NOTES: CH 26 – Phylogeny and the Tree of Life
Phylogeny:
● Systematics: discipline focused on classifying organisms and determining their evolutionary relationships
● The fossil record:
, within layers, or strata, of sedimentary rock
● Paleontologists:
● Taxonomy –
● Systematics – naming & classifying organisms
● Phylogenetics – reconstructing the evolutionary relationships among organisms
Binomial Nomenclature
● In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances
● Two key features of his system remain useful today: two-part names for species and hierarchical classification
● The two-part scientific name of a species is called a binomial
● The first part of the name is the
● The second part is
within the genus
● The first letter of the genus is capitalized, and the entire species name is italicized
● Both parts together name the species
Hierarchical Classification
● The taxonomic groups from broad to narrow are
,
,
,
,
,
, and
● A taxonomic unit at any level of hierarchy is called a
Linking Classification and Phylogeny – PHYLOGENETIC TREES!
● Systematists depict evolutionary relationships in branching
● Phylogenetic tree – hypothesized genealogy
(i.e., the most recent) through hierarchical, dichotomous branching
● A phylogenetic tree represents a hypothesis about evolutionary relationships
● Each branch point represents the
● Sister taxa are groups that
● A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree
● A basal taxon diverges early in the history of a group and originates near the common ancestor of the group
● A polytomy is a branch from which
Constructing Phylogenetic Trees
● Sorting homology vs. analogy...
● Homology:
● Analogy: likenesses attributed to similar ecological roles and natural selection
● Convergent evolution: species from different evolutionary branches that
,
HOMOLOGIES: Similar characters (e.g.,
etc. traits or features) suggest relatedness…
,
● Homologous characters
● As a general rule, the more homologous characters shared by two species,
● Sequences of DNA & RNA (nucleotides) and proteins (amino acids) are used as characters; as a general rule,
the more recently two species shared a common ancestor, the
CONVERGENT EVOLUTION: can produce superficially similar traits that lack homology with one another
● Analogous characters
Evaluating Molecular Homologies:
● Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from
different organisms
● Molecular systematics uses
and other molecular data (i.e.
) to
Shared characters are used to construct phylogenetic trees
● Once homologous characters have been identified, they can be used to infer a phylogeny
CLADISTICS:
● Cladistics groups organisms by
● A clade is a group of species that includes an
● Clades can be nested in larger clades, but not all groupings of organisms
qualify as clades
● A valid clade is
, signifying that it consists of the
ancestor species and all its descendants
●A
grouping consists of an ancestral species and some,
but not all, of the descendants
●A
grouping consists of various species with different ancestors
Shared Ancestral and Shared Derived Characters
● In comparison with its ancestor, an organism has both
and
characteristics
Ancestral vs. Derived Characters
● A shared ancestral character is a character that
● A shared derived character is
of the taxon
(“
”) to a particular clade
● A character can be both ancestral and derived, depending on the context
● When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first
appeared
**The sequence of branching in a cladogram then represents the sequence in which
(
) evolved
Ingroup vs. Outgroup
● An OUTGROUP is a species or group of species that is closely related to the INGROUP, the various species
being studied
● The outgroup is a group that has
the ingroup
● Systematists compare each ingroup species with the outgroup to differentiate between shared derived and
shared ancestral characteristics
● Characters shared by the outgroup and ingroup are
that
of both groups from a common ancestor
An outgroup helps identify shared ancestral and shared DERIVED CHARACTERS (
)
Phylogenetic Trees with Proportional Branch Lengths
● In some trees, the length of a branch can reflect the
that have taken
place in a particular DNA sequence in that lineage
● In other trees, branch length can represent
, and branching points can be
determined from the
Phylogenetic Trees as Hypotheses
● The best hypotheses for phylogenetic trees fit the most data:
,
and
● Phylogenetic bracketing allows us to predict features of an ancestor from features of its descendants
-For example, phylogenetic bracketing allows us to infer characteristics of dinosaurs
● Birds and crocodiles share several features: four-chambered hearts, song, nest building, and brooding
● These characteristics likely evolved in a common ancestor and were shared by all of its descendants, including
● The fossil record supports nest building and brooding in dinosaurs
,
An organism’s evolutionary history is documented in its genome
● Comparing nucleic acids or other molecules to infer relatedness is a valuable approach for tracing organisms’
evolutionary history
● DNA that codes for rRNA
and is useful for investigating branching points
● mtDNA evolves rapidly and can be used to explore recent evolutionary events (i.e.
)
Molecular clocks help track evolutionary time
● To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change
occurs over time
Molecular Clocks
● A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary
change
● In orthologous genes (genes found in different species; e.g.
nucleotide substitutions are proportional to the time since they last shared a common ancestor
● In paralogous genes (similar genes found within one species; e.g.
), nucleotide substitutions are proportional to the time since the genes became duplicated
● Molecular clocks are calibrated against branches whose dates are known from the fossil record
● Individual genes vary in how clocklike they are
),