Reading and Building Trees

Cladograms and Phylogenetic Trees

Cladograms and phylogenetic trees are diagrams used to represent hypotheses about the evolutionary relationships among organisms. Understanding how to read and construct these trees is fundamental to studying evolutionary biology.

• Cladogram: A branching diagram showing hypothesized relationships among organisms. The tips represent the organisms being compared.

• Node (branch point): The point where two branches split, representing a common ancestor—not a living organism at the tip.

• Common ancestor: A species from which two or more groups have descended.

• Most recent common ancestor: The latest ancestor shared by two organisms; the closer the node is to the tips, the more closely related the organisms are.

• Clade: A group consisting of a common ancestor and all its descendants. Excluding any descendant means the group is not a clade.

• Outgroup: The organism that branches off first, used for comparison as it is least related to the others.

• Trait mark: Indicates where a characteristic first evolved; all organisms above this mark possess the trait unless it was lost later.

Key Skills:

• Identify the most closely related organisms by finding the node closest to the tips.

• Explain that nodes represent ancestors, and tips cannot be ancestors of other tips.

• Order traits from oldest (near the root) to newest (near the tips) using trait marks.

• Determine which organisms possess a given trait based on its position on the tree.

• Assess whether a group forms a clade and explain what is missing if not.

• Recognize that rotating branches around a node does not change relationships.

Phylogenetic Trees with a Time Scale

Phylogenetic trees can incorporate time, showing when lineages diverged and how long different groups have existed.

• Phylogenetic tree: A tree that shows both relationships and the timing of divergences.

• Divergence: The splitting of one lineage into two, marked by a node.

• Lineage: A sequence of species each descended from its predecessor.

• Descendants: All organisms that branch off after a given ancestor.

Key Skills:

• Read the time axis to determine when lineages split.

• List all modern descendants of a marked ancestor.

• Identify which pairs of organisms diverged longest ago or most recently.

• Compare relatedness using the age of nodes.

Building a Cladogram from a Trait Table

Cladograms can be constructed using morphological data organized in trait tables, applying the principle of parsimony.

• Morphological data: Physical characteristics such as limbs, hair, or flowers.

• Trait table: A matrix showing which organisms possess which traits.

• Parsimony: The simplest explanation requiring the fewest evolutionary changes is preferred.

• Evolutionary change: Each gain or loss of a trait counts as one change.

Key Skills:

• Sort trait tables by number of shared traits.

• Build cladograms and mark where each trait evolved.

• Place traits shared by all organisms near the root; traits unique to one organism are placed at the tip.

• Count evolutionary changes, including losses.

• Use parsimony to choose between alternative cladograms.

Using Molecular Data (DNA and Proteins)

Molecular data, such as DNA sequences and protein amino acid sequences, provide powerful evidence for evolutionary relationships.

• Molecular data: Information from DNA or protein sequences.

• Amino acid: Building blocks of proteins; sequence comparisons reveal relatedness.

• SNP (Single-nucleotide polymorphism): A single base difference in DNA.

• Sequence divergence: The percentage of positions where two sequences differ, calculated as:

• Fewer differences indicate a more recent common ancestor.

Key Skills:

• Align sequences, count differences, and calculate divergence.

• Rank organisms by relatedness using difference tables.

• Build cladograms from molecular difference tables, pairing the most similar first.

• Explain how DNA differences inform scientists about evolutionary relationships.

When the Evidence Disagrees

Sometimes, different types of evidence (morphological, molecular, fossil) suggest different relationships. Scientists must interpret and reconcile these differences.

• Convergent evolution: Similar traits evolve independently in different lineages due to similar environmental pressures (e.g., wings in bats and birds).

• Adaptation: A trait that increases an organism's fitness in its environment.

• Multiple lines of evidence: Using various data types strengthens hypotheses.

• Cladogram as hypothesis: Trees are hypotheses that can change with new evidence.

Key Skills:

• Identify convergent evolution on trees.

• Explain why similar environments can produce similar traits in unrelated organisms.

• Discuss strengths and weaknesses of morphological and molecular data.

• Describe how scientists revise cladograms as new data emerge.

Our Family Tree, the Evidence, and the Mechanism

Our Family Tree and Hominin Evolution

The human lineage is traced through hominin fossils and genetic evidence, revealing both extinct and living relatives.

• Genus vs. species: Homo is the genus; Homo sapiens, Neanderthals, Denisovans, and others are species within it.

• Hominin: Members of the human branch after splitting from the chimpanzee lineage.

• Extinct vs. living: Extinct species are those whose lineages ended; H. sapiens is the only living Homo species.

• Fossil time range: The period a species is known from fossils.

• Interbreeding: Closely related groups producing offspring (e.g., modern humans with Neanderthals).

• Uncertain placement: Species with limited evidence may have uncertain positions on the tree.

• Ardi (Ardipithecus): A 4.4-million-year-old hominin showing both bipedal and climbing adaptations.

• Bipedal trade-off: Walking on two legs affects balance and energy use; traits can have both benefits and costs. One of the key benefits is that is saves energy and decreases metabolic rate/rate of metabolism.

• Tool use: Homo habilis is the earliest known toolmaker in our lineage.

Key Skills:

• Distinguish living from extinct species on trees and time charts.

