AP Biology 7.5-7.6: Evidence of Evolution and Phylogeny

Taxonomic hierarchy

The major taxonomic ranks from broadest to most specific are domain, kingdom, phylum, class, order, family, genus, and species. Each named group at a rank is a taxon.

Binomial nomenclature

Binomial nomenclature gives an organism a two-part scientific name consisting of its genus and species. The genus is capitalized, the species name is lowercase, and both are italicized when typed.

How does increasing taxonomic specificity affect similarity among organisms?

As classification moves from domain toward species, the groups become smaller and generally more closely related, so their shared characteristics and genetic similarities tend to increase.

What is a subspecies?

A subspecies is a geographically, behaviorally, or otherwise distinct population within a species. Members of different subspecies can mate and produce viable offspring.

Phylogeny

Phylogeny is the evolutionary history of an organism or group and the relationships among its members. It describes shared ancestry and relatedness, not necessarily overall physical similarity.

Systematics

Systematics is the study of organizing and classifying organisms according to their evolutionary relationships. It uses evidence such as fossils, morphology, developmental features, molecules, and DNA sequences.

How are taxonomy, systematics, and phylogeny related?

Taxonomy classifies and names organisms, while systematics uses evidence to study their relationships and organize them accordingly. Phylogeny is the evolutionary history and relationship that systematics attempts to reconstruct.

What is the purpose of a phylogenetic tree?

A phylogenetic tree is a diagram that represents hypothesized evolutionary relationships and pathways among organisms or groups. It can be used to infer common ancestry and the order of divergence.

Why is a phylogenetic tree considered a scientific hypothesis?

The evolutionary relationships represented by a tree cannot be directly observed in the past. New fossil, morphological, or molecular evidence can therefore support, modify, or overturn the tree.

Rooted phylogenetic tree

A rooted tree contains a single ancestral lineage at its root and is intended to show common ancestry and the direction or sequence of evolutionary divergence.

Unrooted phylogenetic tree

An unrooted tree shows relationships among taxa but does not identify a common ancestor or the direction in which evolutionary changes occurred.

What are the three domains of life?

The three domains are Bacteria, Archaea, and Eukarya. In a rooted representation of life's history, these domains diverge from an ancestral lineage.

Branch point

A branch point, or node, represents the divergence of one ancestral lineage into two or more descendant lineages.

Basal taxon

A basal taxon is a lineage that diverged relatively early from the root and remains unbranched in the tree shown. Its position does not necessarily mean it is less evolutionarily advanced.

Sister taxa

Sister taxa are two lineages that originate from the same immediate branch point. They share a more recent common ancestor with each other than with other taxa shown.

Polytomy

A polytomy is a branch point from which more than two lineages emerge. It usually indicates that the exact order of divergence is unresolved or uncertain.

What does rotation around a branch point do to a phylogenetic tree?

Rotating branches around a node changes their visual order but not the relationships represented by the tree. The key information is which taxa share branch points, not their left-to-right arrangement.

What can be inferred by tracing a phylogenetic tree from a species toward the root?

Tracing toward the root identifies shared ancestors and shows where the species shares ancestry with other lineages. It can also indicate the sequence of divergence events in a rooted tree.

Why does branch length usually not indicate elapsed time on a phylogenetic tree?

Unless a diagram explicitly includes a time scale, branch length represents relationships or branching order rather than duration. A longer branch does not automatically mean more time or more evolutionary change.

How can DNA evidence change biological classification?

Molecular comparisons can reveal evolutionary relationships that are not apparent from physical traits alone. As new sequence data become available, classifications and phylogenetic trees may need revision.

Why can closely related organisms look very different?

Different environmental conditions can favor different adaptations in closely related lineages. Consequently, substantial morphological differences do not necessarily indicate distant ancestry.

Why can distantly related organisms look similar?

Similar environmental pressures can independently favor similar adaptations in unrelated lineages. This process can produce analogous traits and misleading phenotypic similarity.

