Taxonomy, Systematics, and Phylogeny Flashcards
Taxonomy
Taxonomy is the scientific discipline concerned with naming and classifying organisms
Nomeneclature
Nomenclature is the system of rules for naming things
What are the problems with common names?
- Different names for the same species.
- Same name for different species
- Common names can imply false relationships
Key features of the Linnaean System of Nomenclature
Hierarchical classification of species into groups (ranks) based on the similarity of structures, functions, and other features.
Unique two-part scientific names for species (binomial nomenclature)
Structure of a binomial name
-
Two parts: genus name (e.g. Homo) followed by a specific epithet (e.g. sapiens).
- Both parts together define the species name (not the specific epithet alone), e.g. Homo sapiens.
- The genus name is CAPITALIZED, and the entire binomial name is italicized.
- The genus name can be abbreviated after the first use, e.g. H. sapiens nstead of Homo sapiens.
- Specific epithets are unique within a genus but can be reused across different genera.
“Great Scientists Investigate Every Animal”.
What are the major ranks of the Linnaean classification system
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
What are the three modern domains?
- Domain Bacteria
- Domain Archaea
- Domain Eukarya (the eukaryotes)
Define
Systematics
Biology
Systematics is the theory and practice of classifying organisms based on evolutionary history (phylogeny)
- Provides a framework for organizing biological diversity and understand evolutionary relationships.
- Modern systematics focuses on the reasons why organisms should be grouped or kept apart and justifies these decisions.
Define
Phylogeny
A phylogeny is the evolutionary relationships among organisms
What is the purpose of a phylogenetic tree?
Phylogenetic trees show hypotheses for the evolutionary relationships between extinct and living organisms as lines of evolutionary descent of different species, organisms, or genes from common ancestors.
It is imposible to porve them to be true, just find evidence to support something
- For long exctinct species, there is no genetic data to make strong evidence of relations
What are some uses of phylogenetic trees?
Organize biological diversity: Groups organisms into groups based on shared evolutionary history.
Visualize evolution: Highlights events like speciation, adaptive radiations, and convergent evolution.
Structure classifications: Align taxonomic classifications to reflect evolutionary relationships.
Guide research: Generates hypotheses on traits and lineage-specific processes.
They also
- connect areas of study
- Enable predictions
What types of data are used to infer phylogenies?
Morphological data: Physical traits such as size, shape, and presence/absence of different anatomical features.
- Useful for living and extinct species
Molecular data: Molecular systematics uses DNA, RNA, and protein structures to infer phylogenies.
- Applies to all extant (living) species, but not to extinct species (fossils)
Sister Taxa
Two descendants that split from the same node are sister taxa.
- Sister taxa share an immediate common ancestor that is not shared with other taxa.
Basal Taxon
A basal taxon diverges early in the history of a group and originates near the common ancestor of the phylogeny
- usually used as a point of contrast
Polytomy
Phyloogenetic Trees
A polytomy is a branch from which more than two groups emerge.
- Polytomies typically represent unresolved patterns of divergence
Clades
Phylogenetic Trees
Clades (clados = branch) are groups that include an ancestor and all its descendants (living and extinct)
Cladograms
Cladograms depict evolutionary relationships where only the branching pattern (topology) is important.
- Branch length and the position of descendant taxa do not convey information about time or evolutionary change
- Cladograms show the relative timing of nodes only when they are on the same direct path from the root, i.e. when one node is a descendant of another.
Phylograms
Phylograms depict evolutionary patterns, but branch lengths represent evolutionary change
Branch Length can represent:
- number of character changes (e.g. morphological or genetic changes) that have occurred along a lineage.
- chronological time, determined through fossil evidence or molecular clock calculations based on DNA sequence changes.
True or false
Phylogenetic trees show evolutionary progress
False
Phylogenetic trees show evolutionary relationships, not evolutionary progress
What’s the key difference between taxonomy and systematics?
A key difference between taxonomy and systematics lies in how groups are defined:
Taxonomy organizes organisms based on similarities and differences into taxonomic ranks (e.g. family, genus, species).
Systematics groups organisms based on their evolutionary relationships, as determined by branching patterns in a phylogenetic tree (i.e. clades)
Homology
Homology is similarity between organisms due to shared ancestry (shared evolutionary origin)
- Homologous structures are anatomical or morphological resemblances representing variations on a structural theme present in a common ancestor
- e.g. the forelimbs of mammals are adapted for different functions (walking, grasping, swimming, flying), but they share a homologous bone structure inherited from a common tetrapod ancestor
Analogy
Biology
Analogy is the similarity between organisms due to convergent evolution
- Convergent evolution occurs when unrelated organisms independently evolve similar traits or adaptations in response to similar environmental conditions and selective pressures
- Convergent evolution does not provide information about shared evolutionary history
Trait Complexity
The more complex two similar structures are, the more likely they are homologous.
Key steps in building a phylogenetic tree
- Select the taxa (choose an ingroup and outgroup)
- Identify homologus traits
- Construct the phylogenetic tree
- Validate the tree
Ingroup
Phylogenetic Trees
Ingroup: the group of taxa whose evolutionary relationships you are studying
Outgroup
phylogenetic tree
Outgroup: one or more taxa related to the ingroup but that diverged earlier
- An outgroup is used as a reference point to help root the tree and distinguish between ancestral and derived traits in the ingroup
Characters
homologous traits
Characters are anatomical, physiological, or molecular features used to compare taxa.
- e.g. DNA sequences, number of
etals, bone structure, etc
Character States
Phylogenetic Tree
The observed variations of a character, which can be used to determine evolutionary changes
- The simplest character states are presence/absence
- More complex characters, like flower petal arrangements, can have multiple states.
- Example: ‘eye colour’ is a character, and in Columba livia the character state is ‘orange’
Cladistics
A method used to infer evolutionary relationships using homologous characters that group taxa based on shared derived characters
Monophyletic Taxa
A group of taxa is monophyletic if it consists of an ancestor taxon, all its descendants, and no other unrelated taxa (mono = one)
Paraphyletic Grouping
A common ancestor, but not all descendants of the common ancestor
- Paraphyletic groups often arise when one or more highly divergent taxa are removed from an otherwise monophyletic clade
- Ex. Removing “Birds” from “Reptiles”
Polyphyletic Grouping
Includes distantly related taxa but does not include the common ancestor of all group members
Reasons for this:
- Incorrect taxonomic classification
- Absence of fossil records
- Multiple common ancestors
Shared derived characters (synapomorphies)
Traits that evolved in the most recent common ancestor of a clade and are unique to that group
- Shared derived characters distinguish clades from one another.
Shared ancestral characters (symplesiomorphies)
Ancestral traits shared by taxa of a clade but are also present in taxa of earlier clades
Synapomorphy
Shared derived characters
A derived character (apomorphy) present in an ancestral taxon and its descendants but is absent from more distant ancestors (syn = together)
Symplesiomorphy
Shared ancestral characters
An ancestral character (plesiomorphy) present in several groups but inherited from a distant common ancestor (sym = together)
Maximum Parsimony
Phylogenetic Trees
When multiple trees are availible to make, choose the one with the fewest number of evolutionary changes
