Systematics and Phylogenetics

Learning Objectives

  • Describe the Linnaean system of classification and explain its limitations.
  • Analyze a phylogenetic tree for a group of organisms and describe the evolutionary history it portrays.
  • Determine if a group of organisms represents a monophyletic, polyphyletic, or paraphyletic taxon.
  • Evaluate evidence that morphological structures are homologous in two or more species or representatives of higher groups.
  • Explain the advantages and disadvantages of using molecular sequence data in a phylogenetic analysis.
  • Generate a parsimonious phylogenetic tree using cladistic methods to analyze a matrix of character states in a set of organisms.
  • Develop a phylogenetic hypothesis that can explain where in an evolutionary lineage a particular trait evolved.
  • Provide support for the idea that the vertical inheritance of genes is not the only mechanism through which genes are transferred from one organism to another.

The Malaria Problem

  • Malaria pathogenesis puzzled scientists for thousands of years.
    • Hippocrates linked fevers and splenomegaly to people living near malodorous marshes.
    • The term malaria arises from Latin meaning “bad air.”
  • By 1900, it was established that mosquitoes transmit the parasite to humans (vectors).
  • Mosquitoes act as intermediate hosts (vectors) for the malaria parasite.
  • Until the 1920s, it was believed that the European malaria was carried by Anopheles maculipennis.
  • Observations showed inconsistencies: areas with huge mosquito populations sometimes had low malaria incidence, and areas with few mosquitoes could have high incidence.
  • Researchers noted variation among mosquitoes; Dutch scientists identified two forms of the so-called species, with only one form seemingly capable of carrying malaria.
  • The field recognized diversity: there may be multiple mosquito forms contributing differently to malaria transmission.

Nomenclature and Classification

  • Carolus Linnaeus: foundational figure in taxonomy; identified, named, and classified new species.
  • Binomial nomenclature: species receive Latinized two-part names (binomial).
    • First part = genus; Second part = specific epithet (species name).
  • For bacteria, species names combine genus and specific epithet to yield a unique name.
  • Examples:
    • Ursus maritimus = polar bear
    • Ursus arctos = brown bear

Taxonomic Hierarchy

  • Similarity increases as you move downward in the hierarchy; organisms in the same group tend to share many characteristics.
  • Trait description: what counts as a trait? An example prompt: how would you describe Loxodonta africana (African elephant)?

Phylogenetic Trees

  • Darwin’s branching evolution complemented Linnaean hierarchy; both are hierarchical representations.

  • Shared ancestry implies that organisms in the same genus typically share a fairly recent common ancestor; higher taxa imply older common ancestors.

  • In the late 19th century, systematists began reconstructing phylogeny; phylogenies are hypotheses about evolutionary relationships, continually revised with new data.

  • Contemporary evolutionary biologists use phylogenetic trees to illustrate hypothesized evolutionary history; the breadth of analyses depends on the research question.

  • Note on interpretation: phylogenies are not fixed facts; they are testable hypotheses.

Reading Phylogenetic Trees: First Principles

  • Taxa: named classification units to which individuals or groups are assigned (the tips of branches).

Nodes and Branches (Example Tree)

  • Tip: Leopard
  • Domestic cat as a related taxon; Leopard and cat are sister species.
  • Node: speciation event representing the divergence from a common ancestor.
  • Root: common ancestor of the entire tree.
  • Branch: lineage segment; a speciation event occurs at nodes; represents an ancestral lineage splitting into descendant lineages.

Representative Phylogenetic Relationships (Illustrative Clades)

  • Examples showing relationships: dog, wolf, otter, striped skunk, leopard, Mephitis, Lutra lutra, Canis, etc.
  • Common ancestor of dog and wolf (Canis lupus familiaris and Canis lupus) and the broader carnivoran groups (e.g., Canidae, Mustelidae, Felidae, Carnivora).
  • A common ancestor of dog, wolf, otter, and skunk is represented at deeper nodes in Carnivora and related clades.
  • These diagrams illustrate how nodes represent common ancestors and how clades (monophyletic groups) are defined by shared ancestry.

