Source: Introduction to Biology I Midterm Examination, University of Washington
Difficulty: Introductory to Intermediate | Prerequisites: Evolution Fundamentals and Evidence for Evolution study notes.
Phylogenetics is how biologists reconstruct evolutionary history: who is related to whom, and how long ago they diverged. Speciation is how one species splits into two or more. These topics build directly on the evidence for evolution and on natural selection. If you understand homology and descent with modification, phylogenetic trees will make sense as visual representations of those relationships. Speciation explains how the diversity you see on a phylogenetic tree came about.
Phylogenetic trees depict evolutionary relationships using branching diagrams. Building them involves assembling a dataset, aligning sequences, choosing a model, and assessing branch support. Gene trees and species trees do not always match, mainly because of incomplete lineage sorting. Speciation, the formation of new species, occurs through several geographic modes (allopatric, peripatric, parapatric, sympatric) and requires the development of reproductive isolation, which can be prezygotic or postzygotic.
Phylogenetic tree
A branching diagram showing the inferred evolutionary relationships among a group of organisms. Think of it as: a family tree for species (or genes), where each branching point represents a common ancestor.
Topology
The order and branching pattern of a phylogenetic tree, showing which taxa are more closely related to each other. In simple terms, topology is about the shape of the tree (who branches off with whom), not the lengths of the branches.
Node (internal node)
A point on a phylogenetic tree where a lineage splits into two or more descendant lineages. Think of it as: the common ancestor from which two or more species diverged.
Clade
A group consisting of a common ancestor and all of its descendants. In simple terms, a complete "branch" of the tree, snipped off at one node.
Gene tree
A phylogenetic tree built from the evolutionary history of a single gene. Gene trees can differ from species trees.
Species tree
A phylogenetic tree representing the actual history of speciation events among species. In simple terms, the "true" tree of how species split from one another over time.
Incomplete lineage sorting (ILS)
A phenomenon where gene trees differ from the species tree because ancestral genetic variation was not fully sorted before subsequent speciation events. This is most likely when ancestral population sizes are large and divergence times between speciation events are short.
Speciation
The process by which new species arise. Think of it as: one lineage splitting into two (or more) that can no longer interbreed.
Allopatric speciation
Speciation caused by geographic separation of populations (e.g. a mountain range or a river dividing a population).
Peripatric speciation
A special case of allopatric speciation where a small peripheral population becomes isolated from the main population. The small population may diverge rapidly due to genetic drift and different selection pressures.
Parapatric speciation
Speciation that occurs when populations are adjacent, with a narrow zone of overlap. There is some gene flow, but divergent selection across the boundary drives divergence.
Sympatric speciation
Speciation that occurs within a single population without geographic separation. In simple terms, a population splits into two species in the same place, often driven by disruptive selection or polyploidy (common in plants).
Reproductive isolation
The inability of two populations to interbreed and produce fertile offspring. This is what defines separate species under the biological species concept.
Prezygotic barriers
Mechanisms that prevent mating or fertilisation from occurring in the first place. Examples: behavioural isolation (different courtship signals), temporal isolation (different breeding seasons), gametic isolation (sperm and egg are incompatible).
Postzygotic barriers
Mechanisms that reduce the viability or fertility of hybrid offspring after fertilisation has occurred. Examples: hybrid inviability (hybrid embryos fail to develop), hybrid sterility (hybrids are infertile, e.g. mules).
Gametic isolation
A prezygotic barrier where sperm and egg are biochemically incompatible, preventing fertilisation even when mating occurs.
Hybrid inviability
A postzygotic barrier where hybrid offspring fail to develop properly or die before reproducing.
Reinforcement
The process by which natural selection strengthens prezygotic barriers to reproduction when hybridisation produces less-fit offspring. Think of it as: evolution "learning" to avoid bad crosses by making mating between the two groups less likely.
A phylogenetic tree is a hypothesis about evolutionary relationships among taxa, depicted as a branching diagram.
Topology refers to the branching pattern: which taxa group together. It does not refer to branch lengths, geographic location, or fossil age.
Each internal node represents a hypothesised common ancestor. A clade is a complete branch: a node plus all its descendants.
Trees can be read in multiple ways. Two trees with the same topology can look different if branches are rotated around a node, since the left-right order of branches has no meaning.
The standard steps for building a phylogenetic tree:
Dataset assembly: Collect the sequences or morphological characters you will analyse.
Sequence alignment: Align corresponding positions across taxa so you are comparing like with like.
