Phylogenetics and Classification (Notes)

A set of practice flashcards covering key concepts from the lecture notes on phylogenetics, classification, and phylogenetic trees.

What is Ontogeny?

The individual growth and development of an organism, from embryo to adult, including morphological changes in the embryo.

What is Phylogeny?

The evolutionary history and relationships of a species, described by morphological or molecular changes in its lineage and often depicted as a phylogenetic tree.

What does Von Baer’s Law state?

Development starts from general features and becomes more specific; embryonic structures tend to be similar across many species, while adult forms diverge.

What is the Biogenetic Law (Recapitulation Theory)?

The idea that ontogeny recapitulates phylogeny (embryonic stages reflect ancestral adult forms); it has been disproven.

Who proposed the Biogenetic Law and when?

Ernst Haeckel in 1866.

What happened to Haeckel’s drawings?

They were found inaccurate; embryonic similarity does not directly reflect adult evolutionary history, leading to the view that ontogeny reflects macroevolutionary patterns rather than precise phylogeny.

What is the Tree of Life?

The most comprehensive map of evolutionary connections across all species.

What is the relationship between phylogenetics and other disciplines like Comparative Biology, Systematics, and Taxonomy?

Phylogenetics uses comparative data to infer evolutionary history (Comparative Biology); Systematics integrates phylogeny into organizing/classifying life; Taxonomy names organisms (binomial nomenclature) within a hierarchical framework (Linnaean system plus Domain).

Why is relying on morphology alone sometimes misleading in classification?

Because morphology can be misleading due to convergent evolution and cryptic species; modern systems reveal more accurate groupings (e.g., Protists spread across six lineages).

What happened to Kingdom Protista in modern classification?

Protists are not a single valid kingdom; they are spread across six distinct eukaryotic lineages, with some algae closer to land plants and others related to apicomplexans.

What is a Character in taxonomy?

A property or feature of an organism (e.g., number of petals).

What is a Character state?

The interpretation of a feature's observable state used to distinguish between characters (e.g., 3, 5, 6, 7, 8 petals).

What is Phenetics?

Classification based on phenotypic similarity without reflecting evolutionary history; produces a phenogram.

What is Cladistics?

Classification based on shared derived traits (synapomorphies) to infer branching patterns; produces a cladogram.

What is Phyletics?

Classification focused on genealogical relationships and the amount of evolutionary change, often with branch lengths indicating time or change.

What is a Phenogram?

A tree showing similarities based on overall phenotypic similarity, not necessarily reflecting evolutionary history.

What is a Cladogram?

A diagram illustrating hypothetical relationships among taxa based on shared derived traits, using maximum parsimony.

What is a Phylogram?

A phylogenetic tree whose branch lengths are proportional to evolutionary time or amount of change, often built from molecular data.

What is the Root of a phylogenetic tree?

The most recent common ancestor (MRCA) of all the organisms in the tree.

What are Branches (Edges) in a phylogenetic tree?

Lines representing evolutionary lineages for the taxa of interest.

What are Nodes?

Branch points representing speciation events or the MRCA itself.

What are Leaves?

The tips of branches representing groups of organisms (taxa), often called OTUs.

What are Sister taxa?

Taxa that share a most recent common ancestor not shared with other taxa.

What is Topology in a phylogenetic tree?

The branching pattern and arrangement of lineages in the tree.

What is Node Rotation?

Rotating branches around a node to produce visually different but equivalent trees without changing relationships.

What is the difference between Rooted and Unrooted trees?

Rooted trees include a common ancestor with directionality; unrooted trees do not specify a common ancestor and show relationships without a specified direction.

What is an Outgroup?

A distant relative used as a reference point for comparing the ingroup sequences.

What is Homology?

Similar traits in different organisms that originated from a common ancestor.

What is Analogy?

Traits with similar function in unrelated organisms due to convergent evolution, not shared ancestry.

What is Homoplasy?

A trait that appears similar in distantly related organisms due to convergent evolution or reversal.

What is a Monophyletic group?

An ancestor and all of its descendants (a clade) favored in modern systematics.

What is a Paraphyletic group?

An ancestral group plus some, but not all, of its descendants.

What is a Polyphyletic group?

Members from different ancestors grouped together.

What is a Plesiomorphy?

An ancestral trait shared by many taxa.

What is a Symplesiomorphy?

An ancestral trait shared by two or more groups.

What is an Apomorphy?

A derived trait unique to a particular group.

What is a Synapomorphy?

A shared derived trait used to define a clade and its branch points.

What is an Autapomorphy?

A derived trait unique to a single taxon; not useful for grouping.

What are common molecular data used in phylogeny?

DNA sequences, RNA, and proteins (e.g., 18S rRNA for eukaryotes, 16S rRNA for prokaryotes, COI, Cytochrome-b, rbcL, matK).

What is 18S rRNA and 16S rRNA used for?

18S rRNA is used for studying eukaryotes; 16S rRNA is used for studying prokaryotes.

What is COI used for in phylogenetics?

Cytochrome c oxidase I; a common animal DNA barcode for species identification.

What is Cytochrome-b used for in barcoding?

Used for identifying closely related taxa; less reliable for deep evolutionary relationships.

What are rbcL and matK used for?

Plant DNA barcoding genes; used in plant phylogenetics.

What is BLAST used for in cladistics?

A tool to align and compare DNA sequences to identify similarities.

What is a Distance Matrix in molecular cladistics?

A matrix that records the number of differences between sequences for clustering.

What is Maximum Parsimony?

The phylogenetic tree with the fewest evolutionary changes is preferred (Occam’s Razor).

What is Maximum Likelihood?

A method that selects the tree with the highest probability of the observed data given a model.

What is Phylogenetic Bracketing?

Predicting unknown traits of extinct organisms by comparing them to their closest living relatives.

What is the general goal of phylogenetics?

To reconstruct evolutionary relationships and history using the best available data.