor plus every one of its descendants. A group that leaves some descendants out is paraphyletic, and a group that pulls together lineages from different ancestors is polyphyletic.
A shared ancestral character was already present in the ancestor of the whole group you're studying, so it can't sort that group. A shared derived character first appeared in one clade's ancestor and marks that clade. Whether a trait counts as ancestral or derived depends on which part of the tree you're looking at.
An outgroup is a lineage known to have split off before the group you're studying (the ingroup) began to branch. Traits the outgroup shares with the ingroup are treated as ancestral, and traits found in only some of the ingroup are derived.
To turn a trait table into a cladogram, place the trait shared by the most taxa nearest the root. Each trait shared by fewer taxa marks a later node.
In a plain cladogram, branch lengths mean nothing. Some trees draw branch lengths to match the amount of genetic change or the passage of time. Every living lineage that descends from one ancestor has been evolving for the same length of time, even if one changed very little.
Maximum parsimony favors the tree that needs the fewest changes, whether trait gains and losses or DNA base changes. Maximum likelihood favors the tree that makes the observed sequences most probable, given a model of how DNA changes. The number of possible trees explodes as species are added, so computers do the search.
Every tree is a hypothesis, and new data can revise it. You can also test it: if two related living groups share a trait, their shared ancestor probably had it too, and so did its other descendants, extinct ones included (phylogenetic bracketing).

Key terms (13)

cladistics: A way of classifying organisms by common ancestry alone, using shared derived characters to find clades.
clade: An ancestor plus all of its descendants. On a tree, you could cut one off with a single snip.
monophyletic group: Another name for a clade: a group made up of one ancestor and every one of its descendants.
paraphyletic group: A group that includes an ancestor and some of its descendants but leaves others out.
polyphyletic group: A group that lumps together lineages from different ancestors without including the ancestor they all share.
shared ancestral character: A trait that was already present in the ancestor of the whole group being studied, so it can't sort members of that group.
shared derived character: A trait that first appeared in the ancestor of one clade and is found only in that clade's members.
outgroup: A lineage that branched off before the group being studied. Comparing it with that group shows which traits are ancestral.
ingroup: The set of species whose relationships a study is trying to work out.
cladogram: A tree that shows only the order of branching. Its branch lengths don't mean anything.
maximum parsimony: Choosing the tree that explains the data with the fewest evolutionary changes.
maximum likelihood: Choosing the tree that makes the observed DNA data most probable, based on rules for how sequences tend to change.
phylogenetic bracketing: Predicting that a trait seen in two related groups also existed in the ancestor they share and in that ancestor's other descendants.

Check yourself: 26.3 Building trees from shared derived traits

4 questions on 26.3 Building trees from shared derived traits. Pick an answer to see if you got it, and why.

Question 1 of 4

The table scores five plants for four traits (1 = present, 0 = absent). The green alga is the outgroup. Plant | Embryo kept inside parent tissue | Vascular tissue | Seeds | Flowers Green alga | 0 | 0 | 0 | 0 Moss | 1 | 0 | 0 | 0 Fern | 1 | 1 | 0 | 0 Pine | 1 | 1 | 1 | 0 Rose | 1 | 1 | 1 | 1 Which statement is supported by the table?

Question 2 of 4

In a tree, the outgroup O splits off first. Next, species K splits off. The remaining lineage divides into species L and a branch that later splits into species M and N. Which grouping is a clade?

Question 3 of 4

In a study of six moth species, a particular wing-scale pattern is found in the outgroup and in two of the moths. The other four moths lack it. How should this pattern be treated when building the moths' tree?

Question 4 of 4

An outgroup lacks all four traits below. Each trait lists the species of A, B and C that have it. Trait 1: A, B Trait 2: A, B Trait 3: B, C Trait 4: A, B, C Using maximum parsimony, which tree is favored, and how many trait changes does it need?

0 of 4 answered

26.4 Genomes as records of history

pp. 548–549

On the AP exam? Background

Shared genes as evidence of common ancestry are in Topics 7.6 and 7.7, mutations are in 6.7 and alternative splicing is in 6.3, but the words orthologous and paralogous aren't in the current course. Treat this section as background.

In the course: Topic 7.6 Evidence of Evolution, Topic 7.7 Common Ancestry, Topic 6.7 Mutations, Topic 6.3 Transcription and RNA Processing (notes, videos and more questions)

Key points

Comparing molecules lets biologists relate groups that have almost no anatomy in common, like plants and fungi, and groups with a poor fossil record or none at all.
Different genes change at different speeds. Slow-changing genes, like those for ribosomal RNA, still show detectable similarity after billions of years, so they're used for the deepest splits. Fast-changing DNA, like mitochondrial DNA, is better for recent events, such as relationships among populations of one species.
Gene duplication makes an extra copy of a gene. Because the original copy keeps doing its job, the spare can pick up mutations and sometimes gains a new function. Repeated duplications build gene families.
Orthologous genes are homologs in different species that trace back to the speciation event that split them. Paralogous genes are homologs within one genome that trace back to a duplication, and they can drift apart within that species.
Even very distantly related species share many orthologous genes. That's why yeast, flies and mice can be used to study how human genes work.
Gene number doesn't track complexity closely: some plants, such as rice, have more protein-coding genes than humans do. One gene can make several proteins (for example, through alternative splicing), and when and where genes are switched on matters as much as how many there are.