Monophyletic Groups (Clades)

  • A monophyletic group includes a common ancestor and all of its descendants.
  • Shared derived characters (synapomorphies) define clades; a synapomorphy is a trait shared among species because their common ancestor possessed that trait.
  • Why are clades meaningful? They reflect true evolutionary relationships and provide a framework for understanding lineage diversification.

Monophyly, Polyphyly, and Paraphyly

  • Monophyletic taxon: ancestor plus all descendants.
  • Paraphyletic taxon: ancestor plus some, but not all, descendants.
  • Polyphyletic taxon: includes species from different evolutionary lineages; most recent common ancestor is not included in the taxon.

Node Rotation and Tree Orientation

  • Node rotation is arbitrary; rotating nodes or reorienting the tree does not change evolutionary relationships.
  • Interpretations may appear different, but underlying relationships remain constant.

Phylogenetic Trees Continued: Primate Cladogram (Illustrative)

  • Example lineage: New World monkeys, Old World monkeys, gibbons, orangutans, humans, chimpanzees, gorillas.
  • Clades indicated: HOMININAE, HOMINIDAE, HOMININI, ANTHROPOIDEA.
  • Time scale: time (millions of years ago) indicated; common ancestors at nodes.
  • Illustrates how a single tree can show relationships among major primate groups and their divergence events.

Data Sources for Phylogenetic Analyses

  • Linnaeus based on morphological similarities and differences (example: birds categorized as oviparous with feathers, two wings, two feet, and a bony beak).
  • Core premise: phenotypic similarities reflect underlying genetic similarities; similarity from shared ancestry = homology.
  • Homology is the study of likeness due to common ancestry; similarity does not imply identical structure or function.

Homology and Non-Homology (Analogies)

  • Homologous structures do not have to be identical in appearance or function.
  • Examples: Pitcher plant leaves modified into pitchers; Venus flytrap leaves modified into jaws; Poinsettia red parts resemble petals but are not petals; cacti spines are modified leaves.
  • Non-homologous (analogous) similarities arise from convergent evolution (homoplasy): different lineages independently evolve similar features (e.g., shark vs whale body plan).

Assessing Homology Through Morphology and Behavior

  • Morphology alone can be insufficient; behavior can help distinguish homologous vs non-homologous traits.
  • Tree frog example: Hyla versicolor and Hyla chrysoscelis show differences in mating calls and chromosome number (H. chrysoscelis is diploid; H. versicolor tetraploid) as prezygotic and postzygotic isolating mechanisms.

Molecular Sequencing and Phylogenetic Data

  • Modern phylogenetics relies on molecular characters: DNA/RNA sequences.
  • Shared changes (insertions, deletions, substitutions) reveal relationships.
  • PCR (polymerase chain reaction) enables amplification of specific DNA segments for analysis; allows use of minute DNA quantities from preserved specimens or fossils; sequencing improves with technology; data are stored in online databases for comparison.

Advantages and Drawbacks of Molecular Sequencing

  • Advantages:
    • Abundant data: every base can be a character for analysis.
    • Can compare distantly related organisms lacking apparent morphological similarity.
    • Can study closely related species with minor morphological differences.
    • Nucleic acids are not directly affected by developmental or environmental factors that confound morphology.
  • Drawbacks (potential disadvantages):
    • Not explicitly listed in the transcript, but challenges include alignment ambiguities, convergent molecular changes, incomplete lineage sorting, and computational demands.
  • Quick question posed: what are the potential disadvantages?

Traditional Classification and Paraphyletic Groups

  • Traditional systematics emphasized phenotypic divergence and branching patterns.
  • Classifications did not always strictly reflect actual branching evolution.

The Cladistic Revolution

  • Cladistics focuses on evolutionary relationships; morphology is largely ignored unless it reflects shared ancestry (synapomorphies).
  • Key terms:
    • Character: a heritable attribute (state: ancestral or derived).
    • Ancestral character state: trait present in a distant common ancestor.
    • Derived character state (apomorphy): a new version found in the most recent common ancestor of a group.
  • Derived character state found in two or more species is essential for grouping in cladistics.
  • Ancient fish example: fins vs limbs as an illustration of character state evolution.

