Chapter 26
Concept 26.1 Phylogenies show evolutionary relationships
Phylogeny: evolutionary history of a species or group
Phylogenetic tree: branching diagram representing evolutionary relationships
Example concept: convergent evolution can produce similar body plans (limbless forms) in unrelated lineages
Binomial Nomenclature
Linnaeus: two-part names for species based on resemblances
First part = genus; second part = specific epithet (unique within genus)
Formatting: genus capitalized, species name italicized (or underlined when handwritten)
Examples: Canis latrans, Canis lupus
Hierarchical Classification
Taxonomic levels from broad to narrow: domain, kingdom, phylum (phyla), class, order, family, genus, species
A taxon = any taxonomic group
Linking Classification and Phylogeny (1 of 2)
Linnaean classification does not always reflect evolutionary relationships due to feature loss or convergent similarity
Current practice: classification based on evolutionary relationships
Monophyly: groups that include a common ancestor and all its descendants
Classification may be revised with DNA or other evidence to reflect evolutionary history
Linking Classification and Phylogeny (2 of 2)
Reclassification occurs when needed to reflect true relationships
What We Can and Cannot Learn from Phylogenetic Trees (1 of 4)
Phylogenetic tree = hypothesis of evolutionary relationships
Each branch point represents divergence from a common ancestor; sister taxa share a unique common ancestor not shared with other groups
What We Can and Cannot Learn from Phylogenetic Trees (2 of 4)
Trees can be drawn in different orientations without changing relationships
What We Can and Cannot Learn from Phylogenetic Trees (3 of 4)
Rooted tree includes the most recent common ancestor of all taxa in the tree
Basal taxon: lineage that diverged early in the history of the group
What We Can and Cannot Learn from Phylogenetic Trees (4 of 4)
Trees show patterns of descent, not phenotypic similarity
Trees do not indicate when species evolved or how much change occurred
Do not assume a taxon evolved from the taxon next to it
Applying Phylogenies
Phylogenies have practical applications (eg, determining if whale meat samples come from legally harvested species)
Concept 26.2: Phylogenies are inferred from morphological and molecular data
Data types: morphology, genes, biochemistry
Only features from common ancestry are informative for relationships
Homology: similarity due to shared ancestry; Analogy: similarity due to convergent evolution
Morphological and Molecular Homologies
Homologies: phenotypic and genetic similarities due to shared ancestry
Closer relatedness often reflected by similar morphology or DNA sequence
Morphological divergence can be large even when genetically similar (example: Hawaiian silverswords)
Sorting Homology from Analogy (1 of 2)
Convergent evolution yields superficial similarities in unrelated species due to similar environments
Example: Australian mole vs African golden mole illustrating analogy due to lifestyle
Sorting Homology from Analogy (2 of 2)
Complex characters help distinguish homology from analogy
Greater similarity in complex structures or many shared gene regions suggests homology
Coincidental matches can occur; use statistical tools to distinguish distant homologies
Evaluating Molecular Homologies
After DNA sequencing, align comparable sequences
Closely related species differ at few sites; distant ones differ at many sites
Insertions/deletions (indels) shift downstream sequence; alignment programs identify best matches
Concept 26.3: Shared characters are used to construct phylogenetic trees
Cladistics: grouping by common ancestry
Clade: an ancestral species and all its descendants; can be nested within larger clades
Cladistics
Monophyletic groups constitute clades
Paraphyletic group: ancestral species and some, but not all, descendants
Polyphyletic group: includes distantly related species not sharing the most recent common ancestor
Shared Ancestral and Shared Derived Characters
Shared ancestral character: originated in an ancestor of the taxon
Shared derived character: evolutionary novelty unique to a clade
Lost features can also be shared derived (eg, loss of limbs in snakes or whales)
Relative nature: a feature can be ancestral in one context and derived in another (eg, backbone in vertebrates)
Inferring Phylogenies Using Derived Characters
Outgroup vs ingroup: outgroup is closely related but not part of the study group
Characters shared by outgroup and ingroup assumed ancestral
Each derived character is assumed to have arisen only once in the ingroup
Figure 26.12 Using derived characters to infer phylogeny
Concept: derived characters used to construct a phylogeny (example table and tree with outgroup and ingroup)
Maximum Parsimony and Maximum Likelihood (1 of 2)
When several trees are possible, parsimony: the simplest explanation with the fewest evolutionary changes is preferred
Likelihood: identifies the tree most likely to produce the observed DNA data given models of DNA change over time
Maximum Parsimony and Maximum Likelihood (2 of 2)
Computers search for trees that are both parsimonious and likely
Phylogenetic Trees as Hypotheses (1 of 2)
Phylogenetic bracketing: features shared by two closely related groups are predicted in their common ancestor and all descendants
Phylogenetic Trees as Hypotheses (2 of 2)
Use in predicting traits in extinct relatives (eg, dinosaurs given bird and crocodile shared features such as four-chambered heart, nesting, brooding)