• Interpret time-range charts to determine coexisting species.

• Differentiate between shared and direct ancestors.

• Identify closest relatives on hominin trees.

• Explain evidence for interbreeding and its modern implications.

• Infer locomotion from fossil features and explain transitional forms.

• Discuss benefits and costs of bipedalism and evidence for ancient habitats.

Your Inner Animals: Evidence for Common Descent

Multiple lines of evidence support the theory of common descent, including anatomical, fossil, developmental, and genetic data.

• Common descent: All species descend from shared ancestors.

• Homologous structures: Similar body parts inherited from a common ancestor, even if they serve different functions (e.g., human arm, chicken wing, fish fin).

• Analogous structure: Similar body parts in function or appearance but evolved independently because the species faced similar environmental challenges, not because they share a close ancestor.

• Tetrapod: Four-limbed vertebrates; Tiktaalik is a transitional form between fish and tetrapods.

• Transitional form: Fossils with features intermediate between major groups, showing gradual evolutionary change.

• Developmental evidence: Embryonic development reveals evolutionary history (e.g., ear bones in mammals).

• Genetic evidence: Shared genes (e.g., EDA gene) indicate common ancestry.

• Vestige: Structures that have lost their original function (e.g., human coccyx).

• Inferring function: Structure of bones and teeth can reveal diet and lifestyle.

Key Skills:

• Explain why homologous structures indicate common ancestry.

• Distinguish homologous from convergent traits using trees.

• Describe sequences of transitional fossils.

• List and explain fossil, anatomical, developmental, and genetic evidence for common descent.

• Infer animal lifestyle from anatomical features.

• Define vestigial structures and their evolutionary significance.

• Explain the significance of shared genes in different species.

Natural Selection: The Mechanism Behind the Tree

Principles of Natural Selection

Natural selection is the process by which heritable traits that confer a survival or reproductive advantage become more common in a population over generations.

• Natural selection: The mechanism driving evolutionary change through differential survival and reproduction.

• Variation: Differences among individuals; selection acts only on existing variation.

• Heritable trait: Traits passed from parent to offspring via genes.

• Mutation: Random changes in DNA that introduce new variation.

• Differential survival and reproduction: Some individuals leave more offspring due to advantageous traits.

• Population vs. individual: Populations evolve, not individuals.

• Trade-off: Traits may have both benefits and costs depending on the environment.

• Mismatch: Traits favored in ancestral environments may not fit current ones.

Key Skills:

• Apply the logic of natural selection to novel organisms.

• Explain why individuals do not evolve and why mutations are random.

• Discuss environmental dependence of trait advantages.

• Interpret data to determine which traits are favored.

• Predict changes in trait frequencies over generations.

• Connect natural selection to convergent evolution.

Common Misconceptions and Corrections

Natural Selection in Humans: Skin Color Evidence

Skin Color, UV, and Evolutionary Trade-offs

Human skin color variation is an example of natural selection shaped by environmental pressures, particularly UV radiation.

• Melanin: Pigment determining skin and hair color; protects DNA from UV damage.

• UV index: Measure of UV radiation intensity; highest near the equator and at high elevations.

• Skin color prediction model: Predicts ancestral skin color based on local UV levels.

• Selective pressure: Environmental factors influencing which traits are favored.

• Folate: B vitamin degraded by UV; essential for fetal development.

• Vitamin D: Produced in skin via UV exposure; lighter skin synthesizes more vitamin D in low-UV environments.

• Trade-off: Darker skin protects folate in high UV; lighter skin aids vitamin D production in low UV.

• Exceptions: Some populations (e.g., Inuit) have darker skin than predicted due to dietary vitamin D.

• Mismatch: Modern environments and behaviors can create mismatches between ancestral adaptations and current needs.

Key Skills:

• Interpret UV maps and skin color graphs to explain evolutionary patterns.

• Explain why ancestral populations are used in models, not recent migrants.

• Discuss why skin cancer is not a major selective pressure (typically affects after reproductive age).

• Analyze data to support claims about folate and vitamin D selection.

• Explain the evolutionary trade-off between folate protection and vitamin D synthesis.

• Predict effects of diet and lifestyle on selection for skin color.

• Correct misconceptions about inheritance and adaptation.

• Identify modern factors affecting vitamin D and folate levels.

Putting It All Together

Connecting Trees, Evidence, and Selection

Evolutionary trees (phylogenies) integrate evidence from morphology, fossils, and genetics to show relationships. Natural selection explains how traits change over time, often involving trade-offs shaped by the environment. Modern mismatches arise when ancestral adaptations do not fit current conditions.

• Trees show relatedness: Nodes indicate common ancestors; closer nodes mean closer relatives.

• Evidence for common descent: Homologous structures, transitional fossils, shared genes, and developmental clues all support shared ancestry.

• Selection explains changes: Variation is inherited; advantageous traits become more common.

• Traits involve trade-offs: The best trait depends on environmental context.

• Mismatch: Traits shaped by past environments may not suit present ones.

Essential Skills for Exam Success

• Read and interpret unfamiliar cladograms and phylogenetic trees.

• Construct trees from trait or molecular difference tables.

• Apply parsimony to select the simplest evolutionary explanation.

• Interpret data in tables and graphs.

• Make evidence-based claims and support them with data.