Key terms (7)

gene duplication: A mutation that leaves an extra copy of a gene in the genome. The spare copy is free to change.
gene family: A set of related genes in one genome that arose from repeated duplications of an ancestral gene.
orthologous genes: Versions of a gene found in different species that trace back to one gene in their common ancestor, before speciation split them.
paralogous genes: Related genes within one genome that arose when an ancestral gene was duplicated.
ribosomal RNA (rRNA) genes: Genes for the RNA in ribosomes. They change so slowly that they're useful for comparing very distant groups.
mitochondrial DNA (mtDNA): The small DNA molecule inside mitochondria. It changes quickly, so it's useful for recent history within or between close species.
alternative splicing: Joining different combinations of a gene's exons, so one gene can code for more than one protein.

Check yourself: 26.4 Genomes as records of history

4 questions on 26.4 Genomes as records of history. Pick an answer to see if you got it, and why.

Question 1 of 4

Salamander populations on four mountaintops have been cut off from one another for about 10,000 years. To work out how the populations are related, which DNA would be most informative to compare?

Question 2 of 4

How are the α-globin genes of a horse and of a rabbit, and the α- and β-globin genes within a single horse, best described?

Question 3 of 4

Species 1 and 2 split about 10 million years ago. A researcher compares gene G-a from species 1 with gene G-b from species 2, not realizing that G-a and G-b are copies made by a gene duplication about 300 million years ago. How will this mistake most likely affect the estimate of when the species split?

Question 4 of 4

After a gene duplication, one copy keeps its original job while the other gradually picks up many mutations and eventually codes for a protein with a new function. Why can the second copy change so much without harming the organism?

0 of 4 answered

26.5 Molecular clocks

pp. 549–551

On the AP exam? Yes

Topic 7.9 says trees can be calibrated with fossils or a molecular clock, so expect to estimate a split date from a rate. Neutral theory and the debate over how reliable clocks are count as background.

In the course: Topic 7.9 Phylogeny, Topic 7.4 Population Genetics, Topic 6.7 Mutations (notes, videos and more questions)

Key points

A molecular clock estimates when two lineages split from how much their DNA or proteins differ. It works only for sequences that pick up changes at a fairly steady average rate.
The clock has to be calibrated. Plot sequence differences against split dates known from dated fossils, find the rate, then use that rate to date splits with no fossil record.
For orthologous genes, the differences measure time since the species split. For paralogs, they measure time since the gene was duplicated.
Neutral theory proposes that many sequence changes have no effect on fitness, so they spread or disappear by genetic drift at a fairly regular pace. That's why some sequences tick like clocks. Genes whose exact sequence is critical change slowly, because most changes to them are harmful and get removed by selection.
Clocks have limits. Rates differ from gene to gene and lineage to lineage, selection can speed or slow change, and dates older than the rich fossil record, which reaches back only about 540 million years, assume a constant rate over huge spans. Building a clock from many genes helps average out the irregularities.
RNA viruses mutate fast enough that samples collected over a few decades show measurable change. A clock built from such samples can estimate when a virus first started spreading in a new host.

Key terms (7)

molecular clock: A method that estimates when lineages split by using how many sequence differences have built up between them, at a known average rate.
calibration: Setting a clock's rate with splits whose dates are already known, usually from dated fossils.
divergence time: How long ago two lineages split from their common ancestor.
neutral theory: The idea that many changes in DNA and proteins neither help nor hurt survival, so their fate is set by chance (genetic drift).
neutral mutation: A change in DNA that has no effect on an organism's survival or reproduction.
genetic drift: Random shifts in allele frequencies between generations. Its effects are strongest in small populations.
silent mutation: A base change that doesn't change the amino acid, because more than one codon codes for it.

Check yourself: 26.5 Molecular clocks

4 questions on 26.5 Molecular clocks. Pick an answer to see if you got it, and why.

Question 1 of 4Calculator allowed

In a group of lizards, differences in one gene build up between two diverging lineages at about 1.5 differences per million years. Two species differ at 27 sites in this gene. About how long ago did they share a common ancestor?