Distinguishing Ancestral and Derived States

  • Outgroup comparison: identify ancestral vs derived characters by comparing the study group to a more distant related group not included in the analysis.

Using Synapomorphies to Reconstruct Evolutionary History

  • Cladistic method: group species that share derived character states.
  • Why avoid ancestral traits? Ancestral characters are not informative for resolving recent branching; derived traits define clades.
  • Outcomes presented as a phylogenetic tree illustrating the hypothesized branching sequence that produced the studied organisms.
  • Key concepts:
    • A common ancestor is hypothesized at each node.
    • The node and all branches from it portray a strictly monophyletic group.

Practical Example: Step-by-Step Practice (Vertebrates)

  • Step 1: Choose nine vertebrate groups: lampreys, sharks and close relatives, bony fishes, amphibians (frogs and salamanders), turtles, lizards (including snakes), crocodilians (including alligators), birds, and mammals. Include lancelets (Chordata, Cephalochordata) as the outgroup.
  • Step 2: Choose characters for the phylogenetic tree:
    • Vertebral column
    • Jaws
    • Swim bladder or lungs
    • Paired limbs (one bone connecting each limb to the body)
    • Extraembryonic membranes (e.g., amnion)
    • Mammary glands
    • Dry, scaly skin somewhere on the body
    • One opening on each side of the skull in front of the eye
    • Feathers
  • Step 3: Score the character states for each group using + (presence) and - (absence) or other symbols as shown in the example matrix.
    • Example excerpt from the scoring (simplified):
    • Lancelets: Vertebrae -, Jaws -, Swim bladder/lungs -, Paired limbs -, Extraembryonic membranes -, Mammary glands -, Dry, scaly skin -, One opening front of eye -, Feathers -
    • Lampreys: Vertebrae -, Jaws -, Swim bladder/lungs -, Paired limbs -, Extraembryonic membranes -, Mammary glands -, Dry, scaly skin -, One opening front of eye -, Feathers -
    • Sharks: Vertebrae +, Jaws +, Swim bladder/lungs -, Paired limbs -, Extraembryonic membranes -, Mammary glands -, Dry, scaly skin -, One opening front of eye -, Feathers -
    • (and so on for each group: bony fishes, amphibians, mammals, etc.)
  • Step 4: Construct the phylogenetic tree from the table by grouping organisms that share derived character states.
  • Step 5: Extend the tree to separate remaining groups; interpret results and consider incorporating molecular sequence data.

Optimizing Phylogenetic Trees

  • Real studies involve hundreds of characters across dozens of species; analysis yields many alternative trees.
  • Example counts:
    • With five species, about 15 possible phylogenetic trees.
    • With 50 species, about 3imes10763 imes 10^{76} possible trees.
  • The challenge is identifying the most representative hypothesis among a vast set of possibilities.

Parsimony Approach

  • Principle of parsimony: traits are unlikely to evolve independently in separate lineages.
  • The best tree minimizes the number of evolutionary changes needed to explain observed character states within a clade.
  • Parsimony reduces homoplasy but is not always ideal for molecular data.

Statistical Approaches to Phylogenetics

  • Methods that account for variation in evolutionary rates across positions, genes, and species; also variations over time.
  • Examples include:
    • Maximum likelihood method
    • Genetic distance method

Genetic Distance Method

  • Concept: closely related species have smaller genetic distances than distantly related species because they accumulated mutations for shorter times.
  • Tree construction is based on pairwise genetic distances; branch lengths reflect amount of genetic change since divergence.
  • Pros: less computationally demanding; does not rely on assumptions about mutation likelihoods.
  • Cons: generally less powerful than maximum likelihood for resolving complex relationships.

Applying the Genetic Distance Method (Illustrative)

  • Example: genetic distances between humans and three great apes are compared.
  • Identify the pair with the smallest distance (e.g., chimpanzee and human).
  • Calculate the average distances between the chimp–human cluster and other species (gorilla, orangutan).
  • Determine the outgroup (orangutan in this example).
  • Resulting tree is defined by these distance calculations.

