Introduction to Phylogenetics

Overview: Key ideas in phylogenetic trees

• Cladogenesis vs. Anagenesis
  • Cladogenesis: branching of lineages (splitting into two or more lineages).
  • Anagenesis: evolutionary change that occurs along a lineage between ancestors and descendants (gradual change without branching).
  • In diagrams, branches represent bifurcations (speciation events) and the time between these events is shown by the internodes.
• Purpose of a phylogenetic tree
  • Diagrammatic representation of evolutionary relationships among groups of organisms.
  • Often resembles a tree; used to visualize relatedness, not just similarity of appearance.
  • Similar idea to a family genealogy: individuals, parents, siblings, and ancestors can be mapped similarly among species.

Tree anatomy: tips, nodes, internodes, root, and outgroups

• Tips (taxa)
  • The endpoints of the tree; they represent taxa at various levels (species, genera, families, etc.).
  • Tips can be individual species or broader groups depending on the focus.
• Nodes
  • The most recent common ancestors of the descendants above them.
  • Deep nodes represent more ancient common ancestors; shallow nodes represent more recent common ancestors.
• Internodes (branches)
  • The time and evolutionary change between speciation events.
  • Represent the lineage segments between nodes; in morphology-based trees, changes along these segments reflect anagenesis.
• Root
  • The most ancestral node from which all other nodes descend.
  • Rooting indicates orientation in time (which lineage is older).
• Outgroup
  • A taxon related to the group of interest but that diverged earlier than the group being studied.
  • Used to root the tree and infer ancestral states.
• Rooted vs. unrooted trees
  • Rooted trees have a defined direction in time (ancestral to descendant).
  • Unrooted trees show relationships without specifying ancestry direction.
• Reading the tree: tips vs nodes vs clades
  • Common approach is to focus on nodes and branching patterns to assess relationships rather than just tip labels.
  • Swiveling (rotating) nodes does not change relationships; clades remain the same even if the diagram is rearranged.

Terminology: clades, monophyly, and related groupings

• Clade
  • A group consisting of a common ancestor and all its descendants.
  • A clade is defined by a common ancestry and includes all descendants of that ancestor.
• Monophyletic group
  • A clade that includes a common ancestor and all of its descendants.
• Polyphyly
  • A grouping that does not include the most recent common ancestor of all members; composed of taxa from different lineages.
• Paraphyly
  • A grouping that includes a common ancestor and some, but not all, of its descendants.
• Sister taxa / sister clades
  • Two taxa or two clades that share an immediate most recent common ancestor.
• Outgroup and ingroup in practice
  • Outgroup helps determine which characters are ancestral vs. derived within the ingroup.
• Cystotaxa (sister-taxa concept)
  • A term used for two closely related species sharing their most recent common ancestor; often used to describe very close sister relationships.
• Reading clades vs individual tips
  • A clade is defined by nodes and ancestors; tips may be rearranged in different drawings, but clades should be stable.

Reading and comparing phylogenetic trees

• Different representations convey the same relationships
  • Rectangular, circular (radial), and other layouts can all depict identical relationships.
  • If the nodes (ancestors) and their descendants are the same, different drawings can be considered identical in terms of relationships.
• Identifying relationships from a tree
  • Look for common ancestors (nodes) and the descendants of those ancestors to determine relationships.
  • If two trees share the same set of ancestors and descendants, they are effectively the same tree, despite the drawing style.
• Common pitfalls
  • Don’t rely solely on tip proximity to infer relatedness; focus on the branching pattern and shared nodes.
  • Rotating nodes can change the visual layout but not the underlying relationships.

Practical examples and illustrations from the lecture

• Simple four-taxon example (A, B, C, D)
  • A and B share a more recent common ancestor; C and D share a more recent common ancestor; A/B and C/D share an older common ancestor.
  • Different drawings can place A next to C or D, but the node relationships (common ancestors and their descendants) stay the same.
• Clades and connections
  • A clade can be a small group (e.g., two sister taxa) or a larger group (e.g., all birds and crocodiles together as a broader clade in some diagrams).
• Reading a circle tree
  • Start from the root and follow nodes to see which tips group together at each node; the same relationships appear as in rectangular trees.

Modern vs. traditional taxonomy: monophyly and reclassification

• Monophyly as a guiding principle
  • Modern taxonomy aims to group organisms into monophyletic groups (clades) that include all descendants of a common ancestor.
• Reptilia and fishes as paraphyletic groups in some traditional schemes
  • Reptiles (as traditionally defined) omit birds, making them non-monophyletic if birds are excluded.
  • Fishes as a group is paraphyletic because tetrapods (amphibians, reptiles, birds, mammals) evolved from fish ancestors, so “fish” does not include all descendants.
• Amniota, Archosauromorpha, and Archosauria in a phylogenetic view
  • Amniota: egg-laying membrane that prevents desiccation; separates amniotes from amphibians.
  • Archosauromorpha and Archosauria: nested monophyletic groups used to redefine relationships among reptiles, birds, and their extinct relatives.
  • Birds are descended from theropod dinosaurs, illustrating why traditional “reptilia” is problematic as a monophyletic group.
• Mammal groups
  • Monotremes: egg-laying mammals (e.g., platypus and echidnas).
  • Marsupials: pouches and different reproductive strategy.
  • Placental mammals: young develop within the placenta inside the mother.