Fossil record provides support for some predictions
Concept 26.4: An organism’s evolutionary history is documented in its genome
Molecular comparisons reveal relatedness across morphologically distinct groups
Gene number does not scale with phenotypic complexity; many genes encode multiple proteins and functions across tissues
Concept 26.6: Our understanding of the tree of life continues to change based on new data
DNA sequence data illuminate deepest branches of life
Historical view shifted from two kingdoms to five kingdoms (Monera, Protista, Plantae, Fungi, Animalia) by the 1960s
Three-domain system: Bacteria, Archaea, Eukarya
Protista is not a kingdom; some protists relate more closely to plants, fungi, or animals
From Two Kingdoms to Three Domains
Prokaryotes form two domains (Bacteria and Archaea); Eukarya includes Plantae, Fungi, Animalia; Protista is not a single kingdom
The Important Role of Horizontal Gene Transfer
rRNA-based trees suggested eukaryotes and archaea are closely related; other genes show different histories
Horizontal gene transfer (HGT): movement of genes between genomes via transposons/plasmids, viral infection, or fusion
HGT is important in evolution of prokaryotes and eukaryotes; eukaryotes can acquire nuclear genes from bacteria/archaea (example: Galdieria sulphuraria acquired ~5% of its genes)
Some biologists view early life as a network with tangled gene transfer rather than a simple branching tree
Phylogeny is the evolutionary history of a species or group, represented by a branching phylogenetic tree. While convergent evolution can create similar body plans in unrelated lineages, Linnaeus established binomial nomenclature for species with a genus and specific epithet, formatted with the genus capitalized and species italicized.
Hierarchical classification organizes life into nested taxonomic levels: domain, kingdom, phylum, class, order, family, genus, and species. Modern classification aims to reflect evolutionary relationships, unlike early Linnaean systems which sometimes failed to capture true ancestry due to feature loss or convergent similarity. Monophyletic groups, which include a common ancestor and all its descendants, are key to current classification, leading to revisions based on new evidence like DNA.
Phylogenetic trees are hypotheses of evolutionary relationships, with each branch point signifying divergence from a common ancestor. Sister taxa share a unique common ancestor. Trees can have various orientations, and a rooted tree includes the most recent common ancestor, with a basal taxon diverging early. Importantly, trees illustrate patterns of descent, not phenotypic similarity, evolution time, or direct lineage of adjacent taxa. They have practical applications, such as identifying if whale meat is from legally harvested species.
Phylogenies are constructed from morphological, genetic, and biochemical data. Only features from common ancestry, known as homologies (similarities due to shared ancestry), are informative. Analogies, by contrast, are superficial similarities resulting from convergent evolution in similar environments. Complex characters and extensive genetic similarities help distinguish homology from analogy, with statistical tools used for more distant homologies. Molecular homologies are evaluated by aligning DNA sequences, noting that insertions/deletions (indels) can shift sequences.
Cladistics groups organisms by common ancestry. A clade is a monophyletic group, comprising an ancestor and all its descendants. Paraphyletic groups include some but not all descendants, while polyphyletic groups include distantly related species without their most recent common ancestor. Characters are classified as shared ancestral (originated in an ancestor of the taxon) or shared derived (unique evolutionary novelty to a clade). A character's classification is relative; for instance, a backbone is ancestral for mammals but derived for vertebrates compared to non-vertebrates. Phylogenies are inferred using an outgroup (closely related but outside the study group) to identify ancestral characters, assuming each derived character arose only once. When multiple trees are possible, maximum parsimony favors the simplest explanation (fewest evolutionary changes), while maximum likelihood identifies the tree most probable given observed DNA data and models of genetic change. These trees serve as hypotheses, enabling phylogenetic bracketing to predict traits in extinct relatives, such as the four-chambered heart in dinosaurs based on birds and crocodiles.
An organism's genome documents its evolutionary history; molecular comparisons unveil relatedness even among morphologically distinct groups. The number of genes does not directly correlate with phenotypic complexity as many genes perform multiple functions. Our understanding of the tree of life has evolved significantly, shifting from two kingdoms to five (Monera, Protista, Plantae, Fungi, Animalia) and now to a three-domain system: Bacteria, Archaea, and Eukarya, acknowledging that Protista is not a single kingdom. Horizontal gene transfer (HGT), the movement of genes between genomes via mechanisms like transposons, viral infection, or fusion, plays a crucial role in the evolution of both prokaryotes and eukaryotes, including eukaryotes acquiring nuclear genes from bacteria/archaea. This concept suggests early life might be better viewed as a tangled network of gene transfers rather than a simple branching tree.