Model selection: Choose a statistical model of how sequences evolve. The model affects the tree you infer, so this step matters.
Tree inference: Use the model and data to infer the best tree (e.g. maximum likelihood, Bayesian methods).
Branch support assessment: Evaluate how confident you can be in each node of the tree (e.g. bootstrap values). Low support means the relationship at that node is uncertain.
"Direct observation of speciation events" is not a step in this workflow. That is a common trick answer on the exam.
A gene tree traces the evolutionary history of a single gene. A species tree traces the actual branching history of species.
Gene trees and species trees are not always identical. The main cause of discordance is incomplete lineage sorting (ILS).
ILS is most likely when the ancestral population size is large and the time between successive speciation events is short. Under these conditions, ancestral alleles may not sort cleanly into the descendant lineages before the next split.
Other causes of gene-tree/species-tree discordance include hybridisation and horizontal gene transfer.
Allopatric speciation: Populations separated by a physical barrier (e.g. a mountain range, a river, continental drift). Gene flow is completely interrupted. The most commonly cited mode. Example: squirrel populations on opposite sides of the Grand Canyon.
Peripatric speciation: A small population at the edge of the species' range becomes isolated. Its small size makes genetic drift a strong force, accelerating divergence. Example: island populations budding off from a mainland species.
Parapatric speciation: Populations are adjacent with partial overlap. Some gene flow occurs, but divergent selection pressures across the boundary drive the populations apart. Example: grass species adapting to different soil types on either side of a mine boundary.
Sympatric speciation: A population splits into two species in the same geographic area, without any physical barrier. This is the hardest mode to demonstrate. Most commonly documented through polyploidy in plants. Example: a tetraploid plant arising within a diploid population and being reproductively isolated from it immediately.
Speciation can occur without complete geographic isolation. Sympatric and parapatric speciation show that geography is not the only driver.
Prezygotic barriers prevent mating or fertilisation:
Behavioural isolation: different courtship rituals or signals.
Temporal isolation: different breeding times.
Habitat isolation: species live in different habitats within the same area.
Mechanical isolation: reproductive organs are physically incompatible.
Gametic isolation: sperm and egg cannot fuse, even if mating occurs. This is a prezygotic barrier that prevents fertilisation after mating.
Postzygotic barriers act after fertilisation:
Hybrid inviability: the hybrid embryo fails to develop or dies.
Hybrid sterility: the hybrid is viable but infertile (e.g. mules, which are horse-donkey crosses).
Hybrid breakdown: first-generation hybrids are fertile, but their offspring have reduced fitness.
Reinforcement occurs when natural selection strengthens prezygotic barriers in response to hybridisation producing less-fit offspring.
If two populations come back into contact and hybrids are less fit than purebreds, individuals that avoid mating with the other group will have higher fitness. Over time, this favours stronger mating preferences and greater prezygotic isolation.
Reinforcement strengthens reproductive isolation to prevent hybridisation.
"Gene trees and species trees are always identical." They are not. Incomplete lineage sorting, hybridisation, and horizontal gene transfer can all cause them to disagree.
"Speciation requires complete geographic isolation." Sympatric and parapatric speciation show that populations can diverge into new species without a physical barrier between them.
"Phylogenetic trees show which species are more "advanced."" Trees show patterns of relatedness, not a progression from simple to complex. All living species on the tips of a tree have been evolving for the same total time.
"The left-right order of branches matters." It does not. Branches can be rotated around any node without changing the topology. What matters is which taxa share a more recent common ancestor.
"Gametic isolation is a postzygotic barrier." Gametic isolation prevents fertilisation (a prezygotic barrier), even though mating has occurred. No zygote forms, so it is prezygotic.
⚠️ Know the definition of "topology" precisely: the branching pattern showing evolutionary relationships, not branch lengths or geography.
⚠️ The phylogenetic analysis workflow steps are tested directly. "Direct observation of speciation events" is the decoy answer.
⚠️ Incomplete lineage sorting: know the two conditions that make it likely (large ancestral population, short divergence times).
⚠️ Be able to distinguish all four modes of speciation and provide an example for each. Peripatric is the one students confuse with allopatric; the key difference is the small peripheral population.
⚠️ Know at least one prezygotic and one postzygotic barrier by name and definition. Gametic isolation (prezygotic, prevents fertilisation) and hybrid inviability (postzygotic, hybrid fails to develop) are the pair tested on this exam.
⚠️ Reinforcement is tested as a true/false: it strengthens reproductive isolation to prevent hybridisation. True.