Molecular Clocks and Dating Divergence

  • Molecular clock concept: if mutations accumulate at a reasonably constant rate, DNA sequence differences can date divergence times.
  • Formula of intuition: more differences imply older divergence; fewer differences imply recent divergence.
  • Each molecule can be treated as an independent clock, ticking at its own rate (different substitution rates across genes, genomes).
  • Calibration requires correlating genetic differences with fossil-record estimated divergence times or biogeographic data.
  • Example focus: mitochondrial DNA (mtDNA).

Phylogenetic Trees and the Comparative Method

  • Comparative method: compare characteristics across species to assess homology and infer where a trait evolved on the tree.
  • Examples: parental care behavior in birds vs crocodilians; whether such behavior is a synapomorphy or a convergent trait.
  • Question framing helps interpret whether similarities reflect shared ancestry or downstream adaptations.

Molecular Phylogenetic Analyses: Applications and Implications

  • Can pinpoint disease origins via phylogenetics (e.g., HIV strains):
    • HIV-1 is more prevalent and virulent, while HIV-2 occurs in West Africa.
    • Key question: did these strains evolve within human hosts, or did they exist before transmission to humans?

Horizontal Gene Transfer (HGT)

  • Distinct from vertical gene transfer (grandparent to offspring).
  • In bacteria, three major mechanisms:
    1. Conjugation
    2. Transformation
    3. Transduction
  • HGT is now recognized as common in the history of life, sometimes crossing domains.
  • Estimates suggest that 20% or more of genes in contemporary bacteria entered via HGT.
  • HGT challenges traditional views of evolution and phylogenetic relationships, complicating the reconstruction of vertical lineages.

Key Concepts and Terms (Glossary Highlights)

  • Monophyletic: containing a common ancestor and all its descendants.
  • Paraphyletic: includes a common ancestor and some, but not all, descendants.
  • Polyphyletic: taxa derived from more than one ancestor, excluding the most recent common ancestor.
  • Synapomorphy: shared derived character defining a clade.
  • Homology: similarity due to shared ancestry.
  • Homoplasy (analogous traits): similarity due to convergent evolution or reversal, not common ancestry.
  • Apomorphy: derived character state.
  • Outgroup: a taxon used to root the tree and help determine ancestral vs derived states.
  • Cladistics: classification based on evolutionary relationships inferred from shared derived characters.
  • Parsimony: selecting the simplest explanation (fewest evolutionary changes).
  • Molecular clock: dating divergence by assuming a relatively constant rate of molecular change.
  • HGT: horizontal gene transfer across organisms or domains, altering the vertical inheritance pattern.

Connections to Foundational Principles

  • Linnaean taxonomy provides a nomenclatural framework that is complemented by cladistic concepts based on ancestry and shared derived traits.
  • Phylogenetic trees turn taxonomic hierarchies into testable hypotheses about evolutionary history.
  • Morphology, behavior, and molecular data each contribute to a more complete reconstruction of phylogeny; relying on a single data type can mislead conclusions.
  • The interplay between fossil data, molecular data, and biogeography enables clock calibrations and richer evolutionary timelines.

Practical Takeaways for Exam Preparation

  • Be able to distinguish between monophyletic, paraphyletic, and polyphyletic groups and justify classifications using synapomorphies.
  • Interpret a phylogenetic tree: identify nodes (common ancestors), sister taxa, and the inferred sequence of branching events.
  • Explain how outgroups help determine ancestral vs derived character states and root trees.
  • Compare and contrast parsimony and likelihood-based methods; know when each is most appropriate and typical limitations.
  • Understand how molecular data augment traditional morphology, and recognize issues like HGT that can blur the tree of life.
  • Be able to discuss the concept of the molecular clock and its reliance on fossil calibrations and biogeography for rate estimates.
  • Apply the concept of homology vs homoplasy to morphological traits and to behavior.
  • Remember key examples: synapomorphies define clades; convergence explains analogous structures; the HIV strains illustrate molecular phylogenetics in disease origins.