Homologous structures

Homologous structures share an underlying developmental or anatomical origin because of common ancestry, even if their present functions differ. The forelimb bones of humans, whales, bats, and birds provide examples.

Analogous structures

Analogous structures perform similar functions but arose independently and do not share the same evolutionary or embryonic origin. Insect wings and vertebrate wings are analogous as wings, despite their similar function.

How can the wings of bats, birds, and insects illustrate both homology and analogy?

The underlying forelimb bones of bats and birds are homologous because they reflect common ancestry. The wings of bats, birds, and insects are analogous as flight structures because flight evolved independently in these groups.

Homoplasy

Homoplasy is similarity that does not result from recent common ancestry, often because traits evolved independently under similar environmental pressures. Analogous traits are a type of homoplasy.

Molecular systematics

Molecular systematics uses DNA and other molecular data to infer taxonomy, biogeography, and evolutionary relationships. It complements evidence from morphology and fossils.

Why is it most reliable to combine morphological and molecular evidence when reconstructing phylogeny?

Either type of evidence can be misleading because morphology may reflect convergent evolution and DNA comparisons can be complicated by mutations or coincidental sequence similarities. Agreement among independent evidence sources provides stronger support for a relationship.

How can a mutation complicate the use of DNA sequences to infer relatedness?

Insertions or deletions can shift the alignment of nucleotide sequences, making homologous regions appear dissimilar. Conversely, unrelated sequences may coincidentally share similar bases, so sequence data require careful analysis.

Why is physical resemblance alone insufficient for determining evolutionary relationships?

Resemblance may result from either common ancestry or convergent evolution. Scientists must distinguish homologous from analogous features and incorporate molecular, developmental, and fossil evidence.

Descent with modification

Descent with modification describes how descendants inherit traits from ancestors while accumulating genetic changes. Some changes persist and become characteristic of later branches.

Cladistics

Cladistics organizes organisms into clades based on shared derived characteristics. It aims to represent evolutionary relationships through branching patterns.

Clade

A clade is a group consisting of a common ancestor and all of its descendants. It is also called a monophyletic group.

What requirement distinguishes a clade from an arbitrary group of organisms on a phylogenetic tree?

All members of a clade must descend from one common branch point, and the group must include every descendant of that ancestor within the tree's scope. A group that excludes some descendants is not monophyletic.

Shared ancestral character

A shared ancestral character is a trait inherited from an ancestor and present in all members of the relevant taxon or clade. Whether a trait is ancestral depends on the reference group being considered.

Shared derived character

A shared derived character is a trait that evolved in a more recent common ancestor and is present in some, but not all, organisms in the larger group. Such traits help identify clades.

Why are the terms shared ancestral character and shared derived character relative?

The same trait can be ancestral when comparing a smaller subgroup with its members, but derived when comparing that subgroup with a broader group. For example, an amniotic egg is ancestral for amniotes such as lizards and mammals but derived relative to vertebrates that lack it.

What is the difference between a shared trait and evidence of close evolutionary relationship?

A shared trait supports close relationship most strongly when it is homologous and especially when it is a shared derived character. A shared analogous trait may instead reflect convergent evolution and does not reliably indicate recent common ancestry.

Maximum parsimony

Maximum parsimony is the strategy of favoring the evolutionary explanation that requires the fewest major changes while fitting the available evidence. It is used to compare possible phylogenetic trees.

How does maximum parsimony help select among competing phylogenetic trees?

Scientists map homologous traits onto candidate trees and prefer the tree requiring the fewest independent evolutionary changes. This is a simplifying criterion, not proof that the selected tree is certainly correct.

What does a phylogenetic tree show about traits that evolved on one branch?

A trait appearing on one branch does not mean evolution stopped in other branches. It indicates that a new lineage acquired or retained that trait while other lineages continued evolving independently.

How can phylogenetic relationships be useful in biological research?

Related species may share biochemical pathways or useful genes, so phylogeny can help researchers identify organisms likely to produce medicines or other valuable compounds. DNA markers can be used to screen newly discovered species for membership in such groups.