⚠️ The long-answer questions on this exam ask you to compare and contrast all four geographic modes of speciation with examples, and to describe the phylogenetic workflow including model selection and branch support.
True or false: Gene trees and species trees are always identical in phylogenetic analysis. (False. Incomplete lineage sorting, hybridisation, and horizontal gene transfer can cause discordance.)
True or false: Speciation can only occur if populations are completely geographically isolated. (False. Sympatric and parapatric speciation occur without complete geographic separation.)
True or false: Reinforcement strengthens reproductive isolation to prevent hybridisation. (True.)
Fill in the blank: The process by which new species arise is called _______. (speciation)
Fill in the blank: In a phylogenetic tree, the common ancestor from which two or more species diverged is called a _______. (node)
Q: In phylogenetics, what does the term "topology" refer to?
A: The order and branching pattern that shows evolutionary relationships among taxa. It describes which groups are most closely related, not the branch lengths or geographic positions.
Q: Which factor contributes most to incomplete lineage sorting causing discordance between gene trees and species trees?
A: Large ancestral population size and short divergence times between speciation events. Under these conditions, ancestral alleles may not sort into daughter lineages before the next split.
Q: Which of the following is NOT a step in the phylogenetic analysis workflow: dataset assembly, sequence alignment, model selection, or direct observation of speciation events?
A: Direct observation of speciation events. The workflow involves dataset assembly, alignment, model selection, tree inference, and branch support assessment.
Q: Which mode of speciation occurs when a small peripheral population becomes isolated from the main population?
A: Peripatric speciation. It is a special case of allopatric speciation, distinguished by the small size of the isolated population.
Q: Which reproductive isolating mechanism prevents fertilisation even when mating occurs?
A: Gametic isolation. Sperm and egg are biochemically incompatible, so no zygote forms. This is a prezygotic barrier.
Q: Explain the role of reproductive isolation in speciation, naming one prezygotic and one postzygotic barrier.
A: Reproductive isolation is essential for speciation because it prevents gene flow between diverging populations, allowing them to accumulate genetic differences independently. A prezygotic barrier such as gametic isolation prevents fertilisation even after mating. A postzygotic barrier such as hybrid inviability means that even if a hybrid zygote forms, it fails to develop into a viable organism. Together, these barriers ensure that the two populations cannot merge back into a single gene pool.
Q: Describe the workflow of phylogenetic analysis and explain the importance of model selection and branch support.
A: The workflow begins with dataset assembly (gathering sequences or characters), followed by sequence alignment (arranging corresponding positions across taxa). Model selection then chooses a statistical model of sequence evolution; the model affects which tree is inferred, so an inappropriate model can produce misleading results. Tree inference uses the data and model to find the best-supported tree. Branch support (e.g. bootstrap values) quantifies confidence in each node: a well-supported node means the relationship is robust to resampling, while low support means the relationship is uncertain and should be interpreted cautiously.
Q: Compare and contrast the four geographic modes of speciation: allopatric, peripatric, parapatric, and sympatric. Provide an example for each.
A: Allopatric speciation involves complete geographic separation (e.g. squirrels divided by the Grand Canyon). Peripatric speciation is a variant where a small peripheral population is isolated, and genetic drift plays a larger role (e.g. island populations budding off a mainland). Parapatric speciation occurs along a boundary with limited gene flow, driven by divergent selection (e.g. grass species on different soil types near a mine). Sympatric speciation occurs within the same area with no physical barrier, often via polyploidy in plants (e.g. a tetraploid plant arising within a diploid population). The key contrast is the degree of geographic separation and gene flow: allopatric and peripatric involve complete separation, parapatric involves partial contact, and sympatric involves no separation at all.
Phylogenetics relies on the evidence for evolution covered in the previous notes (homology, molecular data). Speciation connects back to natural selection: divergent selection pressures drive populations apart, and reproductive isolation mechanisms prevent them from merging back. The concept of gene flow, important in speciation, also appears in population genetics later in the course.
Phylogenetics, phylogenetic tree, topology, node, clade, gene tree, species tree, incomplete lineage sorting, ILS, speciation, allopatric, peripatric, parapatric, sympatric, reproductive isolation, prezygotic barrier, postzygotic barrier, gametic isolation, hybrid inviability, hybrid sterility, hybrid breakdown, reinforcement, biological species concept, geographic isolation, gene flow, polyploidy, bootstrap, branch support, model selection, sequence alignment, dataset assembly, BIO I, Introduction to Biology, University of Washington, midterm review