Homology, homoplasy, and character data in phylogenetics

• Homology
  • A trait shared by two or more taxa that was inherited from a common ancestor (e.g., limb bone structure in tetrapods: humerus, radius, ulna, carpals, metacarpals, phalanges).
• Plesiomorphy (ancestral state)
  • Ancestral character states shared by two or more lineages within a clade; may be present in multiple lineages due to inheritance from a common ancestor.
• Synapomorphy
  • A derived shared trait that unites a clade; used to define monophyletic groups.
• Homoplasy (convergent evolution or reversal)
  • Similar traits arising independently in separate lineages, not due to common ancestry (e.g., wings in pterosaurs, bats, and birds).
  • Convergence: similar solutions to similar ecological problems in unrelated lineages.
  • Reversal: a trait reverts to an earlier state in a descendant.
• Implication for phylogenetics
  • The challenge is to identify homologous traits and exclude homoplasious traits to avoid incorrect grouping (paraphyly or polyphyly).
• Examples of convergent evolution
  • Flying flight in pterosaurs, bats, and birds; analogous wing function but different lineages.
  • Marsupial and placental mammals showing similar ecological roles but different ancestries.

Data in phylogenetics: how trees are reconstructed

• Types of data used
  • Morphological characteristics (physical traits)
  • Molecular data (DNA sequences: A, T, C, G)
• DNA as a data source
  • DNA consists of long sequences of bases: A, T, C, G
  • Differences between sequences accumulate over time due to replication errors and mutations
  • More differences generally indicate more distant common ancestry; fewer differences indicate more recent common ancestry
• How sequences are analyzed
  • Computer programs align sequences and compare differences across taxa
  • The analysis yields a hypothesis about relationships, depicted as a phylogenetic tree
• Practical tips for interpreting molecular trees
  • Closest related species tend to have the fewest differences in DNA sequences
  • The tree reflects a hypothesis about evolutionary history based on available data; new data can alter the tree

Examples of vertebrate phylogeny and classification refinements

• Vertebrate classes and groupings used in the lecture
  • Amphibia, Mammalia, Squamata (lizards and snakes), Testudines (turtles), Crocodilia (crocodiles), Aves (birds)
  • The traditional Linnaean system uses Class, Order, Family, etc.
• From linnaean to phylogenetic thinking
  • Rank-based classifications (e.g., Class, Order) can conflict with monophyly when birds and reptiles are treated as separate “reptilia” groups.
  • Phylogenetic (cladistic) classification favors monophyletic groups (clades) like Amniota or Archosauria that include all descendants.
• Example of synapomorphies and hierarchical groups
  • Tetrapods: four-limbed vertebrates.
  • Amniotes: includes reptiles, birds, and mammals due to amniotic egg membrane.
  • Archosaurs and their close relatives: a monophyletic group including crocodilians and birds.
• Practical note on terminology usage
  • Always verify whether a term refers to a monophyletic group (clade) or to a broader historical grouping that may be paraphyletic/polyphyletic.

Examples and exam-oriented tips

• How to answer questions about trees in assignments
  • Identify the nodes (common ancestors) and their descendants to determine relationships.
  • Compare two trees by checking whether the same ancestors give rise to the same sets of descendants.
  • Distinguish clades (monophyletic groups) from non-monophyletic groups (paraphyletic or polyphyletic).
  • Recognize sister taxa/clades and understand that rearranging tips does not change the underlying relationships.
• Practical concept: pruning (trimming) a tree
  • You can remove taxa from a large tree to focus on relationships among a smaller group without changing the meaning of the relationships among the remaining taxa.
  • Example: removing unrelated taxa to study relationships among four key taxa; the reduced tree preserves the same branching structure among those taxa.
• Reading circular trees
  • The root is at the center; follow successive nodes from root outward to identify groupings; the layout does not change the relationships.

Practical and ethical notes from the lecture

• Recording policy (pedagogical context)
  • The instructor stated that recordings of lectures are not allowed without explicit permission.
  • Students should not record or share class content without permission.
• Emphasis on careful reading of trees
  • Do not infer relationships from tips alone; focus on the branching patterns and shared ancestors (nodes).
  • The deeper (earlier) a node is in the tree, the more ancestral the group; the shallower (closer to the tips) the node, the more recent.

Summary: core takeaways for the exam

• A phylogenetic tree encodes evolutionary relationships as branching patterns, with nodes representing common ancestors and tips representing taxa.
• Cladogenesis vs. anagenesis describe branching vs. within-lineage change; both contribute to the tree’s structure.
• Monophyly, paraphyly, and polyphyly describe how well a group reflects a single ancestral lineage and its descendants.
• Clades are monophyletic groups; sister taxa/clades share a most recent common ancestor.
• Outgroups are used to root trees and infer ancestral character states.
• Homology vs. homoplasy determines which traits are informative for constructing trees; synapomorphies help define clades, while convergent traits (homoplasy) can mislead.
• DNA data and computational analyses have become central to modern phylogenetics; differences in DNA sequences reflect evolutionary distance.
• In practice, modern taxonomy aims to reflect true evolutionary relationships by using monophyletic groups; traditional groups like “reptilia” or “fish” may be paraphyletic and are sometimes revised.
• For assignments: prioritize nodes and branching patterns, identify clades, and assess whether two trees depict the same relationships by comparing common ancestors and their descendants.
• Examples discussed include the relationship between birds and crocodiles, the position of lizards, and the whale–hippo–artiodactyl discussion, illustrating how data support particular hypotheses over others.