Question 2 of 4Calculator allowed

Geologists have dated several events that cut freshwater fish populations apart, such as rivers being separated by uplift. Researchers counted differences in one gene between the fish on each side (invented data). Age of event (millions of years) | DNA differences 2 | 5 4 | 10 6 | 15 8 | 20 Two fish species whose split has no dated event differ at 11 sites in the same gene. About when did their lineages split?

Question 3 of 4

Researchers estimating when two groups of fish split build their molecular clock from 120 genes instead of just one. What is the main advantage of using so many genes?

Question 4 of 4

In mammals, the amino acid sequence of histone H4 has barely changed. Fibrinopeptides, short pieces cut off and thrown away when blood clots, have changed hundreds of times faster. How does neutral theory best explain the difference?

0 of 4 answered

26.6 Three domains and a changing tree of life

pp. 551–553

On the AP exam? Background

The current course doesn't test the three domains by name, but Topic 7.7 covers evidence that all life shares an ancestor, 2.10 covers the bacterial origin of mitochondria and chloroplasts, and 6.7 includes horizontal gene transfer.

In the course: Topic 7.7 Common Ancestry, Topic 7.9 Phylogeny, Topic 2.10 Origins of Cell Compartmentalization, Topic 6.7 Mutations (notes, videos and more questions)

Key points

Early schemes split life into just plants and animals, and fungi and bacteria were filed with plants mostly because they don't move around. A later five-kingdom scheme (prokaryotes, protists, plants, fungi and animals) set the prokaryotes apart.
Sequence data, especially from ribosomal RNA genes, showed that prokaryotes form two lineages about as different from each other as either is from eukaryotes. Biologists now sort life into three domains, a level above kingdoms: Bacteria, Archaea and Eukarya.
Bacteria include most familiar prokaryotes, plus the groups that gave rise to mitochondria and chloroplasts. Archaea are prokaryotes with their own distinctive chemistry. Many live in extreme places, but they're common in soil and oceans too. Eukarya are all organisms whose cells have a nucleus.
The old single kingdom for prokaryotes doesn't work, because its members fall into two domains. "Protists" aren't a clade either: some protists are closer kin to animals, plants or fungi than to the rest of the protists.
Ribosomal RNA trees put the first split between Bacteria and a lineage leading to Archaea and Eukarya. Newer genome studies go further: eukaryotes seem to have arisen from within the Archaea, from a host cell that took in the bacterium that became the mitochondrion.
Horizontal gene transfer moves genes between organisms, not just from parent to offspring, through plasmids, viruses, mobile DNA and endosymbiosis. It was common in early life and still is among prokaryotes. That's why trees built from different genes can disagree, and why some biologists picture early life as a web more than a tree.
Most of life's history and much of its diversity is single-celled. Among the eukaryotes, only plants, fungi and animals are mostly multicellular.

Key terms (9)

domain: The broadest level of classification. All life falls into three: Bacteria, Archaea and Eukarya.
Bacteria: The domain holding most familiar prokaryotes, from soil and gut microbes to the ancestors of mitochondria and chloroplasts.
Archaea: The domain of prokaryotes with their own distinctive membranes and enzymes. Many thrive in extreme habitats, but they're found nearly everywhere.
Eukarya: The domain of all organisms whose cells have a nucleus and membrane-bound organelles: protists, fungi, plants and animals.
kingdom: The rank just below domain in the Linnaean system, such as Plantae, Fungi and Animalia.
protist: An informal name for any eukaryote that isn't a plant, fungus or animal. Protists don't form a single clade.
horizontal gene transfer: The movement of genes between organisms other than from parent to offspring, for example by plasmids or viruses.
endosymbiosis: One cell living inside another. Mitochondria and chloroplasts descend from bacteria that lived this way inside ancient cells.
Asgard archaea: A group of archaea that carry many genes once thought to be found only in eukaryotes. Eukaryotes appear to have arisen from within or near this group.

Check yourself: 26.6 Three domains and a changing tree of life

4 questions on 26.6 Three domains and a changing tree of life. Pick an answer to see if you got it, and why.

Question 1 of 4

Researchers compared one ribosomal RNA gene from a bacterium, an archaeon and a yeast (invented data). Pair | Sequence identity (%) Bacterium–archaeon | 64 Bacterium–yeast | 61 Archaeon–yeast | 70 Which conclusion is best supported?

Question 2 of 4

A gene for antibiotic resistance in a soil bacterium is 99% identical to one in a distantly related gut bacterium, yet the two species' ribosomal RNA genes are very different. In both species, the resistance gene sits on a plasmid. What best explains this?

Question 3 of 4

A newly discovered single-celled organism has ribosomes, DNA and a plasma membrane. Which further finding would place it in domain Eukarya?

Question 4 of 4

DNA data show that choanoflagellates, a group of single-celled protists, are the sister group of animals, closer to them than to diatoms or most other protists. What does this mean for a kingdom that includes every protist but no animals?

0 of 4 answered